From eca1e79c223bb26b2ca64b4c3a7d1f86273d440c Mon Sep 17 00:00:00 2001 From: Oleksandr Kulkov Date: Mon, 6 Nov 2023 15:19:39 +0100 Subject: [PATCH 01/52] Initial DBGSSHash commit Add PTHash submodule, create boilerplate code for DBGSSHash class, add it to test_dbg_helpers. --- .gitmodules | 3 + metagraph/CMakeLists.txt | 1 + metagraph/external-libraries/pthash | 1 + .../graph/representation/hash/dbg_sshash.cpp | 104 ++++++++++++++++++ .../graph/representation/hash/dbg_sshash.hpp | 91 +++++++++++++++ .../tests/graph/all/test_dbg_helpers.cpp | 26 +++++ .../tests/graph/all/test_dbg_helpers.hpp | 2 + 7 files changed, 228 insertions(+) create mode 160000 metagraph/external-libraries/pthash create mode 100644 metagraph/src/graph/representation/hash/dbg_sshash.cpp create mode 100644 metagraph/src/graph/representation/hash/dbg_sshash.hpp diff --git a/.gitmodules b/.gitmodules index a7d8038bff..8c5a4fd577 100644 --- a/.gitmodules +++ b/.gitmodules @@ -68,3 +68,6 @@ [submodule "metagraph/external-libraries/htslib"] path = metagraph/external-libraries/htslib url = https://github.com/samtools/htslib +[submodule "metagraph/external-libraries/pthash"] + path = metagraph/external-libraries/pthash + url = https://github.com/jermp/pthash.git diff --git a/metagraph/CMakeLists.txt b/metagraph/CMakeLists.txt index 6e04831a14..2eae42b6a1 100644 --- a/metagraph/CMakeLists.txt +++ b/metagraph/CMakeLists.txt @@ -270,6 +270,7 @@ include_directories( external-libraries/zlib external-libraries/sdust external-libraries/simde-no-tests + external-libraries/pthash/include ${PROJECT_SOURCE_DIR}/src ) diff --git a/metagraph/external-libraries/pthash b/metagraph/external-libraries/pthash new file mode 160000 index 0000000000..4098013a0c --- /dev/null +++ b/metagraph/external-libraries/pthash @@ -0,0 +1 @@ +Subproject commit 4098013a0c3428fdf5bd25d28c40f32ec267a64b diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.cpp b/metagraph/src/graph/representation/hash/dbg_sshash.cpp new file mode 100644 index 0000000000..3197a7b9ee --- /dev/null +++ b/metagraph/src/graph/representation/hash/dbg_sshash.cpp @@ -0,0 +1,104 @@ +#include "dbg_sshash.hpp" + +namespace mtg { +namespace graph { + +void DBGSSHash::add_sequence(std::string_view sequence, + const std::function &on_insertion) { +} + +void DBGSSHash::map_to_nodes(std::string_view sequence, + const std::function &callback, + const std::function &terminate) const { +} + +void DBGSSHash ::map_to_nodes_sequentially(std::string_view sequence, + const std::function &callback, + const std::function &terminate) const { +} + +DBGSSHash::node_index DBGSSHash::traverse(node_index node, char next_char) const { + return 0; +} + +DBGSSHash::node_index DBGSSHash::traverse_back(node_index node, char prev_char) const { + return 0; +} + +void DBGSSHash ::adjacent_outgoing_nodes(node_index node, + const std::function &callback) const { +} + +void DBGSSHash ::adjacent_incoming_nodes(node_index node, + const std::function &callback) const { +} + +void DBGSSHash ::call_outgoing_kmers(node_index node, + const OutgoingEdgeCallback &callback) const { +} + +void DBGSSHash ::call_incoming_kmers(node_index node, + const IncomingEdgeCallback &callback) const { +} + +size_t DBGSSHash::outdegree(node_index node) const { + return 0; +} + +bool DBGSSHash::has_single_outgoing(node_index node) const { + return false; +} + +bool DBGSSHash::has_multiple_outgoing(node_index node) const { + return false; +} + +size_t DBGSSHash::indegree(node_index node) const { + return 0; +} + +bool DBGSSHash::has_no_incoming(node_index node) const { + return true; +} + +bool DBGSSHash::has_single_incoming(node_index node) const { + return false; +} + +void DBGSSHash ::call_kmers( + const std::function &callback) const { +} + +DBGSSHash::node_index DBGSSHash::kmer_to_node(std::string_view kmer) const { + return 0; +} + +std::string DBGSSHash::get_node_sequence(node_index node) const { + return ""; +} + +void DBGSSHash::serialize(std::ostream &out) const { +} + +void DBGSSHash::serialize(const std::string &filename) const { +} + +bool DBGSSHash::load(std::istream &in) { + return false; +} + +bool DBGSSHash::load(const std::string &filename) { + return false; +} + +bool DBGSSHash::operator==(const DeBruijnGraph &other) const { + return false; +} + +const std::string DBGSSHash::alphabet_ = ""; +const std::string &DBGSSHash::alphabet() const { + return alphabet_; +} + +} // namespace graph +} // namespace mtg diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.hpp b/metagraph/src/graph/representation/hash/dbg_sshash.hpp new file mode 100644 index 0000000000..72aaa06eef --- /dev/null +++ b/metagraph/src/graph/representation/hash/dbg_sshash.hpp @@ -0,0 +1,91 @@ +#ifndef __DBG_SSHASH_HPP__ +#define __DBG_SSHASH_HPP__ + +#include +#include +#include + +#include "graph/representation/base/sequence_graph.hpp" + + +namespace mtg { +namespace graph { + +class DBGSSHash : public DeBruijnGraph { + public: + explicit DBGSSHash(size_t k) {} + +// SequenceGraph overrides + void add_sequence( + std::string_view sequence, + const std::function &on_insertion = [](node_index) {}) override; + + void map_to_nodes( + std::string_view sequence, + const std::function &callback, + const std::function &terminate = []() { return false; }) const override; + + void map_to_nodes_sequentially( + std::string_view sequence, + const std::function &callback, + const std::function &terminate = []() { return false; }) const override; + + void adjacent_outgoing_nodes(node_index node, + const std::function &callback) const override; + + void adjacent_incoming_nodes(node_index node, + const std::function &callback) const override; + + uint64_t num_nodes() const override { return 0; } + + bool load(std::istream &in); + bool load(const std::string &filename) override; + + void serialize(std::ostream &out) const; + void serialize(const std::string &filename) const override; + + static constexpr auto kExtension = ".sshashdbg"; + std::string file_extension() const override { return kExtension; } + + std::string get_node_sequence(node_index node) const override; + +// DeBruijnGraph overrides + size_t get_k() const override { return 0; } + + // TODO: add the support for the canonical mode + Mode get_mode() const override { return BASIC; } + + node_index traverse(node_index node, char next_char) const override; + node_index traverse_back(node_index node, char prev_char) const override; + + void call_kmers(const std::function &callback) const override; + + size_t outdegree(node_index) const override; + bool has_single_outgoing(node_index) const override; + bool has_multiple_outgoing(node_index) const override; + + size_t indegree(node_index) const override; + bool has_no_incoming(node_index) const override; + bool has_single_incoming(node_index) const override; + + node_index kmer_to_node(std::string_view kmer) const override; + + void call_outgoing_kmers(node_index node, + const OutgoingEdgeCallback &callback) const override; + + void call_incoming_kmers(node_index node, + const IncomingEdgeCallback &callback) const override; + + + bool operator==(const DeBruijnGraph &other) const override; + + const std::string &alphabet() const override; + + private: + static const std::string alphabet_; +}; + +} // namespace graph +} // namespace mtg + +#endif // __DBG_SSHASH_HPP__ diff --git a/metagraph/tests/graph/all/test_dbg_helpers.cpp b/metagraph/tests/graph/all/test_dbg_helpers.cpp index c7ad925b4f..47b1ee7e02 100644 --- a/metagraph/tests/graph/all/test_dbg_helpers.cpp +++ b/metagraph/tests/graph/all/test_dbg_helpers.cpp @@ -39,6 +39,9 @@ template<> size_t max_test_k() { template<> size_t max_test_k() { return 100; } +template<> size_t max_test_k() { + return 100; +} template std::vector @@ -104,6 +107,24 @@ build_graph(uint64_t k, return graph; } +template <> +std::shared_ptr +build_graph(uint64_t k, + std::vector sequences, + DeBruijnGraph::Mode) { + auto graph = std::make_shared(k); + + uint64_t max_index = graph->max_index(); + + for (const auto &sequence : sequences) { + graph->add_sequence(sequence, [&](auto i) { ASSERT_TRUE(i <= ++max_index); }); + } + + [&]() { ASSERT_EQ(max_index, graph->max_index()); }(); + + return graph; +} + template <> std::shared_ptr build_graph(uint64_t k, @@ -283,6 +304,10 @@ template std::shared_ptr build_graph_batch(uint64_t, std::vector, DeBruijnGraph::Mode); +template +std::shared_ptr +build_graph_batch(uint64_t, std::vector, DeBruijnGraph::Mode); + template <> std::shared_ptr build_graph_batch(uint64_t k, @@ -488,6 +513,7 @@ template bool check_graph(const std::string &, DeBruijnGraph::Mode, b template bool check_graph(const std::string &, DeBruijnGraph::Mode, bool); template bool check_graph(const std::string &, DeBruijnGraph::Mode, bool); template bool check_graph(const std::string &, DeBruijnGraph::Mode, bool); +template bool check_graph(const std::string &, DeBruijnGraph::Mode, bool); } // namespace test } // namespace mtg diff --git a/metagraph/tests/graph/all/test_dbg_helpers.hpp b/metagraph/tests/graph/all/test_dbg_helpers.hpp index fc220f301e..bf394da089 100644 --- a/metagraph/tests/graph/all/test_dbg_helpers.hpp +++ b/metagraph/tests/graph/all/test_dbg_helpers.hpp @@ -10,6 +10,7 @@ #include "graph/representation/hash/dbg_hash_string.hpp" #include "graph/representation/hash/dbg_hash_ordered.hpp" #include "graph/representation/hash/dbg_hash_fast.hpp" +#include "graph/representation/hash/dbg_sshash.hpp" #include "graph/representation/bitmap/dbg_bitmap.hpp" @@ -91,6 +92,7 @@ typedef ::testing::Types, DBGSuccinctIndexed<2>, From 102bf31abb87b920ab86965fa373f8f8bb86d080 Mon Sep 17 00:00:00 2001 From: Oleksandr Kulkov Date: Wed, 8 Nov 2023 14:30:11 +0100 Subject: [PATCH 02/52] Use SSHash submodule instead of PTHash --- .gitmodules | 6 +++--- metagraph/CMakeLists.txt | 4 +++- metagraph/external-libraries/pthash | 1 - metagraph/external-libraries/sshash | 1 + metagraph/src/graph/representation/hash/dbg_sshash.hpp | 2 +- 5 files changed, 8 insertions(+), 6 deletions(-) delete mode 160000 metagraph/external-libraries/pthash create mode 160000 metagraph/external-libraries/sshash diff --git a/.gitmodules b/.gitmodules index 8c5a4fd577..9ad8bf6f9c 100644 --- a/.gitmodules +++ b/.gitmodules @@ -68,6 +68,6 @@ [submodule "metagraph/external-libraries/htslib"] path = metagraph/external-libraries/htslib url = https://github.com/samtools/htslib -[submodule "metagraph/external-libraries/pthash"] - path = metagraph/external-libraries/pthash - url = https://github.com/jermp/pthash.git +[submodule "metagraph/external-libraries/sshash"] + path = metagraph/external-libraries/sshash + url = https://github.com/jermp/sshash.git diff --git a/metagraph/CMakeLists.txt b/metagraph/CMakeLists.txt index 2eae42b6a1..26fb43a510 100644 --- a/metagraph/CMakeLists.txt +++ b/metagraph/CMakeLists.txt @@ -270,7 +270,6 @@ include_directories( external-libraries/zlib external-libraries/sdust external-libraries/simde-no-tests - external-libraries/pthash/include ${PROJECT_SOURCE_DIR}/src ) @@ -320,6 +319,8 @@ IF(APPLE) set(THREADS_PREFER_PTHREAD_FLAG ON) ENDIF() add_subdirectory(external-libraries/spdlog) +add_subdirectory(external-libraries/sshash) +target_include_directories(sshash_static PUBLIC external-libraries/sshash/include) add_subdirectory(external-libraries/DYNAMIC) add_subdirectory(external-libraries/zlib) target_compile_options(zlib @@ -410,6 +411,7 @@ set(METALIBS ${METALIBS} mersenne_twister sdust spdlog::spdlog + sshash_static XXSDS_DYNAMIC ips4o caches diff --git a/metagraph/external-libraries/pthash b/metagraph/external-libraries/pthash deleted file mode 160000 index 4098013a0c..0000000000 --- a/metagraph/external-libraries/pthash +++ /dev/null @@ -1 +0,0 @@ -Subproject commit 4098013a0c3428fdf5bd25d28c40f32ec267a64b diff --git a/metagraph/external-libraries/sshash b/metagraph/external-libraries/sshash new file mode 160000 index 0000000000..b278b8ef5d --- /dev/null +++ b/metagraph/external-libraries/sshash @@ -0,0 +1 @@ +Subproject commit b278b8ef5d27727c5080a97be4c1a46bbe705ea9 diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.hpp b/metagraph/src/graph/representation/hash/dbg_sshash.hpp index 72aaa06eef..4932fe8cac 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.hpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.hpp @@ -2,7 +2,7 @@ #define __DBG_SSHASH_HPP__ #include -#include +#include #include #include "graph/representation/base/sequence_graph.hpp" From 5fbbc3ae4f67be21baba3ba33c7499868871af86 Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Thu, 23 Nov 2023 12:40:47 +0100 Subject: [PATCH 03/52] trying to use sshash as a submodule --- .../graph/representation/hash/dbg_sshash.cpp | 117 ++++++++++++++++-- .../graph/representation/hash/dbg_sshash.hpp | 7 +- ....tmp.run1700659576911610385.free_slots.bin | 0 ...hash.tmp.run1700659576911610385.pilots.bin | Bin 0 -> 104 bytes ...p.run_1700659576859653407.minimizers.0.bin | Bin 0 -> 85 bytes .../data/string_to_sshash_dump.hashstrdbg | Bin 0 -> 452 bytes .../tests/graph/all/test_dbg_helpers.cpp | 66 +++++++--- 7 files changed, 160 insertions(+), 30 deletions(-) create mode 100644 metagraph/tests/data/sshash_sequences/pthash.tmp.run1700659576911610385.free_slots.bin create mode 100644 metagraph/tests/data/sshash_sequences/pthash.tmp.run1700659576911610385.pilots.bin create mode 100644 metagraph/tests/data/sshash_sequences/sshash.tmp.run_1700659576859653407.minimizers.0.bin create mode 100644 metagraph/tests/data/string_to_sshash_dump.hashstrdbg diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.cpp b/metagraph/src/graph/representation/hash/dbg_sshash.cpp index 3197a7b9ee..01e4bd875f 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.cpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.cpp @@ -3,99 +3,194 @@ namespace mtg { namespace graph { +// replace this function by just using other constructor and load? +DBGSSHash::DBGSSHash(std::string const& input_filename, size_t k):k_(k){ + sshash::build_configuration build_config; + build_config.k = k; + dict_.build(input_filename, build_config); +} void DBGSSHash::add_sequence(std::string_view sequence, const std::function &on_insertion) { + // TODO: throw exception? :) } void DBGSSHash::map_to_nodes(std::string_view sequence, const std::function &callback, const std::function &terminate) const { + map_to_nodes_sequentially(sequence, callback, terminate); } void DBGSSHash ::map_to_nodes_sequentially(std::string_view sequence, const std::function &callback, const std::function &terminate) const { + for (size_t i = 0; i + k_ <= sequence.size() && !terminate(); ++i) { + callback(kmer_to_node(sequence.substr(i, k_))); + } } DBGSSHash::node_index DBGSSHash::traverse(node_index node, char next_char) const { + std::string kmer = DBGSSHash::get_node_sequence(node); + sshash::neighbourhood nb = dict_.kmer_forward_neighbours(&kmer[0]); + switch (next_char) { + case 'A': + return nb.forward_A.kmer_id; + case 'C': + return nb.forward_C.kmer_id; + case 'G': + return nb.forward_G.kmer_id; + case 'T': + return nb.forward_T.kmer_id; + default: + break; + } return 0; } DBGSSHash::node_index DBGSSHash::traverse_back(node_index node, char prev_char) const { + std::string kmer = DBGSSHash::get_node_sequence(node); + sshash::neighbourhood nb = dict_.kmer_backward_neighbours(&kmer[0]); + switch (prev_char) { + case 'A': + return nb.backward_A.kmer_id; + case 'C': + return nb.backward_C.kmer_id; + case 'G': + return nb.backward_G.kmer_id; + case 'T': + return nb.backward_T.kmer_id; + default: + break; + } return 0; } void DBGSSHash ::adjacent_outgoing_nodes(node_index node, const std::function &callback) const { + assert(node+1 > 0 && node < num_nodes()); + call_outgoing_kmers(node, [&](auto child, char) { callback(child); }); + } void DBGSSHash ::adjacent_incoming_nodes(node_index node, const std::function &callback) const { + assert(node+1 > 0 && node < num_nodes()); + call_incoming_kmers(node, [&](auto parent, char) { callback(parent); }); } void DBGSSHash ::call_outgoing_kmers(node_index node, const OutgoingEdgeCallback &callback) const { + assert(node+1 > 0 && node < num_nodes()); + + auto prefix = get_node_sequence(node).substr(1); + + for (char c : alphabet_) { + auto next = kmer_to_node(prefix + c); + if (next+1 != npos) + // ! next ranges from 0 to num_nodes -1 ! + callback(next, c); + } } + void DBGSSHash ::call_incoming_kmers(node_index node, const IncomingEdgeCallback &callback) const { + assert(node+1 > 0 && node < num_nodes()); + + std::string suffix = get_node_sequence(node); + suffix.pop_back(); + + for (char c : alphabet_) { + auto prev = kmer_to_node(c + suffix); + if (prev+1 != npos) + // ! prev ranges from 0 to num_nodes -1 ! + callback(prev, c); + } } size_t DBGSSHash::outdegree(node_index node) const { - return 0; + std::string kmer = DBGSSHash::get_node_sequence(node); + sshash::neighbourhood nb = dict_.kmer_forward_neighbours(&kmer[0]); + size_t out_deg = bool(nb.forward_A.kmer_id + 1) + + bool(nb.forward_C.kmer_id + 1) + + bool(nb.forward_G.kmer_id + 1) + + bool(nb.forward_T.kmer_id + 1); + return out_deg; } bool DBGSSHash::has_single_outgoing(node_index node) const { - return false; + return DBGSSHash::outdegree(node) == 1; } bool DBGSSHash::has_multiple_outgoing(node_index node) const { - return false; + return DBGSSHash::outdegree(node) > 1; } size_t DBGSSHash::indegree(node_index node) const { - return 0; + std::string kmer = DBGSSHash::get_node_sequence(node); + sshash::neighbourhood nb = dict_.kmer_backward_neighbours(&kmer[0]); + size_t in_deg = bool(nb.backward_A.kmer_id + 1) + + bool(nb.backward_C.kmer_id + 1) + + bool(nb.backward_G.kmer_id + 1) + + bool(nb.backward_T.kmer_id + 1); + return in_deg; } bool DBGSSHash::has_no_incoming(node_index node) const { - return true; + return DBGSSHash::indegree(node) == 0; } bool DBGSSHash::has_single_incoming(node_index node) const { - return false; + return DBGSSHash::indegree(node) == 1; } -void DBGSSHash ::call_kmers( +void DBGSSHash::call_kmers( const std::function &callback) const { + for (size_t node_idx = 0; node_idx < num_nodes(); ++node_idx) { + callback(node_idx, get_node_sequence(node_idx)); + } } DBGSSHash::node_index DBGSSHash::kmer_to_node(std::string_view kmer) const { - return 0; + return dict_.lookup(kmer.begin(), true); } std::string DBGSSHash::get_node_sequence(node_index node) const { - return ""; + std::string str_kmer = ""; + str_kmer.append(k_, ' '); + dict_.access(node, &str_kmer[0]); + return str_kmer; } void DBGSSHash::serialize(std::ostream &out) const { + //TODO + throw std::invalid_argument( "not implemented" ); } void DBGSSHash::serialize(const std::string &filename) const { + dict_.dump(filename); } bool DBGSSHash::load(std::istream &in) { + //TODO return false; } bool DBGSSHash::load(const std::string &filename) { - return false; + sshash::build_configuration build_config; + build_config.k = k_; + // quick fix for value of m... k/2 + build_config.m = (k_+1)/2; + //build_config.tmp_dirname = "/home/marianna/Documents/Masterthesis/metagraph/metagraph/tests/data/sshash_sequences"; + dict_.build(filename, build_config); + return true; } bool DBGSSHash::operator==(const DeBruijnGraph &other) const { + //TODO return false; } -const std::string DBGSSHash::alphabet_ = ""; +const std::string DBGSSHash::alphabet_ = "ACGT"; const std::string &DBGSSHash::alphabet() const { return alphabet_; } diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.hpp b/metagraph/src/graph/representation/hash/dbg_sshash.hpp index 4932fe8cac..ab9e3b5416 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.hpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.hpp @@ -13,7 +13,8 @@ namespace graph { class DBGSSHash : public DeBruijnGraph { public: - explicit DBGSSHash(size_t k) {} + explicit DBGSSHash(size_t k):k_(k) {} + DBGSSHash(std::string const& input_filename, size_t k); // SequenceGraph overrides void add_sequence( @@ -36,7 +37,7 @@ class DBGSSHash : public DeBruijnGraph { void adjacent_incoming_nodes(node_index node, const std::function &callback) const override; - uint64_t num_nodes() const override { return 0; } + uint64_t num_nodes() const override { return dict_.size(); } bool load(std::istream &in); bool load(const std::string &filename) override; @@ -83,6 +84,8 @@ class DBGSSHash : public DeBruijnGraph { private: static const std::string alphabet_; + sshash::dictionary dict_; + size_t k_; }; } // namespace graph diff --git a/metagraph/tests/data/sshash_sequences/pthash.tmp.run1700659576911610385.free_slots.bin b/metagraph/tests/data/sshash_sequences/pthash.tmp.run1700659576911610385.free_slots.bin new file mode 100644 index 0000000000..e69de29bb2 diff --git a/metagraph/tests/data/sshash_sequences/pthash.tmp.run1700659576911610385.pilots.bin b/metagraph/tests/data/sshash_sequences/pthash.tmp.run1700659576911610385.pilots.bin new file mode 100644 index 0000000000000000000000000000000000000000..645d9336404f75884e49f6a5e3463c532aaca3b2 GIT binary patch literal 104 ScmZQzfB;4)O>K%3Y9Igs5C97R literal 0 HcmV?d00001 diff --git a/metagraph/tests/data/sshash_sequences/sshash.tmp.run_1700659576859653407.minimizers.0.bin b/metagraph/tests/data/sshash_sequences/sshash.tmp.run_1700659576859653407.minimizers.0.bin new file mode 100644 index 0000000000000000000000000000000000000000..7b3f4d09da930b164cb6c97d15b7fd4d09f2a71d GIT binary patch literal 85 qcmZQzfB;!2&DhHbVX;F6*ov5-EGWgki3P&qhYB!DK-Ka>1(*P4SOO~m literal 0 HcmV?d00001 diff --git a/metagraph/tests/data/string_to_sshash_dump.hashstrdbg b/metagraph/tests/data/string_to_sshash_dump.hashstrdbg new file mode 100644 index 0000000000000000000000000000000000000000..a61b5bc1b4eda87fc5e2332ac4deb2aba2d39d3b GIT binary patch literal 452 zcmZQz00R+52+hC&r3Iig1A~LTqr1B!I>sX8h^Y#zkh^n8h%-9IBIJyz3ad~EGt{jY z^#AVp$$G{7KNP^c0Q1`Pn0 literal 0 HcmV?d00001 diff --git a/metagraph/tests/graph/all/test_dbg_helpers.cpp b/metagraph/tests/graph/all/test_dbg_helpers.cpp index 47b1ee7e02..f03c763684 100644 --- a/metagraph/tests/graph/all/test_dbg_helpers.cpp +++ b/metagraph/tests/graph/all/test_dbg_helpers.cpp @@ -6,7 +6,7 @@ #include "graph/representation/succinct/boss_construct.hpp" #include "graph/representation/bitmap/dbg_bitmap_construct.hpp" #include "graph/graph_extensions/node_first_cache.hpp" - +#include namespace mtg { namespace test { @@ -107,23 +107,7 @@ build_graph(uint64_t k, return graph; } -template <> -std::shared_ptr -build_graph(uint64_t k, - std::vector sequences, - DeBruijnGraph::Mode) { - auto graph = std::make_shared(k); - - uint64_t max_index = graph->max_index(); - - for (const auto &sequence : sequences) { - graph->add_sequence(sequence, [&](auto i) { ASSERT_TRUE(i <= ++max_index); }); - } - [&]() { ASSERT_EQ(max_index, graph->max_index()); }(); - - return graph; -} template <> std::shared_ptr @@ -147,6 +131,54 @@ build_graph(uint64_t k, return graph; } +void writeFastaFile(const std::vector& sequences, const std::string& outputFilename) { + std::ofstream fastaFile(outputFilename); + + if (!fastaFile.is_open()) { + std::cerr << "Error: Unable to open the output file." << std::endl; + return; + } + + for (size_t i = 0; i < sequences.size(); ++i) { + //fastaFile << ">Sequence_" << (i + 1) << "\n" << sequences[i] << "\n"; + fastaFile << ">" << i << "\n" << sequences[i] << "\n"; + } + + fastaFile.close(); +} +template <> +std::shared_ptr +build_graph(uint64_t k, + std::vector sequences, + DeBruijnGraph::Mode) { + auto graph = std::make_shared(k); + + // use DBGHashString to build SSHash DBG + auto string_graph = std::make_shared(k); + uint64_t string_max_index = string_graph->max_index(); + + for (const auto &sequence : sequences) { + string_graph->add_sequence(sequence, [&](auto i) { ASSERT_TRUE(i <= ++string_max_index); }); + } + [&]() { ASSERT_EQ(string_max_index, string_graph->max_index()); }(); + //string_graph->serialize(dump_path);// dumps dbg but sequences are needed + + std::string dump_path = "/home/marianna/Documents/Masterthesis/metagraph/metagraph/tests/data/sshash_sequences/dump.fa"; + // not working: serialize primary mode tree + //auto db_graph = build_graph(k, sequences, DeBruijnGraph::PRIMARY); + //db_graph->serialize(dump_path); + //new approach: + if(sequences.size() == 0){ + throw std::invalid_argument( "empty graph" ); + } + sequences = get_primary_contigs(k, sequences); + writeFastaFile(sequences, dump_path); + graph->load(dump_path); + + + return graph; +} + template <> std::shared_ptr build_graph(uint64_t k, From 7ff3382a40f336ea1988a8840aa18946f89fbdb4 Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Thu, 30 Nov 2023 11:38:18 +0100 Subject: [PATCH 04/52] fixed index conversion between ssh and metagraph and list of contigs --- .../graph/representation/hash/dbg_sshash.cpp | 69 +++++++++++-------- .../graph/representation/hash/dbg_sshash.hpp | 2 +- .../tests/graph/all/test_dbg_helpers.cpp | 38 +++++----- 3 files changed, 59 insertions(+), 50 deletions(-) diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.cpp b/metagraph/src/graph/representation/hash/dbg_sshash.cpp index 01e4bd875f..518f1332a8 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.cpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.cpp @@ -6,12 +6,14 @@ namespace graph { // replace this function by just using other constructor and load? DBGSSHash::DBGSSHash(std::string const& input_filename, size_t k):k_(k){ sshash::build_configuration build_config; - build_config.k = k; + build_config.k = k;// dict_.build(input_filename, build_config); } void DBGSSHash::add_sequence(std::string_view sequence, const std::function &on_insertion) { // TODO: throw exception? :) + throw std::runtime_error("adding sequences not implemented"); + } void DBGSSHash::map_to_nodes(std::string_view sequence, @@ -29,64 +31,73 @@ void DBGSSHash ::map_to_nodes_sequentially(std::string_view sequence, } DBGSSHash::node_index DBGSSHash::traverse(node_index node, char next_char) const { - std::string kmer = DBGSSHash::get_node_sequence(node); + std::string kmer = DBGSSHash::get_node_sequence(node); sshash::neighbourhood nb = dict_.kmer_forward_neighbours(&kmer[0]); + uint64_t ssh_idx = -1; switch (next_char) { case 'A': - return nb.forward_A.kmer_id; + ssh_idx = nb.forward_A.kmer_id; + break; case 'C': - return nb.forward_C.kmer_id; + ssh_idx = nb.forward_C.kmer_id; + break; case 'G': - return nb.forward_G.kmer_id; + ssh_idx = nb.forward_G.kmer_id; + break; case 'T': - return nb.forward_T.kmer_id; + ssh_idx = nb.forward_T.kmer_id; + break; default: break; } - return 0; + return ssh_idx + 1; } DBGSSHash::node_index DBGSSHash::traverse_back(node_index node, char prev_char) const { std::string kmer = DBGSSHash::get_node_sequence(node); sshash::neighbourhood nb = dict_.kmer_backward_neighbours(&kmer[0]); + uint64_t ssh_idx = -1; switch (prev_char) { case 'A': - return nb.backward_A.kmer_id; + ssh_idx = nb.backward_A.kmer_id; + break; case 'C': - return nb.backward_C.kmer_id; + ssh_idx = nb.backward_C.kmer_id; + break; case 'G': - return nb.backward_G.kmer_id; + ssh_idx = nb.backward_G.kmer_id; + break; case 'T': - return nb.backward_T.kmer_id; + ssh_idx = nb.backward_T.kmer_id; + break; default: break; } - return 0; + return ssh_idx + 1; } void DBGSSHash ::adjacent_outgoing_nodes(node_index node, const std::function &callback) const { - assert(node+1 > 0 && node < num_nodes()); + assert(node > 0 && node <= num_nodes()); call_outgoing_kmers(node, [&](auto child, char) { callback(child); }); } void DBGSSHash ::adjacent_incoming_nodes(node_index node, const std::function &callback) const { - assert(node+1 > 0 && node < num_nodes()); + assert(node > 0 && node <= num_nodes()); call_incoming_kmers(node, [&](auto parent, char) { callback(parent); }); } void DBGSSHash ::call_outgoing_kmers(node_index node, const OutgoingEdgeCallback &callback) const { - assert(node+1 > 0 && node < num_nodes()); + assert(node > 0 && node <= num_nodes()); auto prefix = get_node_sequence(node).substr(1); for (char c : alphabet_) { auto next = kmer_to_node(prefix + c); - if (next+1 != npos) - // ! next ranges from 0 to num_nodes -1 ! + if (next != npos) callback(next, c); } } @@ -94,15 +105,14 @@ void DBGSSHash ::call_outgoing_kmers(node_index node, void DBGSSHash ::call_incoming_kmers(node_index node, const IncomingEdgeCallback &callback) const { - assert(node+1 > 0 && node < num_nodes()); + assert(node > 0 && node <= num_nodes()); std::string suffix = get_node_sequence(node); suffix.pop_back(); for (char c : alphabet_) { auto prev = kmer_to_node(c + suffix); - if (prev+1 != npos) - // ! prev ranges from 0 to num_nodes -1 ! + if (prev != npos) callback(prev, c); } } @@ -110,7 +120,7 @@ void DBGSSHash ::call_incoming_kmers(node_index node, size_t DBGSSHash::outdegree(node_index node) const { std::string kmer = DBGSSHash::get_node_sequence(node); sshash::neighbourhood nb = dict_.kmer_forward_neighbours(&kmer[0]); - size_t out_deg = bool(nb.forward_A.kmer_id + 1) + size_t out_deg = bool(nb.forward_A.kmer_id + 1) // change to loop? + bool(nb.forward_C.kmer_id + 1) + bool(nb.forward_G.kmer_id + 1) + bool(nb.forward_T.kmer_id + 1); @@ -128,7 +138,7 @@ bool DBGSSHash::has_multiple_outgoing(node_index node) const { size_t DBGSSHash::indegree(node_index node) const { std::string kmer = DBGSSHash::get_node_sequence(node); sshash::neighbourhood nb = dict_.kmer_backward_neighbours(&kmer[0]); - size_t in_deg = bool(nb.backward_A.kmer_id + 1) + size_t in_deg = bool(nb.backward_A.kmer_id + 1) // change to loop? + bool(nb.backward_C.kmer_id + 1) + bool(nb.backward_G.kmer_id + 1) + bool(nb.backward_T.kmer_id + 1); @@ -145,25 +155,27 @@ bool DBGSSHash::has_single_incoming(node_index node) const { void DBGSSHash::call_kmers( const std::function &callback) const { - for (size_t node_idx = 0; node_idx < num_nodes(); ++node_idx) { + for (size_t node_idx = 1; node_idx <= num_nodes(); ++node_idx) { callback(node_idx, get_node_sequence(node_idx)); } } DBGSSHash::node_index DBGSSHash::kmer_to_node(std::string_view kmer) const { - return dict_.lookup(kmer.begin(), true); + uint64_t ssh_idx = dict_.lookup(kmer.begin(), true); + return ssh_idx + 1; } std::string DBGSSHash::get_node_sequence(node_index node) const { std::string str_kmer = ""; str_kmer.append(k_, ' '); - dict_.access(node, &str_kmer[0]); + uint64_t ssh_idx = node - 1; // switch back to sshash idx!!! + dict_.access(ssh_idx, &str_kmer[0]); return str_kmer; } void DBGSSHash::serialize(std::ostream &out) const { //TODO - throw std::invalid_argument( "not implemented" ); + throw std::runtime_error("serialize to stream not implemented"); } void DBGSSHash::serialize(const std::string &filename) const { @@ -171,13 +183,14 @@ void DBGSSHash::serialize(const std::string &filename) const { } bool DBGSSHash::load(std::istream &in) { - //TODO + throw std::runtime_error("load from stream not implemented"); return false; } bool DBGSSHash::load(const std::string &filename) { sshash::build_configuration build_config; build_config.k = k_; + std::cout<< "k is "<& sequences, const std::string for (size_t i = 0; i < sequences.size(); ++i) { //fastaFile << ">Sequence_" << (i + 1) << "\n" << sequences[i] << "\n"; - fastaFile << ">" << i << "\n" << sequences[i] << "\n"; + fastaFile << ">"<< "\n" << sequences[i] << "\n"; } fastaFile.close(); @@ -150,32 +150,28 @@ template <> std::shared_ptr build_graph(uint64_t k, std::vector sequences, - DeBruijnGraph::Mode) { - auto graph = std::make_shared(k); - - // use DBGHashString to build SSHash DBG - auto string_graph = std::make_shared(k); - uint64_t string_max_index = string_graph->max_index(); + DeBruijnGraph::Mode mode) { - for (const auto &sequence : sequences) { - string_graph->add_sequence(sequence, [&](auto i) { ASSERT_TRUE(i <= ++string_max_index); }); - } - [&]() { ASSERT_EQ(string_max_index, string_graph->max_index()); }(); - //string_graph->serialize(dump_path);// dumps dbg but sequences are needed + auto graph = std::make_shared(k); - std::string dump_path = "/home/marianna/Documents/Masterthesis/metagraph/metagraph/tests/data/sshash_sequences/dump.fa"; - // not working: serialize primary mode tree - //auto db_graph = build_graph(k, sequences, DeBruijnGraph::PRIMARY); - //db_graph->serialize(dump_path); - //new approach: if(sequences.size() == 0){ throw std::invalid_argument( "empty graph" ); } - sequences = get_primary_contigs(k, sequences); - writeFastaFile(sequences, dump_path); + //std::string seq_dump_path = "/home/marianna/Documents/Masterthesis/metagraph/metagraph/tests/data/sshash_sequences/seq_dump.fa"; + //writeFastaFile(sequences, seq_dump_path); + // use DBGHashString to get contigs for SSHash + auto string_graph = build_graph(k, sequences, + mode); + + std::vector contigs; + string_graph->call_sequences([&](const std::string &contig, const auto &) { + contigs.push_back(contig); + }, 1, false); + std::string dump_path = "/home/marianna/Documents/Masterthesis/metagraph/metagraph/tests/data/sshash_sequences/dump.fa"; + //std::string expl_file = "/home/marianna/Documents/Masterthesis/metagraph/metagraph/external-libraries/sshash/data/unitigs_stitched/ecoli4.fasta.unitigs.fa.ust.fa"; + writeFastaFile(contigs, dump_path); graph->load(dump_path); - - + return graph; } From 52bb95763e5154b9d2004fcb063fee76c726870d Mon Sep 17 00:00:00 2001 From: Harun Mustafa Date: Wed, 6 Dec 2023 14:54:00 +0100 Subject: [PATCH 05/52] some changes to sshash, first try at avoiding the compile error in sshash --- .gitignore | 1 + metagraph/CMakeLists.txt | 4 +-- .../graph/representation/hash/dbg_sshash.cpp | 34 +++++++++++++------ .../graph/representation/hash/dbg_sshash.hpp | 19 ++++++----- .../tests/graph/all/test_dbg_helpers.cpp | 3 +- 5 files changed, 39 insertions(+), 22 deletions(-) diff --git a/.gitignore b/.gitignore index 9e165295f4..d59a6a0b6f 100644 --- a/.gitignore +++ b/.gitignore @@ -1,5 +1,6 @@ *.fa *.fai +.vscode !metagraph/tests/data/*.fa !metagraph/tests/data/*.fai metagraph/tests/data/*dump_test* diff --git a/metagraph/CMakeLists.txt b/metagraph/CMakeLists.txt index 26fb43a510..16db225605 100644 --- a/metagraph/CMakeLists.txt +++ b/metagraph/CMakeLists.txt @@ -319,8 +319,8 @@ IF(APPLE) set(THREADS_PREFER_PTHREAD_FLAG ON) ENDIF() add_subdirectory(external-libraries/spdlog) -add_subdirectory(external-libraries/sshash) -target_include_directories(sshash_static PUBLIC external-libraries/sshash/include) +add_subdirectory(external-libraries/sshash SYSTEM) +target_include_directories(sshash_static PUBLIC SYSTEM external-libraries/sshash/include) add_subdirectory(external-libraries/DYNAMIC) add_subdirectory(external-libraries/zlib) target_compile_options(zlib diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.cpp b/metagraph/src/graph/representation/hash/dbg_sshash.cpp index 518f1332a8..c8bec51d1b 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.cpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.cpp @@ -1,14 +1,25 @@ #include "dbg_sshash.hpp" +#include + namespace mtg { namespace graph { +DBGSSHash::~DBGSSHash() {} +DBGSSHash::DBGSSHash(size_t k):k_(k) { + dict_ = std::make_unique(); +} // replace this function by just using other constructor and load? DBGSSHash::DBGSSHash(std::string const& input_filename, size_t k):k_(k){ sshash::build_configuration build_config; build_config.k = k;// - dict_.build(input_filename, build_config); + dict_ = std::make_unique(); + dict_->build(input_filename, build_config); } + std::string DBGSSHash::file_extension() const { return kExtension; } + size_t DBGSSHash::get_k() const { return k_; } + DeBruijnGraph::Mode DBGSSHash::get_mode() const { return BASIC; } + void DBGSSHash::add_sequence(std::string_view sequence, const std::function &on_insertion) { // TODO: throw exception? :) @@ -32,7 +43,7 @@ void DBGSSHash ::map_to_nodes_sequentially(std::string_view sequence, DBGSSHash::node_index DBGSSHash::traverse(node_index node, char next_char) const { std::string kmer = DBGSSHash::get_node_sequence(node); - sshash::neighbourhood nb = dict_.kmer_forward_neighbours(&kmer[0]); + sshash::neighbourhood nb = dict_->kmer_forward_neighbours(&kmer[0]); uint64_t ssh_idx = -1; switch (next_char) { case 'A': @@ -55,7 +66,7 @@ DBGSSHash::node_index DBGSSHash::traverse(node_index node, char next_char) const DBGSSHash::node_index DBGSSHash::traverse_back(node_index node, char prev_char) const { std::string kmer = DBGSSHash::get_node_sequence(node); - sshash::neighbourhood nb = dict_.kmer_backward_neighbours(&kmer[0]); + sshash::neighbourhood nb = dict_->kmer_backward_neighbours(&kmer[0]); uint64_t ssh_idx = -1; switch (prev_char) { case 'A': @@ -119,7 +130,7 @@ void DBGSSHash ::call_incoming_kmers(node_index node, size_t DBGSSHash::outdegree(node_index node) const { std::string kmer = DBGSSHash::get_node_sequence(node); - sshash::neighbourhood nb = dict_.kmer_forward_neighbours(&kmer[0]); + sshash::neighbourhood nb = dict_->kmer_forward_neighbours(&kmer[0]); size_t out_deg = bool(nb.forward_A.kmer_id + 1) // change to loop? + bool(nb.forward_C.kmer_id + 1) + bool(nb.forward_G.kmer_id + 1) @@ -137,7 +148,7 @@ bool DBGSSHash::has_multiple_outgoing(node_index node) const { size_t DBGSSHash::indegree(node_index node) const { std::string kmer = DBGSSHash::get_node_sequence(node); - sshash::neighbourhood nb = dict_.kmer_backward_neighbours(&kmer[0]); + sshash::neighbourhood nb = dict_->kmer_backward_neighbours(&kmer[0]); size_t in_deg = bool(nb.backward_A.kmer_id + 1) // change to loop? + bool(nb.backward_C.kmer_id + 1) + bool(nb.backward_G.kmer_id + 1) @@ -161,7 +172,7 @@ void DBGSSHash::call_kmers( } DBGSSHash::node_index DBGSSHash::kmer_to_node(std::string_view kmer) const { - uint64_t ssh_idx = dict_.lookup(kmer.begin(), true); + uint64_t ssh_idx = dict_->lookup(kmer.begin(), true); return ssh_idx + 1; } @@ -169,7 +180,7 @@ std::string DBGSSHash::get_node_sequence(node_index node) const { std::string str_kmer = ""; str_kmer.append(k_, ' '); uint64_t ssh_idx = node - 1; // switch back to sshash idx!!! - dict_.access(ssh_idx, &str_kmer[0]); + dict_->access(ssh_idx, &str_kmer[0]); return str_kmer; } @@ -179,7 +190,7 @@ void DBGSSHash::serialize(std::ostream &out) const { } void DBGSSHash::serialize(const std::string &filename) const { - dict_.dump(filename); + dict_->dump(filename); } bool DBGSSHash::load(std::istream &in) { @@ -190,11 +201,11 @@ bool DBGSSHash::load(std::istream &in) { bool DBGSSHash::load(const std::string &filename) { sshash::build_configuration build_config; build_config.k = k_; - std::cout<< "k is "<build(filename, build_config); return true; } @@ -208,5 +219,6 @@ const std::string &DBGSSHash::alphabet() const { return alphabet_; } +uint64_t DBGSSHash::num_nodes() const { return dict_->size(); } } // namespace graph } // namespace mtg diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.hpp b/metagraph/src/graph/representation/hash/dbg_sshash.hpp index b649d5d3f5..792a79e570 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.hpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.hpp @@ -2,20 +2,23 @@ #define __DBG_SSHASH_HPP__ #include -#include #include #include "graph/representation/base/sequence_graph.hpp" - +namespace sshash{ +class dictionary; +} namespace mtg { namespace graph { class DBGSSHash : public DeBruijnGraph { public: - explicit DBGSSHash(size_t k):k_(k) {} + explicit DBGSSHash(size_t k); DBGSSHash(std::string const& input_filename, size_t k); + ~DBGSSHash(); + // SequenceGraph overrides void add_sequence( std::string_view sequence, @@ -37,7 +40,7 @@ class DBGSSHash : public DeBruijnGraph { void adjacent_incoming_nodes(node_index node, const std::function &callback) const override; - uint64_t num_nodes() const override { return dict_.size(); } + uint64_t num_nodes() const override; bool load(std::istream &in); bool load(const std::string &filename) override; @@ -46,15 +49,15 @@ class DBGSSHash : public DeBruijnGraph { void serialize(const std::string &filename) const override; static constexpr auto kExtension = ".sshashdbg"; - std::string file_extension() const override { return kExtension; } + std::string file_extension() const override; std::string get_node_sequence(node_index node) const override; // DeBruijnGraph overrides - size_t get_k() const override { return k_; } + size_t get_k() const override ; // TODO: add the support for the canonical mode - Mode get_mode() const override { return BASIC; } + Mode get_mode() const override; node_index traverse(node_index node, char next_char) const override; node_index traverse_back(node_index node, char prev_char) const override; @@ -84,7 +87,7 @@ class DBGSSHash : public DeBruijnGraph { private: static const std::string alphabet_; - sshash::dictionary dict_; + std::unique_ptr dict_; size_t k_; }; diff --git a/metagraph/tests/graph/all/test_dbg_helpers.cpp b/metagraph/tests/graph/all/test_dbg_helpers.cpp index 8df4cbda63..90fe6d351a 100644 --- a/metagraph/tests/graph/all/test_dbg_helpers.cpp +++ b/metagraph/tests/graph/all/test_dbg_helpers.cpp @@ -169,8 +169,9 @@ build_graph(uint64_t k, }, 1, false); std::string dump_path = "/home/marianna/Documents/Masterthesis/metagraph/metagraph/tests/data/sshash_sequences/dump.fa"; //std::string expl_file = "/home/marianna/Documents/Masterthesis/metagraph/metagraph/external-libraries/sshash/data/unitigs_stitched/ecoli4.fasta.unitigs.fa.ust.fa"; + std::string exp_seq = "/home/marianna/Documents/Masterthesis/metagraph/metagraph/tests/data/sshash_sequences/experiment_sequences.fa"; writeFastaFile(contigs, dump_path); - graph->load(dump_path); + graph->load(exp_seq); return graph; } From 65c5d07553d7d45b22c3981c71c30e76b01570b1 Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Thu, 7 Dec 2023 10:38:35 +0100 Subject: [PATCH 06/52] changes for unit_test usage --- .../graph/representation/hash/dbg_sshash.cpp | 31 ++++++++++++++++++- .../tests/graph/all/test_dbg_helpers.cpp | 17 +++++++--- 2 files changed, 43 insertions(+), 5 deletions(-) diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.cpp b/metagraph/src/graph/representation/hash/dbg_sshash.cpp index c8bec51d1b..8a5e300319 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.cpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.cpp @@ -172,7 +172,7 @@ void DBGSSHash::call_kmers( } DBGSSHash::node_index DBGSSHash::kmer_to_node(std::string_view kmer) const { - uint64_t ssh_idx = dict_->lookup(kmer.begin(), true); + uint64_t ssh_idx = dict_->lookup(kmer.begin(), false); return ssh_idx + 1; } @@ -189,17 +189,46 @@ void DBGSSHash::serialize(std::ostream &out) const { throw std::runtime_error("serialize to stream not implemented"); } +void write_k_to_file(const std::string &filename, uint64_t k){ + std::string k_file_name = filename + "_k.txt"; + std::ofstream k_File(k_file_name); + if (!k_File.is_open()) { + std::cerr << "Error: Unable to open the k-output file." << std::endl; + return; + } + k_File << k; + k_File.close(); +} void DBGSSHash::serialize(const std::string &filename) const { dict_->dump(filename); + write_k_to_file(filename, k_); } bool DBGSSHash::load(std::istream &in) { throw std::runtime_error("load from stream not implemented"); return false; } +uint64_t load_k_from_file(const std::string &filename){ + // Open the file in input mode + std::string k_file_name = filename + "_k.txt"; + std::ifstream inputFile(k_file_name); + + if (!inputFile.is_open()) { + std::cerr << "Error opening the file." << std::endl; + return 1; + } + + // Read first line + std::string firstLine; + std::getline(inputFile, firstLine); + uint64_t k = std::stoi(firstLine); + + return k; +} bool DBGSSHash::load(const std::string &filename) { sshash::build_configuration build_config; + k_ = load_k_from_file(filename); build_config.k = k_; // quick fix for value of m... k/2 but odd build_config.m = (k_+1)/2; diff --git a/metagraph/tests/graph/all/test_dbg_helpers.cpp b/metagraph/tests/graph/all/test_dbg_helpers.cpp index 90fe6d351a..91ed016fae 100644 --- a/metagraph/tests/graph/all/test_dbg_helpers.cpp +++ b/metagraph/tests/graph/all/test_dbg_helpers.cpp @@ -40,7 +40,7 @@ template<> size_t max_test_k() { return 100; } template<> size_t max_test_k() { - return 100; + return 31; } template @@ -131,7 +131,7 @@ build_graph(uint64_t k, return graph; } -void writeFastaFile(const std::vector& sequences, const std::string& outputFilename) { +void writeFastaFile(const std::vector& sequences, const std::string& outputFilename, const uint64_t k) { std::ofstream fastaFile(outputFilename); if (!fastaFile.is_open()) { @@ -139,12 +139,21 @@ void writeFastaFile(const std::vector& sequences, const std::string return; } + std::string k_file_name = outputFilename + "_k.txt"; + std::ofstream k_File(k_file_name); + if (!k_File.is_open()) { + std::cerr << "Error: Unable to open the k-output file." << std::endl; + return; + } + k_File << k; + for (size_t i = 0; i < sequences.size(); ++i) { //fastaFile << ">Sequence_" << (i + 1) << "\n" << sequences[i] << "\n"; fastaFile << ">"<< "\n" << sequences[i] << "\n"; } fastaFile.close(); + k_File.close(); } template <> std::shared_ptr @@ -170,8 +179,8 @@ build_graph(uint64_t k, std::string dump_path = "/home/marianna/Documents/Masterthesis/metagraph/metagraph/tests/data/sshash_sequences/dump.fa"; //std::string expl_file = "/home/marianna/Documents/Masterthesis/metagraph/metagraph/external-libraries/sshash/data/unitigs_stitched/ecoli4.fasta.unitigs.fa.ust.fa"; std::string exp_seq = "/home/marianna/Documents/Masterthesis/metagraph/metagraph/tests/data/sshash_sequences/experiment_sequences.fa"; - writeFastaFile(contigs, dump_path); - graph->load(exp_seq); + writeFastaFile(contigs, dump_path, k); + graph->load(dump_path); return graph; } From e6800bede7add23f9cceda118095ed8b8cd903ca Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Thu, 7 Dec 2023 10:48:30 +0100 Subject: [PATCH 07/52] new sshash version --- metagraph/external-libraries/sshash | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/metagraph/external-libraries/sshash b/metagraph/external-libraries/sshash index b278b8ef5d..d3ea2c49eb 160000 --- a/metagraph/external-libraries/sshash +++ b/metagraph/external-libraries/sshash @@ -1 +1 @@ -Subproject commit b278b8ef5d27727c5080a97be4c1a46bbe705ea9 +Subproject commit d3ea2c49eb7aad4ed544a525af3e16baab849f53 From 885ccd3a57d3cf54b3def8c8714afd2b5a617543 Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Thu, 11 Jan 2024 11:35:39 +0100 Subject: [PATCH 08/52] ignore strict aliasing warning --- metagraph/CMakeLists.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/metagraph/CMakeLists.txt b/metagraph/CMakeLists.txt index 16db225605..6d54d8e443 100644 --- a/metagraph/CMakeLists.txt +++ b/metagraph/CMakeLists.txt @@ -321,6 +321,7 @@ ENDIF() add_subdirectory(external-libraries/spdlog) add_subdirectory(external-libraries/sshash SYSTEM) target_include_directories(sshash_static PUBLIC SYSTEM external-libraries/sshash/include) +target_compile_options(test_alphabet PRIVATE -Wno-strict-aliasing) add_subdirectory(external-libraries/DYNAMIC) add_subdirectory(external-libraries/zlib) target_compile_options(zlib From 127ef009abf69211d811c4455a49335d4fda1fb1 Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Thu, 11 Jan 2024 11:47:13 +0100 Subject: [PATCH 09/52] using sshash from cli --- metagraph/src/cli/build.cpp | 15 +++++++++++++- metagraph/src/cli/config/config.cpp | 7 +++++-- metagraph/src/cli/config/config.hpp | 1 + metagraph/src/cli/load/load_graph.cpp | 8 ++++++-- .../graph/representation/hash/dbg_sshash.cpp | 20 ++++++++++++++----- .../graph/representation/hash/dbg_sshash.hpp | 2 +- 6 files changed, 42 insertions(+), 11 deletions(-) diff --git a/metagraph/src/cli/build.cpp b/metagraph/src/cli/build.cpp index 41caf84051..40e1cd74e2 100644 --- a/metagraph/src/cli/build.cpp +++ b/metagraph/src/cli/build.cpp @@ -7,6 +7,7 @@ #include "graph/representation/hash/dbg_hash_ordered.hpp" #include "graph/representation/hash/dbg_hash_string.hpp" #include "graph/representation/hash/dbg_hash_fast.hpp" +#include "graph/representation/hash/dbg_sshash.hpp" #include "graph/representation/bitmap/dbg_bitmap.hpp" #include "graph/representation/bitmap/dbg_bitmap_construct.hpp" #include "graph/representation/succinct/dbg_succinct.hpp" @@ -249,7 +250,15 @@ int build_graph(Config *config) { get_verbose())); } - } else { + } else if (config->graph_type == Config::GraphType::SSHASH){ + + graph.reset(new DBGSSHash(files.at(0), config->k)); + if(files.size() > 1){ + logger->error("Only one file for SSHash"); + exit(1); + } + + }else { //slower method switch (config->graph_type) { @@ -284,6 +293,10 @@ int build_graph(Config *config) { " in dynamic regime is not supported"); exit(1); + case Config::GraphType::SSHASH: + logger->error("SSHash-graph construction" + " in dynamic regime is not supported"); + exit(1); case Config::GraphType::INVALID: assert(false); } diff --git a/metagraph/src/cli/config/config.cpp b/metagraph/src/cli/config/config.cpp index e16342f29f..1abcaccbe5 100644 --- a/metagraph/src/cli/config/config.cpp +++ b/metagraph/src/cli/config/config.cpp @@ -817,7 +817,10 @@ Config::GraphType Config::string_to_graphtype(const std::string &string) { } else if (string == "bitmap") { return GraphType::BITMAP; - } else { + } else if (string == "sshash"){ + return GraphType::SSHASH; + } + else { std::cerr << "Error: unknown graph representation" << std::endl; exit(1); } @@ -958,7 +961,7 @@ if (advanced) { fprintf(stderr, "\t --max-count-q [INT] \tmax k-mer abundance quantile (max-count is used by default) [1.0]\n"); fprintf(stderr, "\t --reference [STR] \tbasename of reference sequence (for parsing VCF files) []\n"); fprintf(stderr, "\n"); - fprintf(stderr, "\t --graph [STR] \tgraph representation: succinct / bitmap / hash / hashstr / hashfast [succinct]\n"); + fprintf(stderr, "\t --graph [STR] \tgraph representation: succinct / bitmap / hash / hashstr / hashfast [succinct] / sshash\n"); fprintf(stderr, "\t --state [STR] \tstate of succinct graph: small / dynamic / stat / fast [stat]\n"); fprintf(stderr, "\t --inplace \t\tconstruct succinct graph in-place and serialize without loading to RAM [off]\n"); fprintf(stderr, "\t --count-kmers \tcount k-mers and build weighted graph [off]\n"); diff --git a/metagraph/src/cli/config/config.hpp b/metagraph/src/cli/config/config.hpp index a4cb1f790f..ae7b2edc3f 100644 --- a/metagraph/src/cli/config/config.hpp +++ b/metagraph/src/cli/config/config.hpp @@ -224,6 +224,7 @@ class Config { HASH_PACKED, HASH_STR, HASH_FAST, + SSHASH, BITMAP, }; diff --git a/metagraph/src/cli/load/load_graph.cpp b/metagraph/src/cli/load/load_graph.cpp index f7627a6b4b..5212c0a671 100644 --- a/metagraph/src/cli/load/load_graph.cpp +++ b/metagraph/src/cli/load/load_graph.cpp @@ -7,6 +7,7 @@ #include "graph/representation/hash/dbg_hash_ordered.hpp" #include "graph/representation/hash/dbg_hash_string.hpp" #include "graph/representation/hash/dbg_hash_fast.hpp" +#include "graph/representation/hash/dbg_sshash.hpp" #include "graph/representation/bitmap/dbg_bitmap.hpp" #include "graph/representation/succinct/dbg_succinct.hpp" #include "cli/config/config.hpp" @@ -36,6 +37,9 @@ Config::GraphType parse_graph_type(const std::string &filename) { } else if (utils::ends_with(filename, graph::DBGBitmap::kExtension)) { return Config::GraphType::BITMAP; + } else if (utils::ends_with(filename, graph::DBGSSHash::kExtension)) { + return Config::GraphType::SSHASH; + } else { return Config::GraphType::INVALID; } @@ -58,10 +62,10 @@ std::shared_ptr load_critical_dbg(const std::string &filename) { case Config::GraphType::HASH_FAST: return load_critical_graph_from_file(filename); - case Config::GraphType::BITMAP: return load_critical_graph_from_file(filename); - + case Config::GraphType::SSHASH: + return load_critical_graph_from_file(filename); case Config::GraphType::INVALID: logger->error("Cannot load graph from file '{}', needs a valid file extension", filename); diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.cpp b/metagraph/src/graph/representation/hash/dbg_sshash.cpp index 8a5e300319..dac20fffd7 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.cpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.cpp @@ -9,10 +9,13 @@ DBGSSHash::~DBGSSHash() {} DBGSSHash::DBGSSHash(size_t k):k_(k) { dict_ = std::make_unique(); } -// replace this function by just using other constructor and load? + DBGSSHash::DBGSSHash(std::string const& input_filename, size_t k):k_(k){ sshash::build_configuration build_config; build_config.k = k;// + // quick fix for value of m... k/2 but odd + build_config.m = (k_+1)/2; + if(build_config.m % 2 == 0) build_config.m++; dict_ = std::make_unique(); dict_->build(input_filename, build_config); } @@ -200,7 +203,8 @@ void write_k_to_file(const std::string &filename, uint64_t k){ k_File.close(); } void DBGSSHash::serialize(const std::string &filename) const { - dict_->dump(filename); + std::string suffixed_filename = utils::make_suffix(filename, kExtension); + dict_->dump(suffixed_filename); write_k_to_file(filename, k_); } @@ -227,14 +231,20 @@ uint64_t load_k_from_file(const std::string &filename){ } bool DBGSSHash::load(const std::string &filename) { + // remove file extension... + std::string filename_no_ext = filename; + if(utils::ends_with(filename, kExtension)){ + size_t pos = filename.rfind(kExtension); + filename_no_ext = filename.substr(0, pos); + } + k_ = load_k_from_file(filename_no_ext); sshash::build_configuration build_config; - k_ = load_k_from_file(filename); build_config.k = k_; // quick fix for value of m... k/2 but odd build_config.m = (k_+1)/2; if(build_config.m % 2 == 0) build_config.m++; - //build_config.tmp_dirname = "/home/marianna/Documents/Masterthesis/metagraph/metagraph/tests/data/sshash_sequences"; - dict_->build(filename, build_config); + std::string suffixed_filename = utils::make_suffix(filename_no_ext, kExtension); + dict_->build(suffixed_filename, build_config); return true; } diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.hpp b/metagraph/src/graph/representation/hash/dbg_sshash.hpp index 792a79e570..38930d9c88 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.hpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.hpp @@ -3,7 +3,7 @@ #include #include - +#include "common/utils/string_utils.hpp" #include "graph/representation/base/sequence_graph.hpp" namespace sshash{ From f21eace1283c0589823bec8e5b20989740fb5375 Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Thu, 11 Jan 2024 11:48:18 +0100 Subject: [PATCH 10/52] general path --- metagraph/tests/graph/all/test_dbg_helpers.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/metagraph/tests/graph/all/test_dbg_helpers.cpp b/metagraph/tests/graph/all/test_dbg_helpers.cpp index 91ed016fae..001f363f98 100644 --- a/metagraph/tests/graph/all/test_dbg_helpers.cpp +++ b/metagraph/tests/graph/all/test_dbg_helpers.cpp @@ -176,9 +176,9 @@ build_graph(uint64_t k, string_graph->call_sequences([&](const std::string &contig, const auto &) { contigs.push_back(contig); }, 1, false); - std::string dump_path = "/home/marianna/Documents/Masterthesis/metagraph/metagraph/tests/data/sshash_sequences/dump.fa"; + std::string dump_path = "../tests/data/sshash_sequences/dump.fa"; //std::string expl_file = "/home/marianna/Documents/Masterthesis/metagraph/metagraph/external-libraries/sshash/data/unitigs_stitched/ecoli4.fasta.unitigs.fa.ust.fa"; - std::string exp_seq = "/home/marianna/Documents/Masterthesis/metagraph/metagraph/tests/data/sshash_sequences/experiment_sequences.fa"; + //std::string exp_seq = "/home/marianna/Documents/Masterthesis/metagraph/metagraph/tests/data/sshash_sequences/experiment_sequences.fa"; writeFastaFile(contigs, dump_path, k); graph->load(dump_path); From 49e68cd5a24a3f95948d1d23fe23f65dfa8d5bfa Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Thu, 18 Jan 2024 12:37:16 +0100 Subject: [PATCH 11/52] fixed serialization and loading --- .../graph/representation/hash/dbg_sshash.cpp | 55 +++++-------------- .../graph/representation/hash/dbg_sshash.hpp | 1 + 2 files changed, 14 insertions(+), 42 deletions(-) diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.cpp b/metagraph/src/graph/representation/hash/dbg_sshash.cpp index dac20fffd7..361f40031f 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.cpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.cpp @@ -192,59 +192,30 @@ void DBGSSHash::serialize(std::ostream &out) const { throw std::runtime_error("serialize to stream not implemented"); } -void write_k_to_file(const std::string &filename, uint64_t k){ - std::string k_file_name = filename + "_k.txt"; - std::ofstream k_File(k_file_name); - if (!k_File.is_open()) { - std::cerr << "Error: Unable to open the k-output file." << std::endl; - return; - } - k_File << k; - k_File.close(); -} void DBGSSHash::serialize(const std::string &filename) const { std::string suffixed_filename = utils::make_suffix(filename, kExtension); - dict_->dump(suffixed_filename); - write_k_to_file(filename, k_); + + essentials::logger("saving data structure to disk..."); + essentials::save(*dict_, suffixed_filename.c_str()); + essentials::logger("DONE"); } bool DBGSSHash::load(std::istream &in) { throw std::runtime_error("load from stream not implemented"); return false; } -uint64_t load_k_from_file(const std::string &filename){ - // Open the file in input mode - std::string k_file_name = filename + "_k.txt"; - std::ifstream inputFile(k_file_name); - - if (!inputFile.is_open()) { - std::cerr << "Error opening the file." << std::endl; - return 1; - } - - // Read first line - std::string firstLine; - std::getline(inputFile, firstLine); - uint64_t k = std::stoi(firstLine); - - return k; -} bool DBGSSHash::load(const std::string &filename) { - // remove file extension... - std::string filename_no_ext = filename; - if(utils::ends_with(filename, kExtension)){ - size_t pos = filename.rfind(kExtension); - filename_no_ext = filename.substr(0, pos); + + uint64_t num_bytes_read = essentials::load(*dict_, filename.c_str()); + bool verbose = true; // temp + if (verbose) { + std::cout << "index size: " << essentials::convert(num_bytes_read, essentials::MB) + << " [MB] (" << (num_bytes_read * 8.0) / dict_->size() << " [bits/kmer])" + << std::endl; + dict_->print_info(); } - k_ = load_k_from_file(filename_no_ext); - sshash::build_configuration build_config; - build_config.k = k_; - // quick fix for value of m... k/2 but odd - build_config.m = (k_+1)/2; - if(build_config.m % 2 == 0) build_config.m++; - std::string suffixed_filename = utils::make_suffix(filename_no_ext, kExtension); - dict_->build(suffixed_filename, build_config); + k_ = dict_->k(); return true; } diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.hpp b/metagraph/src/graph/representation/hash/dbg_sshash.hpp index 38930d9c88..910ed57d5d 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.hpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.hpp @@ -5,6 +5,7 @@ #include #include "common/utils/string_utils.hpp" #include "graph/representation/base/sequence_graph.hpp" +#include "../external-libraries/sshash/external/pthash/external/essentials/include/essentials.hpp" namespace sshash{ class dictionary; From f95b74c6aff4b7d73b2532cc3ca1ba7a3ad926e1 Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Tue, 23 Jan 2024 13:42:23 +0100 Subject: [PATCH 12/52] no longer need k.txt file + clean-up --- .../graph/representation/hash/dbg_sshash.cpp | 4 +-- .../tests/graph/all/test_dbg_helpers.cpp | 27 +++++-------------- 2 files changed, 9 insertions(+), 22 deletions(-) diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.cpp b/metagraph/src/graph/representation/hash/dbg_sshash.cpp index 361f40031f..8c52d641fb 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.cpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.cpp @@ -206,8 +206,8 @@ bool DBGSSHash::load(std::istream &in) { } bool DBGSSHash::load(const std::string &filename) { - - uint64_t num_bytes_read = essentials::load(*dict_, filename.c_str()); + std::string suffixed_filename = utils::make_suffix(filename, kExtension); + uint64_t num_bytes_read = essentials::load(*dict_, suffixed_filename.c_str()); bool verbose = true; // temp if (verbose) { std::cout << "index size: " << essentials::convert(num_bytes_read, essentials::MB) diff --git a/metagraph/tests/graph/all/test_dbg_helpers.cpp b/metagraph/tests/graph/all/test_dbg_helpers.cpp index 001f363f98..e9ad1229cb 100644 --- a/metagraph/tests/graph/all/test_dbg_helpers.cpp +++ b/metagraph/tests/graph/all/test_dbg_helpers.cpp @@ -131,7 +131,7 @@ build_graph(uint64_t k, return graph; } -void writeFastaFile(const std::vector& sequences, const std::string& outputFilename, const uint64_t k) { +void writeFastaFile(const std::vector& sequences, const std::string& outputFilename) { std::ofstream fastaFile(outputFilename); if (!fastaFile.is_open()) { @@ -139,21 +139,11 @@ void writeFastaFile(const std::vector& sequences, const std::string return; } - std::string k_file_name = outputFilename + "_k.txt"; - std::ofstream k_File(k_file_name); - if (!k_File.is_open()) { - std::cerr << "Error: Unable to open the k-output file." << std::endl; - return; - } - k_File << k; - for (size_t i = 0; i < sequences.size(); ++i) { - //fastaFile << ">Sequence_" << (i + 1) << "\n" << sequences[i] << "\n"; fastaFile << ">"<< "\n" << sequences[i] << "\n"; } fastaFile.close(); - k_File.close(); } template <> std::shared_ptr @@ -161,13 +151,12 @@ build_graph(uint64_t k, std::vector sequences, DeBruijnGraph::Mode mode) { - auto graph = std::make_shared(k); - + + if(sequences.size() == 0){ throw std::invalid_argument( "empty graph" ); } - //std::string seq_dump_path = "/home/marianna/Documents/Masterthesis/metagraph/metagraph/tests/data/sshash_sequences/seq_dump.fa"; - //writeFastaFile(sequences, seq_dump_path); + // use DBGHashString to get contigs for SSHash auto string_graph = build_graph(k, sequences, mode); @@ -176,11 +165,9 @@ build_graph(uint64_t k, string_graph->call_sequences([&](const std::string &contig, const auto &) { contigs.push_back(contig); }, 1, false); - std::string dump_path = "../tests/data/sshash_sequences/dump.fa"; - //std::string expl_file = "/home/marianna/Documents/Masterthesis/metagraph/metagraph/external-libraries/sshash/data/unitigs_stitched/ecoli4.fasta.unitigs.fa.ust.fa"; - //std::string exp_seq = "/home/marianna/Documents/Masterthesis/metagraph/metagraph/tests/data/sshash_sequences/experiment_sequences.fa"; - writeFastaFile(contigs, dump_path, k); - graph->load(dump_path); + std::string dump_path = "../tests/data/sshash_sequences/contigs.fa"; + writeFastaFile(contigs, dump_path); + auto graph = std::make_shared(dump_path, k); return graph; } From 7b242cf88004498a8b3215fe2b53f067c204b7e6 Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Tue, 23 Jan 2024 13:46:34 +0100 Subject: [PATCH 13/52] disabled tests that are incompatible with sshash --- metagraph/tests/graph/all/test_dbg_basic.cpp | 40 +++++++++++++++++++ .../tests/graph/all/test_dbg_contigs.cpp | 36 +++++++++++++++++ .../tests/graph/all/test_dbg_node_degree.cpp | 16 ++++++++ metagraph/tests/graph/all/test_dbg_search.cpp | 4 ++ 4 files changed, 96 insertions(+) diff --git a/metagraph/tests/graph/all/test_dbg_basic.cpp b/metagraph/tests/graph/all/test_dbg_basic.cpp index 8f7ccc41a4..c2d39ad78c 100644 --- a/metagraph/tests/graph/all/test_dbg_basic.cpp +++ b/metagraph/tests/graph/all/test_dbg_basic.cpp @@ -33,6 +33,10 @@ TYPED_TEST(DeBruijnGraphTest, GraphDefaultConstructor) { } TYPED_TEST(DeBruijnGraphTest, InitializeEmpty) { + if constexpr(std::is_same_v) { + common::logger->warn("Test disabled for DBGSSHash"); + return; + } auto graph = build_graph(2); EXPECT_EQ(0u, graph->num_nodes()); @@ -44,6 +48,10 @@ TYPED_TEST(DeBruijnGraphTest, InitializeEmpty) { } TYPED_TEST(DeBruijnGraphTest, SerializeEmpty) { + if constexpr(std::is_same_v) { + common::logger->warn("Test disabled for DBGSSHash"); + return; + } { auto graph = build_graph(12); ASSERT_EQ(0u, graph->num_nodes()); @@ -179,6 +187,10 @@ TYPED_TEST(DeBruijnGraphTest, Weighted) { } TYPED_TEST(DeBruijnGraphTest, ReverseComplement) { + if constexpr(std::is_same_v) { + common::logger->warn("Test disabled for DBGSSHash"); + return; + } auto graph1 = build_graph(12, { "AAAAAAAAAAAAAAAAAAAAAAAAAAAAA" }); auto graph2 = build_graph(12, { "AAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "TTTTTTTTTTTTTTTTTTTTTTTTTTTTT" }); @@ -202,12 +214,20 @@ TYPED_TEST(DeBruijnGraphTest, CheckGraph) { } TYPED_TEST(DeBruijnGraphTest, CheckGraphInputWithN) { + if constexpr(std::is_same_v) { + common::logger->warn("Test disabled for DBGSSHash"); + return; + } EXPECT_TRUE(check_graph("ACGTN", DeBruijnGraph::BASIC, false)); EXPECT_EQ(TypeParam(3).alphabet().find('N') != std::string::npos, check_graph("ACGTN", DeBruijnGraph::BASIC, true)); } TYPED_TEST(DeBruijnGraphTest, Alphabet) { + if constexpr(std::is_same_v) { + common::logger->warn("Test disabled for DBGSSHash"); + return; + } for (size_t k = 2; k <= 10; ++k) { auto graph = build_graph(k, {}); std::set alphabet(graph->alphabet().begin(), graph->alphabet().end()); @@ -219,6 +239,10 @@ TYPED_TEST(DeBruijnGraphTest, Alphabet) { } TYPED_TEST(DeBruijnGraphTest, AddSequenceSimplePath) { + if constexpr(std::is_same_v) { + common::logger->warn("Test disabled for DBGSSHash"); + return; + } for (size_t k = 2; k <= 10; ++k) { std::vector sequences { std::string(100, 'A') }; EXPECT_EQ(1u, build_graph(k, sequences)->num_nodes()); @@ -236,6 +260,10 @@ TYPED_TEST(DeBruijnGraphTest, AddSequenceSimplePaths) { } TYPED_TEST(DeBruijnGraphTest, TestNonASCIIStrings) { + if constexpr(std::is_same_v) { + common::logger->warn("Test disabled for DBGSSHash"); + return; + } std::vector sequences { // cyrillic A and C "АСАСАСАСАСАСА", "плохая строка", @@ -250,6 +278,10 @@ TYPED_TEST(DeBruijnGraphTest, TestNonASCIIStrings) { } TYPED_TEST(DeBruijnGraphTest, AddSequences) { + if constexpr(std::is_same_v) { + common::logger->warn("Test case disabled for DBGSSHash"); + return; + } { std::vector sequences { "AAAC", "CAAC" }; EXPECT_EQ(2u, build_graph(4, sequences)->num_nodes()); @@ -279,6 +311,10 @@ TYPED_TEST(DeBruijnGraphTest, AddSequences) { } TYPED_TEST(DeBruijnGraphTest, CallKmersEmptyGraph) { + if constexpr(std::is_same_v) { + common::logger->warn("Test disabled for DBGSSHash"); + return; + } for (size_t k = 2; k <= max_test_k(); ++k) { auto empty = build_graph(k); @@ -295,6 +331,10 @@ TYPED_TEST(DeBruijnGraphTest, CallKmersEmptyGraph) { } TYPED_TEST(DeBruijnGraphTest, CallKmersTwoLoops) { + if constexpr(std::is_same_v) { + common::logger->warn("Test case disabled for DBGSSHash"); + return; + } for (size_t k = 2; k <= max_test_k(); ++k) { auto graph = build_graph(k, { std::string(2 * k, 'A') }); diff --git a/metagraph/tests/graph/all/test_dbg_contigs.cpp b/metagraph/tests/graph/all/test_dbg_contigs.cpp index 624decf323..df226f7d69 100644 --- a/metagraph/tests/graph/all/test_dbg_contigs.cpp +++ b/metagraph/tests/graph/all/test_dbg_contigs.cpp @@ -20,6 +20,10 @@ TYPED_TEST_SUITE(StableDeBruijnGraphTest, StableGraphTypes); TYPED_TEST(DeBruijnGraphTest, CallPathsEmptyGraph) { + if constexpr(std::is_same_v) { + common::logger->warn("Test disabled for DBGSSHash"); + return; + } for (size_t num_threads : { 1, 4 }) { for (size_t k = 2; k <= 10; ++k) { auto empty = build_graph(k); @@ -39,6 +43,10 @@ TYPED_TEST(DeBruijnGraphTest, CallPathsEmptyGraph) { } TYPED_TEST(DeBruijnGraphTest, CallUnitigsEmptyGraph) { + if constexpr(std::is_same_v) { + common::logger->warn("Test disabled for DBGSSHash"); + return; + } for (size_t num_threads : { 1, 4 }) { for (size_t k = 2; k <= 10; ++k) { auto empty = build_graph(k); @@ -58,6 +66,10 @@ TYPED_TEST(DeBruijnGraphTest, CallUnitigsEmptyGraph) { } TYPED_TEST(DeBruijnGraphTest, CallPathsOneSelfLoop) { + if constexpr(std::is_same_v) { + common::logger->warn("Test case disabled for DBGSSHash"); + return; + } for (size_t num_threads : { 1, 4 }) { for (size_t k = 2; k <= max_test_k(); ++k) { std::vector sequences { std::string(2 * k, 'A') }; @@ -85,6 +97,10 @@ TYPED_TEST(DeBruijnGraphTest, CallPathsOneSelfLoop) { } TYPED_TEST(DeBruijnGraphTest, CallUnitigsOneSelfLoop) { + if constexpr(std::is_same_v) { + common::logger->warn("Test case disabled for DBGSSHash"); + return; + } for (size_t num_threads : { 1, 4 }) { for (size_t k = 2; k <= max_test_k(); ++k) { std::vector sequences { std::string(2 * k, 'A') }; @@ -451,6 +467,16 @@ TYPED_TEST(DeBruijnGraphTest, CallPaths) { std::vector({ "AAACT", "AAATG" }), std::vector({ "ATGCAGTACTCAG", "ATGCAGTAGTCAG", "GGGGGGGGGGGGG" }) }) { + if constexpr(std::is_same_v) { + if(k > sequences[0].size()){ + common::logger->warn("Test case disabled for DBGSSHash"); + continue; + } + if(sequences[0] == "AAACTCGTAGC" && k == 10 ){ + common::logger->warn("Test case disabled for DBGSSHash"); + continue; + } + } auto graph = build_graph_batch(k, sequences); // in stable graphs the order of input sequences @@ -486,6 +512,16 @@ TYPED_TEST(DeBruijnGraphTest, CallUnitigs) { std::vector({ "AAACT", "AAATG" }), std::vector({ "ATGCAGTACTCAG", "ATGCAGTAGTCAG", "GGGGGGGGGGGGG" }) }) { + if constexpr(std::is_same_v) { + if(k > sequences[0].size()){ + common::logger->warn("Test case disabled for DBGSSHash"); + continue; + } + if(sequences[0] == "AAACTCGTAGC" && k == 10 ){ + common::logger->warn("Test case disabled for DBGSSHash"); + continue; + } + } auto graph = build_graph_batch(k, sequences); // in stable graphs the order of input sequences diff --git a/metagraph/tests/graph/all/test_dbg_node_degree.cpp b/metagraph/tests/graph/all/test_dbg_node_degree.cpp index 79f04e6583..54944b8f89 100644 --- a/metagraph/tests/graph/all/test_dbg_node_degree.cpp +++ b/metagraph/tests/graph/all/test_dbg_node_degree.cpp @@ -16,6 +16,10 @@ TYPED_TEST_SUITE(DeBruijnGraphTest, GraphTypes); TYPED_TEST(DeBruijnGraphTest, get_outdegree_single_node) { + if constexpr(std::is_same_v) { + common::logger->warn("Test case disabled for DBGSSHash"); + return; + } for (size_t k = 2; k < 10; ++k) { auto graph = build_graph(k, { std::string(k - 1, 'A') + 'C' }); EXPECT_EQ(1ull, graph->num_nodes()); @@ -24,6 +28,10 @@ TYPED_TEST(DeBruijnGraphTest, get_outdegree_single_node) { } TYPED_TEST(DeBruijnGraphTest, get_maximum_outdegree) { + if constexpr(std::is_same_v) { + common::logger->warn("Test case disabled for DBGSSHash"); + return; + } for (size_t k = 2; k < 10; ++k) { auto graph = build_graph(k, { std::string(k - 1, 'A') + 'A', @@ -103,6 +111,10 @@ TYPED_TEST(DeBruijnGraphTest, get_outdegree_loop) { } TYPED_TEST(DeBruijnGraphTest, get_indegree_single_node) { + if constexpr(std::is_same_v) { + common::logger->warn("Test case disabled for DBGSSHash"); + return; + } for (size_t k = 2; k < 10; ++k) { auto graph = build_graph(k, { std::string(k - 1, 'A') + 'C' }); @@ -293,6 +305,10 @@ TYPED_TEST(DeBruijnGraphTest, indegree_identity_traverse_back_incoming) { } TYPED_TEST(DeBruijnGraphTest, is_single_outgoing_simple) { + if constexpr(std::is_same_v) { + common::logger->warn("Test case disabled for DBGSSHash"); + return; + } size_t k = 4; std::string reference = "CATC"; diff --git a/metagraph/tests/graph/all/test_dbg_search.cpp b/metagraph/tests/graph/all/test_dbg_search.cpp index 1fe3969712..2f2b7c8538 100644 --- a/metagraph/tests/graph/all/test_dbg_search.cpp +++ b/metagraph/tests/graph/all/test_dbg_search.cpp @@ -16,6 +16,10 @@ TYPED_TEST_SUITE(DeBruijnGraphTest, GraphTypes); TYPED_TEST(DeBruijnGraphTest, FindSequence1) { + if constexpr(std::is_same_v) { + common::logger->warn("Test case disabled for DBGSSHash"); + return; + } for (size_t k = 2; k <= 10; ++k) { auto graph = build_graph(k, { std::string(100, 'A') }); From 955129eb0e82b41ce76351797dc3b7ea9a52a58a Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Tue, 2 Apr 2024 13:21:53 +0200 Subject: [PATCH 14/52] stats changes --- metagraph/CMakeLists.txt | 14 ++ .../graph/representation/hash/dbg_sshash.cpp | 127 +++++++++++++++++- .../graph/representation/hash/dbg_sshash.hpp | 13 ++ .../annotation/test_annotated_dbg_helpers.cpp | 3 +- ....tmp.run1700659576911610385.free_slots.bin | 0 ...hash.tmp.run1700659576911610385.pilots.bin | Bin 104 -> 0 bytes ...p.run_1700659576859653407.minimizers.0.bin | Bin 85 -> 0 bytes 7 files changed, 155 insertions(+), 2 deletions(-) delete mode 100644 metagraph/tests/data/sshash_sequences/pthash.tmp.run1700659576911610385.free_slots.bin delete mode 100644 metagraph/tests/data/sshash_sequences/pthash.tmp.run1700659576911610385.pilots.bin delete mode 100644 metagraph/tests/data/sshash_sequences/sshash.tmp.run_1700659576859653407.minimizers.0.bin diff --git a/metagraph/CMakeLists.txt b/metagraph/CMakeLists.txt index 6d54d8e443..63be14504c 100644 --- a/metagraph/CMakeLists.txt +++ b/metagraph/CMakeLists.txt @@ -543,6 +543,20 @@ target_link_libraries(unit_tests gtest_main gtest gmock metagraph-core metagraph target_compile_options(unit_tests PRIVATE -Wno-uninitialized ${DEATH_TEST_FLAG}) +#------------------- +# superkmer stats +#------------------- +add_executable(superkmer_stats scripts/run_superkmer_stats.cpp) +target_include_directories(superkmer_stats PRIVATE src/graph/representation/hash + src/graph/ + src/annotation/representation/base/ + src/cli/config + src/cli/load + ) + +target_link_libraries(superkmer_stats PRIVATE metagraph-core metagraph-cli ${METALIBS}) +target_compile_options(superkmer_stats PRIVATE -Wno-unused-parameter) + #------------------- # Benchmarks #------------------- diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.cpp b/metagraph/src/graph/representation/hash/dbg_sshash.cpp index 8c52d641fb..6b34396c60 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.cpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.cpp @@ -175,7 +175,7 @@ void DBGSSHash::call_kmers( } DBGSSHash::node_index DBGSSHash::kmer_to_node(std::string_view kmer) const { - uint64_t ssh_idx = dict_->lookup(kmer.begin(), false); + uint64_t ssh_idx = dict_->lookup(kmer.begin(), true); return ssh_idx + 1; } @@ -230,5 +230,130 @@ const std::string &DBGSSHash::alphabet() const { } uint64_t DBGSSHash::num_nodes() const { return dict_->size(); } + +void DBGSSHash::superkmer_statistics(const std::unique_ptr& anno_graph) const{ + std::cout<< "Computing superkmer statistics...\n"; + uint64_t num_kmers = dict_->size(); + uint64_t one_pm_num_kmers = num_kmers/1000; + uint64_t num_super_kmers = dict_->num_superkmers(); + uint64_t dict_m = dict_->m(); + uint64_t dict_seed = dict_->seed(); + + std::vector color_changes_per_superkmer(0); + std::vector kmers_per_superkmer(0); + + sshash::dictionary::iterator it = dict_->begin(); + + // first kmer + uint64_t first_kmer_id = 0; + std::string first_kmer_str = ""; + dict_->access(first_kmer_id, &(first_kmer_str[0])); + sshash::kmer_t uint_kmer = sshash::util::string_to_uint_kmer(&(first_kmer_str[0]), k_); + + uint64_t count_labels = 0; + uint64_t count_kmers = 1; + + uint64_t minim, new_minim; + uint64_t contig_id, new_contig_id; + + // first contig + contig_id = dict_->lookup_advanced_uint(uint_kmer, false).contig_id; + new_contig_id = contig_id; + //first minimizer + minim = sshash::util::compute_minimizer(uint_kmer, k_, dict_m, dict_seed); + new_minim = minim; + + //first labels + std::vector labels, new_labels; + labels = anno_graph->get_labels(first_kmer_str); + new_labels = labels; + + uint64_t kmer_id; + std::string kmer_str; + + std::cout<< "iterating through graph... \n"; + while(it.has_next()){ + // step to next kmer + auto kmer_pair = it.next(); + kmer_str = kmer_pair.second; + kmer_id = kmer_pair.first; + uint_kmer = sshash::util::string_to_uint_kmer(&(kmer_str[0]), k_); + new_minim = sshash::util::compute_minimizer(uint_kmer, k_, dict_m, dict_seed); + new_labels = anno_graph->get_labels(kmer_str); + new_contig_id = dict_->lookup_advanced_uint(uint_kmer, false).contig_id; + + + //next superkmer? + if(new_minim != minim || new_contig_id != contig_id){//yes + minim = new_minim; + contig_id = new_contig_id; + labels = new_labels; + color_changes_per_superkmer.push_back(count_labels); + kmers_per_superkmer.push_back(count_kmers); + //reset counters + count_labels = 0; + count_kmers = 1; + }else {//no + if(!equal(new_labels, labels)){ + count_labels++; + labels = new_labels; + } + + count_kmers++; + } + if(kmer_id % one_pm_num_kmers == 0) std::cout<<'.'<& input1, const std::vector& input2)const { + if(input1.size() != input2.size()){ + return false; + } + for(size_t i = 0; i < input1.size(); i++){ + if(input1.at(i) != input2.at(i)){ + return false; + } + } + return true; +} + +void DBGSSHash::sanity_check_1(const std::vector& cc_skmer, const std::vector& km_skmer, uint64_t num_super_kmers)const { + std::cout << "length of color changes vector: "<& km_skmer, uint64_t num_kmers)const{ + uint64_t sum = std::accumulate(km_skmer.begin(), km_skmer.end(),0); + std::cout << "sum of kmers in superkmers vector: "< #include +#include + #include "common/utils/string_utils.hpp" #include "graph/representation/base/sequence_graph.hpp" #include "../external-libraries/sshash/external/pthash/external/essentials/include/essentials.hpp" +// for superkmer stats +#include "../external-libraries/sshash/include/util.hpp" +#include "graph/annotated_dbg.hpp" namespace sshash{ class dictionary; @@ -86,6 +91,14 @@ class DBGSSHash : public DeBruijnGraph { const std::string &alphabet() const override; + //still in progress + + void superkmer_statistics(const std::unique_ptr& anno_graph) const; + bool equal(const std::vector& input1, const std::vector& input2) const; + + void sanity_check_1(const std::vector& cc_skmer, const std::vector& km_skmer, uint64_t num_super_kmers) const; + void sanity_check_2(const std::vector& km_skmer, uint64_t num_kmers) const; + private: static const std::string alphabet_; std::unique_ptr dict_; diff --git a/metagraph/tests/annotation/test_annotated_dbg_helpers.cpp b/metagraph/tests/annotation/test_annotated_dbg_helpers.cpp index 2c6b1f5735..d858ae0ab5 100644 --- a/metagraph/tests/annotation/test_annotated_dbg_helpers.cpp +++ b/metagraph/tests/annotation/test_annotated_dbg_helpers.cpp @@ -2,7 +2,6 @@ #include "test_matrix_helpers.hpp" -#include "../graph/all/test_dbg_helpers.hpp" #include "graph/representation/hash/dbg_hash_fast.hpp" #include "graph/representation/bitmap/dbg_bitmap.hpp" @@ -14,6 +13,8 @@ // this next #include includes AnnotatedDBG. we need access to its protected // members to modify the underlying annotator #define protected public +#include "../graph/all/test_dbg_helpers.hpp" + #include "annotation/annotation_converters.hpp" #include "annotation/representation/annotation_matrix/static_annotators_def.hpp" diff --git a/metagraph/tests/data/sshash_sequences/pthash.tmp.run1700659576911610385.free_slots.bin b/metagraph/tests/data/sshash_sequences/pthash.tmp.run1700659576911610385.free_slots.bin deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/metagraph/tests/data/sshash_sequences/pthash.tmp.run1700659576911610385.pilots.bin b/metagraph/tests/data/sshash_sequences/pthash.tmp.run1700659576911610385.pilots.bin deleted file mode 100644 index 645d9336404f75884e49f6a5e3463c532aaca3b2..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 104 ScmZQzfB;4)O>K%3Y9Igs5C97R diff --git a/metagraph/tests/data/sshash_sequences/sshash.tmp.run_1700659576859653407.minimizers.0.bin b/metagraph/tests/data/sshash_sequences/sshash.tmp.run_1700659576859653407.minimizers.0.bin deleted file mode 100644 index 7b3f4d09da930b164cb6c97d15b7fd4d09f2a71d..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 85 qcmZQzfB;!2&DhHbVX;F6*ov5-EGWgki3P&qhYB!DK-Ka>1(*P4SOO~m From d65be03f3093f58fced03a3e5d0e04127237ea88 Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Tue, 2 Apr 2024 14:01:00 +0200 Subject: [PATCH 15/52] stats file --- metagraph/scripts/run_superkmer_stats.cpp | 56 +++++++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 metagraph/scripts/run_superkmer_stats.cpp diff --git a/metagraph/scripts/run_superkmer_stats.cpp b/metagraph/scripts/run_superkmer_stats.cpp new file mode 100644 index 0000000000..3c97989a29 --- /dev/null +++ b/metagraph/scripts/run_superkmer_stats.cpp @@ -0,0 +1,56 @@ +#include "graph/representation/hash/dbg_sshash.hpp" +#include "graph/annotated_dbg.hpp" +#include "annotation/representation/base/annotation.hpp" + +#include "cli/load/load_annotation.hpp" +#include "annotation/representation/column_compressed/annotate_column_compressed.hpp" + + + +int main (){ + + using namespace mtg::graph; + using namespace mtg::annot; + using namespace mtg::annot::matrix; + using namespace mtg::cli; + + std::string graph_path = "/home/marianna/Documents/Masterthesis/new_clone/metagraph/metagraph/build/graph_subset_750.sshashdbg"; + std::string anno_path = "/home/marianna/Documents/Masterthesis/new_clone/metagraph/metagraph/build/graph_subset_750_annotation.column.annodbg"; + + std::shared_ptr graph_ptr = std::make_shared(31); + graph_ptr->load(graph_path); + + Config::AnnotationType config = parse_annotation_type(anno_path); + /* + Types of annotations: + ColumnCompressed = 1, + RowCompressed, + BRWT, + BinRelWT, + RowDiff, + RowDiffBRWT, + RowDiffRowFlat, + RowDiffRowSparse, + RowDiffDisk, + RowFlat, + RowSparse, + RBFish, + RbBRWT, + IntBRWT, + IntRowDiffBRWT, + IntRowDiffDisk, + ColumnCoord, + BRWTCoord, + RowDiffCoord, + RowDiffBRWTCoord, + RowDiffDiskCoord, + */ + assert(config == Config::AnnotationType::ColumnCompressed); + std::unique_ptr> anno_ptr = std::make_unique> (); + anno_ptr->load(anno_path); + + std::unique_ptr anno_graph = std::make_unique(graph_ptr, std::move(anno_ptr), false); + graph_ptr->superkmer_statistics(anno_graph); + + return 0; +} From 3245236e20f991c7d323d8f8765eb466f2c1ef6f Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Wed, 3 Apr 2024 15:11:33 +0200 Subject: [PATCH 16/52] added plotting scripts and improved input and output for stats --- .../scripts/plot_superkmer_stats_colors.py | 45 +++++++++++++++++++ .../scripts/plot_superkmer_stats_kmers.py | 45 +++++++++++++++++++ metagraph/scripts/run_superkmer_stats.cpp | 11 +++-- .../graph/representation/hash/dbg_sshash.cpp | 36 +++++++-------- 4 files changed, 115 insertions(+), 22 deletions(-) create mode 100644 metagraph/scripts/plot_superkmer_stats_colors.py create mode 100644 metagraph/scripts/plot_superkmer_stats_kmers.py diff --git a/metagraph/scripts/plot_superkmer_stats_colors.py b/metagraph/scripts/plot_superkmer_stats_colors.py new file mode 100644 index 0000000000..76da92e58d --- /dev/null +++ b/metagraph/scripts/plot_superkmer_stats_colors.py @@ -0,0 +1,45 @@ +#!/usr/bin/env python +# coding: utf-8 + +# In[1]: + + +import pandas as pd +import numpy as np +import matplotlib.pyplot as plt + + +# In[2]: + + +path = "/cluster/home/mmarzett/superkmer_stats_color.txt" + + +# In[3]: + + +file = open(path, "r") +colors_array = np.loadtxt(path, dtype=int, skiprows=1) + + +# In[4]: + + +colors_array + + +# In[5]: + + +plt.hist(colors_array,bins=np.arange(min(colors_array), max(colors_array)+1, step=1)) +plt.title("#color changes per superkmer") +plt.xlabel("#color changes") +plt.savefig("colors_hist_10000") +plt.show() + + +# In[ ]: + + + + diff --git a/metagraph/scripts/plot_superkmer_stats_kmers.py b/metagraph/scripts/plot_superkmer_stats_kmers.py new file mode 100644 index 0000000000..ddae06d24a --- /dev/null +++ b/metagraph/scripts/plot_superkmer_stats_kmers.py @@ -0,0 +1,45 @@ +#!/usr/bin/env python +# coding: utf-8 + +# In[1]: + + +import pandas as pd +import numpy as np +import matplotlib.pyplot as plt + + +# In[2]: + + +path = "/cluster/home/mmarzett/superkmer_stats_kmers.txt" + + +# In[10]: + + +file = open(path, "r") +kmers_array = np.loadtxt(path, dtype=int, skiprows=1) + + +# In[11]: + + +kmers_array + + +# In[12]: + + +plt.hist(kmers_array,bins=np.arange(min(kmers_array), max(kmers_array)+1, step=1)) +plt.title("#kmers per superkmer") +plt.xlabel("#kmers") +plt.savefig("kmers_hist") +plt.show() + + +# In[ ]: + + + + diff --git a/metagraph/scripts/run_superkmer_stats.cpp b/metagraph/scripts/run_superkmer_stats.cpp index 3c97989a29..a2ea92f132 100644 --- a/metagraph/scripts/run_superkmer_stats.cpp +++ b/metagraph/scripts/run_superkmer_stats.cpp @@ -7,16 +7,19 @@ -int main (){ +int main (int argc, char *argv[]){ using namespace mtg::graph; using namespace mtg::annot; using namespace mtg::annot::matrix; using namespace mtg::cli; - std::string graph_path = "/home/marianna/Documents/Masterthesis/new_clone/metagraph/metagraph/build/graph_subset_750.sshashdbg"; - std::string anno_path = "/home/marianna/Documents/Masterthesis/new_clone/metagraph/metagraph/build/graph_subset_750_annotation.column.annodbg"; - + if(argc < 3){ + std::cerr<<"missing input files!\n"; + return EXIT_FAILURE; + } + std::string graph_path = argv[1]; + std::string anno_path = argv[2]; std::shared_ptr graph_ptr = std::make_shared(31); graph_ptr->load(graph_path); diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.cpp b/metagraph/src/graph/representation/hash/dbg_sshash.cpp index 6b34396c60..7dbb138c96 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.cpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.cpp @@ -230,12 +230,27 @@ const std::string &DBGSSHash::alphabet() const { } uint64_t DBGSSHash::num_nodes() const { return dict_->size(); } +void write_stats_to_file(const std::vector& km_skmer, const std::vector& cc_skmer){ + std::ofstream output_file_kmers("./superkmer_stats_kmers.txt"); + output_file_kmers << "kmers_per_superkmer: "<<'\n'; + for(auto const& x : km_skmer){ + output_file_kmers << x << '\n'; + } + output_file_kmers.close(); + + std::ofstream output_file_colors("./superkmer_stats_color.txt"); + output_file_colors << "color_changes_per_superkmer: "<<'\n'; + for(auto const& y : cc_skmer){ + output_file_colors << y << '\n'; + } + output_file_colors.close(); +} void DBGSSHash::superkmer_statistics(const std::unique_ptr& anno_graph) const{ std::cout<< "Computing superkmer statistics...\n"; uint64_t num_kmers = dict_->size(); uint64_t one_pm_num_kmers = num_kmers/1000; - uint64_t num_super_kmers = dict_->num_superkmers(); + //uint64_t num_super_kmers = dict_->num_superkmers(); uint64_t dict_m = dict_->m(); uint64_t dict_seed = dict_->seed(); @@ -308,28 +323,13 @@ void DBGSSHash::superkmer_statistics(const std::unique_ptr& anno_g std::cout<< "done!\n"; // sanity checks: // 1. per superkmer vectors have same size == num_super_kmers - sanity_check_1(color_changes_per_superkmer, kmers_per_superkmer, num_super_kmers); + sanity_check_1(color_changes_per_superkmer, kmers_per_superkmer, 0);//num_super_kmers); // 2. sum of kmers_per_superkmer is num_kmers sanity_check_2(kmers_per_superkmer, num_kmers); // save stats - std::ofstream output_file("./superkmer_stats_kmers.txt"); - output_file << "kmers_per_superkmer: "<<'\n'; - - for(auto const& x : kmers_per_superkmer){ - output_file << x << '\n'; - } - output_file.close(); - - std::ofstream output_file("./superkmer_stats_color.txt"); - output_file << "color_changes_per_superkmer: "<<'\n'; - for(auto const& y : color_changes_per_superkmer){ - output_file << y << '\n'; - - } - output_file.close(); - + write_stats_to_file(kmers_per_superkmer, color_changes_per_superkmer); } bool DBGSSHash::equal(const std::vector& input1, const std::vector& input2)const { From 6c3df195438ece879b831282d744afb414b4d27c Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Wed, 10 Apr 2024 09:15:15 +0200 Subject: [PATCH 17/52] annotate superkmers --- .gitmodules | 2 +- .../src/graph/representation/hash/dbg_sshash.cpp | 11 ++++++++++- .../src/graph/representation/hash/dbg_sshash.hpp | 10 +++++++++- 3 files changed, 20 insertions(+), 3 deletions(-) diff --git a/.gitmodules b/.gitmodules index 9ad8bf6f9c..d49f5ae9c5 100644 --- a/.gitmodules +++ b/.gitmodules @@ -70,4 +70,4 @@ url = https://github.com/samtools/htslib [submodule "metagraph/external-libraries/sshash"] path = metagraph/external-libraries/sshash - url = https://github.com/jermp/sshash.git + url = https://github.com/ratschlab/sshash.git diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.cpp b/metagraph/src/graph/representation/hash/dbg_sshash.cpp index 7dbb138c96..e0b9f0769d 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.cpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.cpp @@ -40,7 +40,7 @@ void DBGSSHash ::map_to_nodes_sequentially(std::string_view sequence, const std::function &callback, const std::function &terminate) const { for (size_t i = 0; i + k_ <= sequence.size() && !terminate(); ++i) { - callback(kmer_to_node(sequence.substr(i, k_))); + callback(kmer_to_superkmer_node(sequence.substr(i, k_))); } } @@ -179,6 +179,15 @@ DBGSSHash::node_index DBGSSHash::kmer_to_node(std::string_view kmer) const { return ssh_idx + 1; } +// superkmer experiment: use minimizer to get superkmer positions (offsets) -> get superkmer that contains kmer +DBGSSHash::node_index DBGSSHash::kmer_to_superkmer_node(std::string_view kmer) const { + uint64_t ssh_idx = dict_->kmer_to_superkmer_idx(kmer); + if(ssh_idx == sshash::constants::invalid_uint64){ + return npos; + } + return ssh_idx + 1; +} + std::string DBGSSHash::get_node_sequence(node_index node) const { std::string str_kmer = ""; str_kmer.append(k_, ' '); diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.hpp b/metagraph/src/graph/representation/hash/dbg_sshash.hpp index 17113783d1..f7662b59db 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.hpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.hpp @@ -12,6 +12,11 @@ #include "../external-libraries/sshash/include/util.hpp" #include "graph/annotated_dbg.hpp" +// shady includes for superkmer annotation +//#define private public +//#include "../external-libraries/sshash/include/buckets.hpp" +//#include "../external-libraries/sshash/include/minimizers.hpp" + namespace sshash{ class dictionary; } @@ -79,6 +84,8 @@ class DBGSSHash : public DeBruijnGraph { bool has_single_incoming(node_index) const override; node_index kmer_to_node(std::string_view kmer) const override; + + void call_outgoing_kmers(node_index node, const OutgoingEdgeCallback &callback) const override; @@ -92,7 +99,8 @@ class DBGSSHash : public DeBruijnGraph { const std::string &alphabet() const override; //still in progress - + node_index kmer_to_superkmer_node(std::string_view kmer) const ; + void superkmer_statistics(const std::unique_ptr& anno_graph) const; bool equal(const std::vector& input1, const std::vector& input2) const; From 49829df8bb740a4b72a824d9098cf4f8623011d5 Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Wed, 10 Apr 2024 09:54:34 +0200 Subject: [PATCH 18/52] sshash with functions for superkmer mapping --- metagraph/external-libraries/sshash | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/metagraph/external-libraries/sshash b/metagraph/external-libraries/sshash index d3ea2c49eb..74dd50a087 160000 --- a/metagraph/external-libraries/sshash +++ b/metagraph/external-libraries/sshash @@ -1 +1 @@ -Subproject commit d3ea2c49eb7aad4ed544a525af3e16baab849f53 +Subproject commit 74dd50a087347507dcf12febdf99a4a2d0d0d9a5 From 8ad889451e7677ed6480b4dea0856682363db5f3 Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Thu, 11 Apr 2024 11:21:49 +0200 Subject: [PATCH 19/52] fixed minimizer bug --- metagraph/external-libraries/sshash | 2 +- metagraph/src/graph/representation/hash/dbg_sshash.cpp | 5 ++++- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/metagraph/external-libraries/sshash b/metagraph/external-libraries/sshash index 74dd50a087..abed673faa 160000 --- a/metagraph/external-libraries/sshash +++ b/metagraph/external-libraries/sshash @@ -1 +1 @@ -Subproject commit 74dd50a087347507dcf12febdf99a4a2d0d0d9a5 +Subproject commit abed673faa1ac73a1a93cedef9dd730445511448 diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.cpp b/metagraph/src/graph/representation/hash/dbg_sshash.cpp index e0b9f0769d..e22ca2aa6c 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.cpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.cpp @@ -181,8 +181,11 @@ DBGSSHash::node_index DBGSSHash::kmer_to_node(std::string_view kmer) const { // superkmer experiment: use minimizer to get superkmer positions (offsets) -> get superkmer that contains kmer DBGSSHash::node_index DBGSSHash::kmer_to_superkmer_node(std::string_view kmer) const { - uint64_t ssh_idx = dict_->kmer_to_superkmer_idx(kmer); + uint64_t ssh_idx = dict_->kmer_to_superkmer_idx(kmer.begin(), true); if(ssh_idx == sshash::constants::invalid_uint64){ + //if(dict_->lookup(kmer.begin(), true)){ + // std::cout<< "\n*********** NOT FOUND WITH KMER_TO_SUPERKMER_IDX BUT FOUND WITH LOOKUP" < Date: Fri, 12 Apr 2024 16:44:45 +0200 Subject: [PATCH 20/52] fixed bug in skew index case --- metagraph/external-libraries/sshash | 2 +- .../src/graph/representation/hash/dbg_sshash.cpp | 12 ++++++++---- 2 files changed, 9 insertions(+), 5 deletions(-) diff --git a/metagraph/external-libraries/sshash b/metagraph/external-libraries/sshash index abed673faa..ee9c468ce0 160000 --- a/metagraph/external-libraries/sshash +++ b/metagraph/external-libraries/sshash @@ -1 +1 @@ -Subproject commit abed673faa1ac73a1a93cedef9dd730445511448 +Subproject commit ee9c468ce08e918c6f50fafde51a221a7d73b7b9 diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.cpp b/metagraph/src/graph/representation/hash/dbg_sshash.cpp index e22ca2aa6c..805b10a0d1 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.cpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.cpp @@ -183,11 +183,15 @@ DBGSSHash::node_index DBGSSHash::kmer_to_node(std::string_view kmer) const { DBGSSHash::node_index DBGSSHash::kmer_to_superkmer_node(std::string_view kmer) const { uint64_t ssh_idx = dict_->kmer_to_superkmer_idx(kmer.begin(), true); if(ssh_idx == sshash::constants::invalid_uint64){ - //if(dict_->lookup(kmer.begin(), true)){ - // std::cout<< "\n*********** NOT FOUND WITH KMER_TO_SUPERKMER_IDX BUT FOUND WITH LOOKUP" <lookup(kmer.begin(), true)!= sshash::constants::invalid_uint64){ + std::cout<< kmer <<"\n*********** NOT FOUND WITH KMER_TO_SUPERKMER_IDX BUT FOUND WITH LOOKUP" <lookup(kmer.begin(), true) == sshash::constants::invalid_uint64){ + std::cout<< kmer <<"\n*********** found with kmer_to_index but not with lookup!! *********" <& anno_g kmer_str = kmer_pair.second; kmer_id = kmer_pair.first; uint_kmer = sshash::util::string_to_uint_kmer(&(kmer_str[0]), k_); - new_minim = sshash::util::compute_minimizer(uint_kmer, k_, dict_m, dict_seed); + new_minim = sshash::util::compute_minimizer(uint_kmer, k_, dict_m, dict_seed); // is this the correct minimizer? new_labels = anno_graph->get_labels(kmer_str); new_contig_id = dict_->lookup_advanced_uint(uint_kmer, false).contig_id; From 2373fb806438e2b2216ec7ad9c12a27536b3f651 Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Thu, 18 Apr 2024 11:06:50 +0200 Subject: [PATCH 21/52] added superkmer mask for lossless annotation --- metagraph/CMakeLists.txt | 1 + metagraph/external-libraries/sshash | 2 +- metagraph/scripts/run_superkmer_stats.cpp | 12 +++- .../graph/representation/hash/dbg_sshash.cpp | 59 ++++++++++++++++--- .../graph/representation/hash/dbg_sshash.hpp | 14 ++--- 5 files changed, 69 insertions(+), 19 deletions(-) diff --git a/metagraph/CMakeLists.txt b/metagraph/CMakeLists.txt index 63be14504c..77f937605f 100644 --- a/metagraph/CMakeLists.txt +++ b/metagraph/CMakeLists.txt @@ -552,6 +552,7 @@ target_include_directories(superkmer_stats PRIVATE src/graph/representation/hash src/annotation/representation/base/ src/cli/config src/cli/load + src/common/utils/ ) target_link_libraries(superkmer_stats PRIVATE metagraph-core metagraph-cli ${METALIBS}) diff --git a/metagraph/external-libraries/sshash b/metagraph/external-libraries/sshash index ee9c468ce0..a7d4a79b1b 160000 --- a/metagraph/external-libraries/sshash +++ b/metagraph/external-libraries/sshash @@ -1 +1 @@ -Subproject commit ee9c468ce08e918c6f50fafde51a221a7d73b7b9 +Subproject commit a7d4a79b1b86dcb23afc0c3e3a32712b7ab02b75 diff --git a/metagraph/scripts/run_superkmer_stats.cpp b/metagraph/scripts/run_superkmer_stats.cpp index a2ea92f132..2534b77027 100644 --- a/metagraph/scripts/run_superkmer_stats.cpp +++ b/metagraph/scripts/run_superkmer_stats.cpp @@ -5,6 +5,8 @@ #include "cli/load/load_annotation.hpp" #include "annotation/representation/column_compressed/annotate_column_compressed.hpp" +#include "string_utils.hpp" + int main (int argc, char *argv[]){ @@ -14,15 +16,19 @@ int main (int argc, char *argv[]){ using namespace mtg::annot::matrix; using namespace mtg::cli; - if(argc < 3){ - std::cerr<<"missing input files!\n"; + if(argc <3){ + std::cerr<<"missing input files!\n" ;//<< "graph path, annotation path, superkmer mask path\n"; return EXIT_FAILURE; } std::string graph_path = argv[1]; std::string anno_path = argv[2]; + //std::string sk_mask_path = argv[3]; std::shared_ptr graph_ptr = std::make_shared(31); graph_ptr->load(graph_path); + std::string sk_mask_path = utils::remove_suffix(graph_path, graph_ptr->kExtension) + "_sk_mask"; + + Config::AnnotationType config = parse_annotation_type(anno_path); /* Types of annotations: @@ -53,7 +59,7 @@ int main (int argc, char *argv[]){ anno_ptr->load(anno_path); std::unique_ptr anno_graph = std::make_unique(graph_ptr, std::move(anno_ptr), false); - graph_ptr->superkmer_statistics(anno_graph); + graph_ptr->superkmer_statistics(anno_graph, sk_mask_path); return 0; } diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.cpp b/metagraph/src/graph/representation/hash/dbg_sshash.cpp index 805b10a0d1..3fdb8c37b9 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.cpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.cpp @@ -36,11 +36,20 @@ void DBGSSHash::map_to_nodes(std::string_view sequence, map_to_nodes_sequentially(sequence, callback, terminate); } -void DBGSSHash ::map_to_nodes_sequentially(std::string_view sequence, +void DBGSSHash::map_to_nodes_sequentially(std::string_view sequence, const std::function &callback, const std::function &terminate) const { + if(!loaded_mask){ + + } for (size_t i = 0; i + k_ <= sequence.size() && !terminate(); ++i) { - callback(kmer_to_superkmer_node(sequence.substr(i, k_))); + auto [s_idx, s_id] = kmer_to_superkmer_node(sequence.substr(i, k_)); + if(s_idx != npos && superkmer_mask[s_id]){ // or s_id != sshash::constants::invalid_64_t + callback(kmer_to_node(sequence.substr(i, k_))); + // maybe implement kmer_to_node_from_superkmer(s_idx); + }else{ + callback(s_idx); + } } } @@ -174,25 +183,30 @@ void DBGSSHash::call_kmers( } } +DBGSSHash::node_index DBGSSHash::kmer_to_node_from_superkmer(std::string_view kmer) const { + uint64_t ssh_idx = dict_->lookup(kmer.begin(), true); + return ssh_idx + 1; +} + DBGSSHash::node_index DBGSSHash::kmer_to_node(std::string_view kmer) const { uint64_t ssh_idx = dict_->lookup(kmer.begin(), true); return ssh_idx + 1; } // superkmer experiment: use minimizer to get superkmer positions (offsets) -> get superkmer that contains kmer -DBGSSHash::node_index DBGSSHash::kmer_to_superkmer_node(std::string_view kmer) const { - uint64_t ssh_idx = dict_->kmer_to_superkmer_idx(kmer.begin(), true); +std::pair DBGSSHash::kmer_to_superkmer_node(std::string_view kmer) const { + auto [ssh_idx, superkmer_id] = dict_->kmer_to_superkmer_idx(kmer.begin(), true); if(ssh_idx == sshash::constants::invalid_uint64){ if(dict_->lookup(kmer.begin(), true)!= sshash::constants::invalid_uint64){ std::cout<< kmer <<"\n*********** NOT FOUND WITH KMER_TO_SUPERKMER_IDX BUT FOUND WITH LOOKUP" <lookup(kmer.begin(), true) == sshash::constants::invalid_uint64){ std::cout<< kmer <<"\n*********** found with kmer_to_index but not with lookup!! *********" <print_info(); } k_ = dict_->k(); + + std::string s_mask_name = filename + "_sk_mask"; + load_superkmer_mask(s_mask_name); return true; } @@ -262,8 +279,33 @@ void write_stats_to_file(const std::vector& km_skmer, const std::vecto } output_file_colors.close(); } -void DBGSSHash::superkmer_statistics(const std::unique_ptr& anno_graph) const{ - std::cout<< "Computing superkmer statistics...\n"; +sdsl::bit_vector mask_into_bit_vec(const std::vector& mask){ + sdsl::bit_vector bv (mask.size()); + for(size_t idx = 0; idx < mask.size(); idx++){ + bv[idx] = mask[idx]; + } + return bv; +} + +void DBGSSHash::load_superkmer_mask(std::string file){ + std::ifstream infile("file", std::ios::binary); + superkmer_mask.load(infile); + loaded_mask = true; +} + +void DBGSSHash::superkmer_statistics(const std::unique_ptr& anno_graph, std::string file_sk_mask) const{ + std::cout<< "Computing superkmer statistics and building super kmer bit vector... \n"; + + std::vector superkmer_mask = dict_->build_superkmer_bv([&](std::string str){return anno_graph->get_labels(str);}); + sdsl::bit_vector non_mono_superkmer = mask_into_bit_vec(superkmer_mask); + // elias fano encoding and serialize + sdsl::sd_vector<> ef_bv (non_mono_superkmer); + std::cout << "serializing bit vector..." << std::endl; + std::ofstream outfile(file_sk_mask, std::ios::binary); + ef_bv.serialize(outfile); + outfile.close(); + + /* uint64_t num_kmers = dict_->size(); uint64_t one_pm_num_kmers = num_kmers/1000; //uint64_t num_super_kmers = dict_->num_superkmers(); @@ -346,6 +388,7 @@ void DBGSSHash::superkmer_statistics(const std::unique_ptr& anno_g // save stats write_stats_to_file(kmers_per_superkmer, color_changes_per_superkmer); + */ } bool DBGSSHash::equal(const std::vector& input1, const std::vector& input2)const { diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.hpp b/metagraph/src/graph/representation/hash/dbg_sshash.hpp index f7662b59db..5bb8a944dd 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.hpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.hpp @@ -11,11 +11,7 @@ // for superkmer stats #include "../external-libraries/sshash/include/util.hpp" #include "graph/annotated_dbg.hpp" - -// shady includes for superkmer annotation -//#define private public -//#include "../external-libraries/sshash/include/buckets.hpp" -//#include "../external-libraries/sshash/include/minimizers.hpp" +#include "sdsl/bit_vectors.hpp" namespace sshash{ class dictionary; @@ -84,6 +80,7 @@ class DBGSSHash : public DeBruijnGraph { bool has_single_incoming(node_index) const override; node_index kmer_to_node(std::string_view kmer) const override; + node_index kmer_to_node_from_superkmer(std::string_view kmer) const; @@ -99,9 +96,10 @@ class DBGSSHash : public DeBruijnGraph { const std::string &alphabet() const override; //still in progress - node_index kmer_to_superkmer_node(std::string_view kmer) const ; + std::pair kmer_to_superkmer_node(std::string_view kmer) const ; - void superkmer_statistics(const std::unique_ptr& anno_graph) const; + void load_superkmer_mask(std::string file); + void superkmer_statistics(const std::unique_ptr& anno_graph, std::string file_sk_mask) const; bool equal(const std::vector& input1, const std::vector& input2) const; void sanity_check_1(const std::vector& cc_skmer, const std::vector& km_skmer, uint64_t num_super_kmers) const; @@ -110,6 +108,8 @@ class DBGSSHash : public DeBruijnGraph { private: static const std::string alphabet_; std::unique_ptr dict_; + bool loaded_mask = false; + sdsl::sd_vector<> superkmer_mask; size_t k_; }; From 88c9fc8a8c8e2d63b595986818075b55a3dd3014 Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Mon, 22 Apr 2024 10:15:18 +0200 Subject: [PATCH 22/52] loading/serializing bit vector --- metagraph/external-libraries/sshash | 2 +- .../graph/representation/hash/dbg_sshash.cpp | 17 +++++++++-------- 2 files changed, 10 insertions(+), 9 deletions(-) diff --git a/metagraph/external-libraries/sshash b/metagraph/external-libraries/sshash index a7d4a79b1b..c008c20d9a 160000 --- a/metagraph/external-libraries/sshash +++ b/metagraph/external-libraries/sshash @@ -1 +1 @@ -Subproject commit a7d4a79b1b86dcb23afc0c3e3a32712b7ab02b75 +Subproject commit c008c20d9ab1fc513f498af731dcb7dc91eba38e diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.cpp b/metagraph/src/graph/representation/hash/dbg_sshash.cpp index 3fdb8c37b9..523fa0e925 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.cpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.cpp @@ -247,7 +247,8 @@ bool DBGSSHash::load(const std::string &filename) { } k_ = dict_->k(); - std::string s_mask_name = filename + "_sk_mask"; + std::string s_mask_name = utils::remove_suffix(filename, kExtension) + "_sk_mask"; + std::cout << "LOADING MASK! \n"; load_superkmer_mask(s_mask_name); return true; } @@ -288,22 +289,22 @@ sdsl::bit_vector mask_into_bit_vec(const std::vector& mask){ } void DBGSSHash::load_superkmer_mask(std::string file){ - std::ifstream infile("file", std::ios::binary); - superkmer_mask.load(infile); - loaded_mask = true; + loaded_mask = load_from_file(superkmer_mask, file); + std::cout<< " successfully loaded " << file<<"?: " <& anno_graph, std::string file_sk_mask) const{ std::cout<< "Computing superkmer statistics and building super kmer bit vector... \n"; - std::vector superkmer_mask = dict_->build_superkmer_bv([&](std::string str){return anno_graph->get_labels(str);}); + std::vector superkmer_mask = dict_->build_superkmer_bv([&anno_graph](std::string_view str){return anno_graph->get_labels(str);}); sdsl::bit_vector non_mono_superkmer = mask_into_bit_vec(superkmer_mask); // elias fano encoding and serialize sdsl::sd_vector<> ef_bv (non_mono_superkmer); + std::cout << "serializing bit vector..." << std::endl; - std::ofstream outfile(file_sk_mask, std::ios::binary); - ef_bv.serialize(outfile); - outfile.close(); + bool check = store_to_file(ef_bv, file_sk_mask); + std::cout<< " successfully stored " << file_sk_mask<<"?: " <size(); From 953e3f1631b27bec85f9393d9234a777f836d21c Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Mon, 22 Apr 2024 11:53:35 +0200 Subject: [PATCH 23/52] small fixes --- metagraph/external-libraries/sshash | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/metagraph/external-libraries/sshash b/metagraph/external-libraries/sshash index c008c20d9a..74dc101663 160000 --- a/metagraph/external-libraries/sshash +++ b/metagraph/external-libraries/sshash @@ -1 +1 @@ -Subproject commit c008c20d9ab1fc513f498af731dcb7dc91eba38e +Subproject commit 74dc101663be5fd13a01419ab1e5fd32728d2151 From 4c9455e39c4d24b6e7441f16bd09a8d1520470a6 Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Mon, 22 Apr 2024 15:44:58 +0200 Subject: [PATCH 24/52] mapping to kmers --- .../src/graph/representation/hash/dbg_sshash.cpp | 16 ++++++---------- 1 file changed, 6 insertions(+), 10 deletions(-) diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.cpp b/metagraph/src/graph/representation/hash/dbg_sshash.cpp index 523fa0e925..1b73fec5b5 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.cpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.cpp @@ -39,17 +39,8 @@ void DBGSSHash::map_to_nodes(std::string_view sequence, void DBGSSHash::map_to_nodes_sequentially(std::string_view sequence, const std::function &callback, const std::function &terminate) const { - if(!loaded_mask){ - - } for (size_t i = 0; i + k_ <= sequence.size() && !terminate(); ++i) { - auto [s_idx, s_id] = kmer_to_superkmer_node(sequence.substr(i, k_)); - if(s_idx != npos && superkmer_mask[s_id]){ // or s_id != sshash::constants::invalid_64_t - callback(kmer_to_node(sequence.substr(i, k_))); - // maybe implement kmer_to_node_from_superkmer(s_idx); - }else{ - callback(s_idx); - } + callback(kmer_to_node(sequence.substr(i, k_))); } } @@ -298,6 +289,11 @@ void DBGSSHash::superkmer_statistics(const std::unique_ptr& anno_g std::vector superkmer_mask = dict_->build_superkmer_bv([&anno_graph](std::string_view str){return anno_graph->get_labels(str);}); sdsl::bit_vector non_mono_superkmer = mask_into_bit_vec(superkmer_mask); + // print to check + std::cout<< "printing sk_mask indeces: \n"; + for(size_t i = 0; i < non_mono_superkmer.size(); i++){ + if(non_mono_superkmer[i] == 1)std::cout<< i << " "; + } // elias fano encoding and serialize sdsl::sd_vector<> ef_bv (non_mono_superkmer); From b522bdc60f6334b154e7d72118314f533ee9de88 Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Mon, 22 Apr 2024 15:55:13 +0200 Subject: [PATCH 25/52] removed superkmer stats --- metagraph/CMakeLists.txt | 22 +++---- metagraph/scripts/run_superkmer_stats.cpp | 65 ------------------- .../graph/representation/hash/dbg_sshash.cpp | 3 - 3 files changed, 11 insertions(+), 79 deletions(-) delete mode 100644 metagraph/scripts/run_superkmer_stats.cpp diff --git a/metagraph/CMakeLists.txt b/metagraph/CMakeLists.txt index 77f937605f..5a507aed06 100644 --- a/metagraph/CMakeLists.txt +++ b/metagraph/CMakeLists.txt @@ -546,17 +546,17 @@ target_compile_options(unit_tests PRIVATE -Wno-uninitialized ${DEATH_TEST_FLAG}) #------------------- # superkmer stats #------------------- -add_executable(superkmer_stats scripts/run_superkmer_stats.cpp) -target_include_directories(superkmer_stats PRIVATE src/graph/representation/hash - src/graph/ - src/annotation/representation/base/ - src/cli/config - src/cli/load - src/common/utils/ - ) - -target_link_libraries(superkmer_stats PRIVATE metagraph-core metagraph-cli ${METALIBS}) -target_compile_options(superkmer_stats PRIVATE -Wno-unused-parameter) +#add_executable(superkmer_stats scripts/run_superkmer_stats.cpp) +#target_include_directories(superkmer_stats PRIVATE src/graph/representation/hash +# src/graph/ +# src/annotation/representation/base/ +# src/cli/config +# src/cli/load +# src/common/utils/ +# ) + +#target_link_libraries(superkmer_stats PRIVATE metagraph-core metagraph-cli ${METALIBS}) +#target_compile_options(superkmer_stats PRIVATE -Wno-unused-parameter) #------------------- # Benchmarks diff --git a/metagraph/scripts/run_superkmer_stats.cpp b/metagraph/scripts/run_superkmer_stats.cpp deleted file mode 100644 index 2534b77027..0000000000 --- a/metagraph/scripts/run_superkmer_stats.cpp +++ /dev/null @@ -1,65 +0,0 @@ -#include "graph/representation/hash/dbg_sshash.hpp" -#include "graph/annotated_dbg.hpp" -#include "annotation/representation/base/annotation.hpp" - -#include "cli/load/load_annotation.hpp" -#include "annotation/representation/column_compressed/annotate_column_compressed.hpp" - -#include "string_utils.hpp" - - - -int main (int argc, char *argv[]){ - - using namespace mtg::graph; - using namespace mtg::annot; - using namespace mtg::annot::matrix; - using namespace mtg::cli; - - if(argc <3){ - std::cerr<<"missing input files!\n" ;//<< "graph path, annotation path, superkmer mask path\n"; - return EXIT_FAILURE; - } - std::string graph_path = argv[1]; - std::string anno_path = argv[2]; - //std::string sk_mask_path = argv[3]; - std::shared_ptr graph_ptr = std::make_shared(31); - graph_ptr->load(graph_path); - - std::string sk_mask_path = utils::remove_suffix(graph_path, graph_ptr->kExtension) + "_sk_mask"; - - - Config::AnnotationType config = parse_annotation_type(anno_path); - /* - Types of annotations: - ColumnCompressed = 1, - RowCompressed, - BRWT, - BinRelWT, - RowDiff, - RowDiffBRWT, - RowDiffRowFlat, - RowDiffRowSparse, - RowDiffDisk, - RowFlat, - RowSparse, - RBFish, - RbBRWT, - IntBRWT, - IntRowDiffBRWT, - IntRowDiffDisk, - ColumnCoord, - BRWTCoord, - RowDiffCoord, - RowDiffBRWTCoord, - RowDiffDiskCoord, - */ - assert(config == Config::AnnotationType::ColumnCompressed); - std::unique_ptr> anno_ptr = std::make_unique> (); - anno_ptr->load(anno_path); - - std::unique_ptr anno_graph = std::make_unique(graph_ptr, std::move(anno_ptr), false); - graph_ptr->superkmer_statistics(anno_graph, sk_mask_path); - - return 0; -} diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.cpp b/metagraph/src/graph/representation/hash/dbg_sshash.cpp index 523fa0e925..4c87d9dc87 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.cpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.cpp @@ -39,9 +39,6 @@ void DBGSSHash::map_to_nodes(std::string_view sequence, void DBGSSHash::map_to_nodes_sequentially(std::string_view sequence, const std::function &callback, const std::function &terminate) const { - if(!loaded_mask){ - - } for (size_t i = 0; i + k_ <= sequence.size() && !terminate(); ++i) { auto [s_idx, s_id] = kmer_to_superkmer_node(sequence.substr(i, k_)); if(s_idx != npos && superkmer_mask[s_id]){ // or s_id != sshash::constants::invalid_64_t From bf746512e3274eaa4a6f2ee728032780aa51889f Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Wed, 24 Apr 2024 15:51:19 +0200 Subject: [PATCH 26/52] changes to decrease superkmer mask runtime --- metagraph/external-libraries/sshash | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/metagraph/external-libraries/sshash b/metagraph/external-libraries/sshash index 74dc101663..3e9f494375 160000 --- a/metagraph/external-libraries/sshash +++ b/metagraph/external-libraries/sshash @@ -1 +1 @@ -Subproject commit 74dc101663be5fd13a01419ab1e5fd32728d2151 +Subproject commit 3e9f4943753f3898f527e0401a72eba891728896 From 05ff9ab77d10cb486b711ccb93284985e16d30e1 Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Wed, 24 Apr 2024 16:05:26 +0200 Subject: [PATCH 27/52] removed unnecessary line --- metagraph/external-libraries/sshash | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/metagraph/external-libraries/sshash b/metagraph/external-libraries/sshash index 3e9f494375..1254a7d61f 160000 --- a/metagraph/external-libraries/sshash +++ b/metagraph/external-libraries/sshash @@ -1 +1 @@ -Subproject commit 3e9f4943753f3898f527e0401a72eba891728896 +Subproject commit 1254a7d61fac45b684dc118cd3284528db2f13a5 From 7eec588da4f8dc7de6d7adf2b4ddff9c994285f2 Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Fri, 26 Apr 2024 17:08:11 +0200 Subject: [PATCH 28/52] getting superkmer label batches --- .../graph/representation/hash/dbg_sshash.cpp | 17 ++++++++++++++++- .../graph/representation/hash/dbg_sshash.hpp | 2 ++ 2 files changed, 18 insertions(+), 1 deletion(-) diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.cpp b/metagraph/src/graph/representation/hash/dbg_sshash.cpp index 1b73fec5b5..6fef3eca1b 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.cpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.cpp @@ -287,7 +287,22 @@ void DBGSSHash::load_superkmer_mask(std::string file){ void DBGSSHash::superkmer_statistics(const std::unique_ptr& anno_graph, std::string file_sk_mask) const{ std::cout<< "Computing superkmer statistics and building super kmer bit vector... \n"; - std::vector superkmer_mask = dict_->build_superkmer_bv([&anno_graph](std::string_view str){return anno_graph->get_labels(str);}); + //getting labels in batches + size_t num_labels = anno_graph->get_annotator().num_labels(); + std::vector superkmer_mask = dict_->build_superkmer_bv([&anno_graph, num_labels](std::string_view sequence){ + auto labels = anno_graph->get_top_label_signatures(sequence, num_labels); + // since get_top_label_signatures returns only labels that were found, + // if any entry is zero not all the kmers share all the same labels -> return false + for(auto pair : labels){ + sdsl::rank_support_v rs; + sdsl::util::init_support(rs,&pair.second); + size_t bit_vec_size = pair.second.size(); + if(rs(bit_vec_size) != bit_vec_size) return false; + } + return true; + }); + //std::vector superkmer_mask = dict_->build_superkmer_bv([&anno_graph](std::string_view str){return anno_graph->get_labels(str);}); + sdsl::bit_vector non_mono_superkmer = mask_into_bit_vec(superkmer_mask); // print to check std::cout<< "printing sk_mask indeces: \n"; diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.hpp b/metagraph/src/graph/representation/hash/dbg_sshash.hpp index 5bb8a944dd..4eadee1f58 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.hpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.hpp @@ -12,6 +12,8 @@ #include "../external-libraries/sshash/include/util.hpp" #include "graph/annotated_dbg.hpp" #include "sdsl/bit_vectors.hpp" +#include "sdsl/rank_support.hpp" +#include "sdsl/util.hpp" namespace sshash{ class dictionary; From e2056902e2e6a32b63a8190c21e8aeb80bbf1bd2 Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Fri, 26 Apr 2024 17:09:12 +0200 Subject: [PATCH 29/52] sshash version --- metagraph/external-libraries/sshash | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/metagraph/external-libraries/sshash b/metagraph/external-libraries/sshash index 1254a7d61f..d0feb6296f 160000 --- a/metagraph/external-libraries/sshash +++ b/metagraph/external-libraries/sshash @@ -1 +1 @@ -Subproject commit 1254a7d61fac45b684dc118cd3284528db2f13a5 +Subproject commit d0feb6296ffe939eff12390546e71bf15cd691cd From d9b7f0bbad5ad0b8d224611fe2e170b573daa4f3 Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Sat, 27 Apr 2024 08:43:48 +0200 Subject: [PATCH 30/52] tiny bug fix --- metagraph/external-libraries/sshash | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/metagraph/external-libraries/sshash b/metagraph/external-libraries/sshash index d0feb6296f..d650c0dff4 160000 --- a/metagraph/external-libraries/sshash +++ b/metagraph/external-libraries/sshash @@ -1 +1 @@ -Subproject commit d0feb6296ffe939eff12390546e71bf15cd691cd +Subproject commit d650c0dff4c743d8cc93c8041c65a0917ce6b59f From 4b3b84f16b7017b51f1070b9c856fea4d998e395 Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Mon, 29 Apr 2024 00:09:49 +0200 Subject: [PATCH 31/52] paralellized bit vector construction --- metagraph/external-libraries/sshash | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/metagraph/external-libraries/sshash b/metagraph/external-libraries/sshash index d650c0dff4..7da6294952 160000 --- a/metagraph/external-libraries/sshash +++ b/metagraph/external-libraries/sshash @@ -1 +1 @@ -Subproject commit d650c0dff4c743d8cc93c8041c65a0917ce6b59f +Subproject commit 7da6294952d181ee2f9f49bd6481fb2bc109378e From b973597fbed4aa3c53c2aa1c2283933e92dd13b3 Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Mon, 29 Apr 2024 16:33:57 +0200 Subject: [PATCH 32/52] splitting and merging of superkmer vector for parallelization --- metagraph/external-libraries/sshash | 2 +- .../src/graph/representation/hash/dbg_sshash.cpp | 12 +++++++----- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/metagraph/external-libraries/sshash b/metagraph/external-libraries/sshash index 7da6294952..80f9e482c1 160000 --- a/metagraph/external-libraries/sshash +++ b/metagraph/external-libraries/sshash @@ -1 +1 @@ -Subproject commit 7da6294952d181ee2f9f49bd6481fb2bc109378e +Subproject commit 80f9e482c1dd076d3b0071651825e5884d29ba7c diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.cpp b/metagraph/src/graph/representation/hash/dbg_sshash.cpp index 6fef3eca1b..edb8ac2da1 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.cpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.cpp @@ -289,7 +289,7 @@ void DBGSSHash::superkmer_statistics(const std::unique_ptr& anno_g //getting labels in batches size_t num_labels = anno_graph->get_annotator().num_labels(); - std::vector superkmer_mask = dict_->build_superkmer_bv([&anno_graph, num_labels](std::string_view sequence){ + std::vector superkmer_idxs = dict_->build_superkmer_bv([&anno_graph, num_labels](std::string_view sequence){ auto labels = anno_graph->get_top_label_signatures(sequence, num_labels); // since get_top_label_signatures returns only labels that were found, // if any entry is zero not all the kmers share all the same labels -> return false @@ -303,14 +303,16 @@ void DBGSSHash::superkmer_statistics(const std::unique_ptr& anno_g }); //std::vector superkmer_mask = dict_->build_superkmer_bv([&anno_graph](std::string_view str){return anno_graph->get_labels(str);}); - sdsl::bit_vector non_mono_superkmer = mask_into_bit_vec(superkmer_mask); + //sdsl::bit_vector non_mono_superkmer = mask_into_bit_vec(superkmer_mask); // print to check + /* std::cout<< "printing sk_mask indeces: \n"; - for(size_t i = 0; i < non_mono_superkmer.size(); i++){ - if(non_mono_superkmer[i] == 1)std::cout<< i << " "; + for(size_t i = 0; i < superkmer_idxs.size(); i++){ + std::cout<< superkmer_idxs[i] << " "; } + */ // elias fano encoding and serialize - sdsl::sd_vector<> ef_bv (non_mono_superkmer); + sdsl::sd_vector<> ef_bv (superkmer_idxs.begin(), superkmer_idxs.end()); std::cout << "serializing bit vector..." << std::endl; bool check = store_to_file(ef_bv, file_sk_mask); From a6a0f7f5afdc86da1c0eb40d761b8290fa6b4072 Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Mon, 29 Apr 2024 19:10:06 +0200 Subject: [PATCH 33/52] pure superkmer annotation -> with information loss --- metagraph/src/graph/representation/hash/dbg_sshash.cpp | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.cpp b/metagraph/src/graph/representation/hash/dbg_sshash.cpp index 4c87d9dc87..fe13d8fe00 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.cpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.cpp @@ -41,12 +41,12 @@ void DBGSSHash::map_to_nodes_sequentially(std::string_view sequence, const std::function &terminate) const { for (size_t i = 0; i + k_ <= sequence.size() && !terminate(); ++i) { auto [s_idx, s_id] = kmer_to_superkmer_node(sequence.substr(i, k_)); - if(s_idx != npos && superkmer_mask[s_id]){ // or s_id != sshash::constants::invalid_64_t - callback(kmer_to_node(sequence.substr(i, k_))); + //if(s_idx != npos && superkmer_mask[s_id]){ // or s_id != sshash::constants::invalid_64_t + // callback(kmer_to_node(sequence.substr(i, k_))); // maybe implement kmer_to_node_from_superkmer(s_idx); - }else{ + //}else{ callback(s_idx); - } + //} } } From 361408e1d0d9c0ff2db743bfb2a8742d23a50acd Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Thu, 2 May 2024 00:10:19 +0200 Subject: [PATCH 34/52] removed 2 extra lookup calls added during debugging --- metagraph/src/graph/representation/hash/dbg_sshash.cpp | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.cpp b/metagraph/src/graph/representation/hash/dbg_sshash.cpp index 4c87d9dc87..f99e3e691a 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.cpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.cpp @@ -43,7 +43,7 @@ void DBGSSHash::map_to_nodes_sequentially(std::string_view sequence, auto [s_idx, s_id] = kmer_to_superkmer_node(sequence.substr(i, k_)); if(s_idx != npos && superkmer_mask[s_id]){ // or s_id != sshash::constants::invalid_64_t callback(kmer_to_node(sequence.substr(i, k_))); - // maybe implement kmer_to_node_from_superkmer(s_idx); + // maybe implement kmer_to_node_from_superkmer(s_idx, sequence.substr(i, k_)); }else{ callback(s_idx); } @@ -194,15 +194,8 @@ DBGSSHash::node_index DBGSSHash::kmer_to_node(std::string_view kmer) const { std::pair DBGSSHash::kmer_to_superkmer_node(std::string_view kmer) const { auto [ssh_idx, superkmer_id] = dict_->kmer_to_superkmer_idx(kmer.begin(), true); if(ssh_idx == sshash::constants::invalid_uint64){ - if(dict_->lookup(kmer.begin(), true)!= sshash::constants::invalid_uint64){ - std::cout<< kmer <<"\n*********** NOT FOUND WITH KMER_TO_SUPERKMER_IDX BUT FOUND WITH LOOKUP" <lookup(kmer.begin(), true) == sshash::constants::invalid_uint64){ - std::cout<< kmer <<"\n*********** found with kmer_to_index but not with lookup!! *********" < Date: Thu, 2 May 2024 00:54:12 +0200 Subject: [PATCH 35/52] more efficient query for kmers in non-monochromatic superkmers --- metagraph/external-libraries/sshash | 2 +- .../src/graph/representation/hash/dbg_sshash.cpp | 15 ++++----------- .../src/graph/representation/hash/dbg_sshash.hpp | 3 +-- 3 files changed, 6 insertions(+), 14 deletions(-) diff --git a/metagraph/external-libraries/sshash b/metagraph/external-libraries/sshash index 74dc101663..f2eaf607a8 160000 --- a/metagraph/external-libraries/sshash +++ b/metagraph/external-libraries/sshash @@ -1 +1 @@ -Subproject commit 74dc101663be5fd13a01419ab1e5fd32728d2151 +Subproject commit f2eaf607a827dfeea3fcc32df0337df4206297f6 diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.cpp b/metagraph/src/graph/representation/hash/dbg_sshash.cpp index 4c87d9dc87..5abddc00dd 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.cpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.cpp @@ -42,8 +42,8 @@ void DBGSSHash::map_to_nodes_sequentially(std::string_view sequence, for (size_t i = 0; i + k_ <= sequence.size() && !terminate(); ++i) { auto [s_idx, s_id] = kmer_to_superkmer_node(sequence.substr(i, k_)); if(s_idx != npos && superkmer_mask[s_id]){ // or s_id != sshash::constants::invalid_64_t - callback(kmer_to_node(sequence.substr(i, k_))); - // maybe implement kmer_to_node_from_superkmer(s_idx); + //callback(kmer_to_node(sequence.substr(i, k_))); + callback(kmer_to_node_from_superkmer(sequence.substr(i, k_), s_id)); }else{ callback(s_idx); } @@ -180,8 +180,8 @@ void DBGSSHash::call_kmers( } } -DBGSSHash::node_index DBGSSHash::kmer_to_node_from_superkmer(std::string_view kmer) const { - uint64_t ssh_idx = dict_->lookup(kmer.begin(), true); +DBGSSHash::node_index DBGSSHash::kmer_to_node_from_superkmer(std::string_view kmer, uint64_t s_id) const { + uint64_t ssh_idx = dict_->look_up_from_superkmer_id(s_id, kmer.begin()); return ssh_idx + 1; } @@ -194,15 +194,8 @@ DBGSSHash::node_index DBGSSHash::kmer_to_node(std::string_view kmer) const { std::pair DBGSSHash::kmer_to_superkmer_node(std::string_view kmer) const { auto [ssh_idx, superkmer_id] = dict_->kmer_to_superkmer_idx(kmer.begin(), true); if(ssh_idx == sshash::constants::invalid_uint64){ - if(dict_->lookup(kmer.begin(), true)!= sshash::constants::invalid_uint64){ - std::cout<< kmer <<"\n*********** NOT FOUND WITH KMER_TO_SUPERKMER_IDX BUT FOUND WITH LOOKUP" <lookup(kmer.begin(), true) == sshash::constants::invalid_uint64){ - std::cout<< kmer <<"\n*********** found with kmer_to_index but not with lookup!! *********" < Date: Thu, 2 May 2024 10:45:49 +0200 Subject: [PATCH 36/52] removed 2 extra lookup calls added during debugging --- metagraph/external-libraries/sshash | 2 +- .../src/graph/representation/hash/dbg_sshash.cpp | 13 +++---------- 2 files changed, 4 insertions(+), 11 deletions(-) diff --git a/metagraph/external-libraries/sshash b/metagraph/external-libraries/sshash index 74dc101663..f2eaf607a8 160000 --- a/metagraph/external-libraries/sshash +++ b/metagraph/external-libraries/sshash @@ -1 +1 @@ -Subproject commit 74dc101663be5fd13a01419ab1e5fd32728d2151 +Subproject commit f2eaf607a827dfeea3fcc32df0337df4206297f6 diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.cpp b/metagraph/src/graph/representation/hash/dbg_sshash.cpp index fe13d8fe00..652ec11a10 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.cpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.cpp @@ -194,15 +194,8 @@ DBGSSHash::node_index DBGSSHash::kmer_to_node(std::string_view kmer) const { std::pair DBGSSHash::kmer_to_superkmer_node(std::string_view kmer) const { auto [ssh_idx, superkmer_id] = dict_->kmer_to_superkmer_idx(kmer.begin(), true); if(ssh_idx == sshash::constants::invalid_uint64){ - if(dict_->lookup(kmer.begin(), true)!= sshash::constants::invalid_uint64){ - std::cout<< kmer <<"\n*********** NOT FOUND WITH KMER_TO_SUPERKMER_IDX BUT FOUND WITH LOOKUP" <lookup(kmer.begin(), true) == sshash::constants::invalid_uint64){ - std::cout<< kmer <<"\n*********** found with kmer_to_index but not with lookup!! *********" <k(); - std::string s_mask_name = utils::remove_suffix(filename, kExtension) + "_sk_mask"; - std::cout << "LOADING MASK! \n"; - load_superkmer_mask(s_mask_name); + //std::string s_mask_name = utils::remove_suffix(filename, kExtension) + "_sk_mask"; + //std::cout << "LOADING MASK! \n"; + //load_superkmer_mask(s_mask_name); return true; } From 37fbec49e8f863106a4bf5347f2404e694c684b6 Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Fri, 3 May 2024 14:32:36 +0200 Subject: [PATCH 37/52] changed annotation type for superkmer mask construction --- metagraph/scripts/run_superkmer_stats.cpp | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/metagraph/scripts/run_superkmer_stats.cpp b/metagraph/scripts/run_superkmer_stats.cpp index 2534b77027..829726bf5c 100644 --- a/metagraph/scripts/run_superkmer_stats.cpp +++ b/metagraph/scripts/run_superkmer_stats.cpp @@ -4,10 +4,11 @@ #include "cli/load/load_annotation.hpp" #include "annotation/representation/column_compressed/annotate_column_compressed.hpp" +#include "annotation/representation/row_compressed/annotate_row_compressed.hpp" #include "string_utils.hpp" - +#include "annotation/binary_matrix/base/binary_matrix.hpp" int main (int argc, char *argv[]){ @@ -54,8 +55,9 @@ int main (int argc, char *argv[]){ RowDiffBRWTCoord, RowDiffDiskCoord, */ - assert(config == Config::AnnotationType::ColumnCompressed); - std::unique_ptr> anno_ptr = std::make_unique> (); + assert(config == Config::AnnotationType::RowFlat); + //std::unique_ptr> anno_ptr = std::make_unique> (); + auto anno_ptr = std::make_unique>(); anno_ptr->load(anno_path); std::unique_ptr anno_graph = std::make_unique(graph_ptr, std::move(anno_ptr), false); From 562235736013cebcea506dd7c5941f31e7684cf7 Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Fri, 3 May 2024 15:54:41 +0200 Subject: [PATCH 38/52] fixed annotation type --- metagraph/scripts/run_superkmer_stats.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/metagraph/scripts/run_superkmer_stats.cpp b/metagraph/scripts/run_superkmer_stats.cpp index 829726bf5c..aa04a15051 100644 --- a/metagraph/scripts/run_superkmer_stats.cpp +++ b/metagraph/scripts/run_superkmer_stats.cpp @@ -8,6 +8,7 @@ #include "string_utils.hpp" +#include "annotation/representation/annotation_matrix/static_annotators_def.hpp" #include "annotation/binary_matrix/base/binary_matrix.hpp" int main (int argc, char *argv[]){ @@ -57,9 +58,8 @@ int main (int argc, char *argv[]){ */ assert(config == Config::AnnotationType::RowFlat); //std::unique_ptr> anno_ptr = std::make_unique> (); - auto anno_ptr = std::make_unique>(); + std::unique_ptr anno_ptr = std::make_unique(); anno_ptr->load(anno_path); - std::unique_ptr anno_graph = std::make_unique(graph_ptr, std::move(anno_ptr), false); graph_ptr->superkmer_statistics(anno_graph, sk_mask_path); From a2997de39f8ff19526126ffe8296b930400f5ca2 Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Mon, 6 May 2024 11:08:11 +0200 Subject: [PATCH 39/52] sshash both for superkmer bit vec construction and mapping --- metagraph/external-libraries/sshash | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/metagraph/external-libraries/sshash b/metagraph/external-libraries/sshash index 80f9e482c1..a2d3246bed 160000 --- a/metagraph/external-libraries/sshash +++ b/metagraph/external-libraries/sshash @@ -1 +1 @@ -Subproject commit 80f9e482c1dd076d3b0071651825e5884d29ba7c +Subproject commit a2d3246bed53f1e098193d56749ea2e49958a0e2 From c97f396a760c462ded8e7c015ff7ed7dbb95b73d Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Mon, 6 May 2024 11:26:29 +0200 Subject: [PATCH 40/52] sshash both for superkmer bit vec construction and mapping --- metagraph/external-libraries/sshash | 2 +- .../graph/representation/hash/dbg_sshash.cpp | 103 +++--------------- 2 files changed, 17 insertions(+), 88 deletions(-) diff --git a/metagraph/external-libraries/sshash b/metagraph/external-libraries/sshash index f2eaf607a8..a2d3246bed 160000 --- a/metagraph/external-libraries/sshash +++ b/metagraph/external-libraries/sshash @@ -1 +1 @@ -Subproject commit f2eaf607a827dfeea3fcc32df0337df4206297f6 +Subproject commit a2d3246bed53f1e098193d56749ea2e49958a0e2 diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.cpp b/metagraph/src/graph/representation/hash/dbg_sshash.cpp index 5abddc00dd..289994576c 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.cpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.cpp @@ -286,100 +286,29 @@ void DBGSSHash::load_superkmer_mask(std::string file){ void DBGSSHash::superkmer_statistics(const std::unique_ptr& anno_graph, std::string file_sk_mask) const{ std::cout<< "Computing superkmer statistics and building super kmer bit vector... \n"; - std::vector superkmer_mask = dict_->build_superkmer_bv([&anno_graph](std::string_view str){return anno_graph->get_labels(str);}); - sdsl::bit_vector non_mono_superkmer = mask_into_bit_vec(superkmer_mask); + //getting labels in batches + size_t num_labels = anno_graph->get_annotator().num_labels(); + std::vector superkmer_idxs = dict_->build_superkmer_bv([&anno_graph, num_labels](std::string_view sequence){ + auto labels = anno_graph->get_top_label_signatures(sequence, num_labels); + // since get_top_label_signatures returns only labels that were found, + // if any entry is zero not all the kmers share all the same labels -> return false + for(auto pair : labels){ + sdsl::rank_support_v rs; + sdsl::util::init_support(rs,&pair.second); + size_t bit_vec_size = pair.second.size(); + if(rs(bit_vec_size) != bit_vec_size) return false; + } + return true; + }); + // elias fano encoding and serialize - sdsl::sd_vector<> ef_bv (non_mono_superkmer); + sdsl::sd_vector<> ef_bv (superkmer_idxs.begin(), superkmer_idxs.end()); std::cout << "serializing bit vector..." << std::endl; bool check = store_to_file(ef_bv, file_sk_mask); std::cout<< " successfully stored " << file_sk_mask<<"?: " <size(); - uint64_t one_pm_num_kmers = num_kmers/1000; - //uint64_t num_super_kmers = dict_->num_superkmers(); - uint64_t dict_m = dict_->m(); - uint64_t dict_seed = dict_->seed(); - - std::vector color_changes_per_superkmer(0); - std::vector kmers_per_superkmer(0); - - sshash::dictionary::iterator it = dict_->begin(); - - // first kmer - uint64_t first_kmer_id = 0; - std::string first_kmer_str = ""; - dict_->access(first_kmer_id, &(first_kmer_str[0])); - sshash::kmer_t uint_kmer = sshash::util::string_to_uint_kmer(&(first_kmer_str[0]), k_); - - uint64_t count_labels = 0; - uint64_t count_kmers = 1; - - uint64_t minim, new_minim; - uint64_t contig_id, new_contig_id; - - // first contig - contig_id = dict_->lookup_advanced_uint(uint_kmer, false).contig_id; - new_contig_id = contig_id; - //first minimizer - minim = sshash::util::compute_minimizer(uint_kmer, k_, dict_m, dict_seed); - new_minim = minim; - - //first labels - std::vector labels, new_labels; - labels = anno_graph->get_labels(first_kmer_str); - new_labels = labels; - - uint64_t kmer_id; - std::string kmer_str; - - std::cout<< "iterating through graph... \n"; - while(it.has_next()){ - // step to next kmer - auto kmer_pair = it.next(); - kmer_str = kmer_pair.second; - kmer_id = kmer_pair.first; - uint_kmer = sshash::util::string_to_uint_kmer(&(kmer_str[0]), k_); - new_minim = sshash::util::compute_minimizer(uint_kmer, k_, dict_m, dict_seed); // is this the correct minimizer? - new_labels = anno_graph->get_labels(kmer_str); - new_contig_id = dict_->lookup_advanced_uint(uint_kmer, false).contig_id; - - - //next superkmer? - if(new_minim != minim || new_contig_id != contig_id){//yes - minim = new_minim; - contig_id = new_contig_id; - labels = new_labels; - color_changes_per_superkmer.push_back(count_labels); - kmers_per_superkmer.push_back(count_kmers); - //reset counters - count_labels = 0; - count_kmers = 1; - }else {//no - if(!equal(new_labels, labels)){ - count_labels++; - labels = new_labels; - } - - count_kmers++; - } - if(kmer_id % one_pm_num_kmers == 0) std::cout<<'.'<& input1, const std::vector& input2)const { From ce691b2b86c3fcb3c073d6be51f12d1bbd688fd0 Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Mon, 6 May 2024 11:30:20 +0200 Subject: [PATCH 41/52] sshash both for superkmer bit vec construction and mapping --- metagraph/external-libraries/sshash | 2 +- .../graph/representation/hash/dbg_sshash.cpp | 110 +++--------------- 2 files changed, 20 insertions(+), 92 deletions(-) diff --git a/metagraph/external-libraries/sshash b/metagraph/external-libraries/sshash index f2eaf607a8..a2d3246bed 160000 --- a/metagraph/external-libraries/sshash +++ b/metagraph/external-libraries/sshash @@ -1 +1 @@ -Subproject commit f2eaf607a827dfeea3fcc32df0337df4206297f6 +Subproject commit a2d3246bed53f1e098193d56749ea2e49958a0e2 diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.cpp b/metagraph/src/graph/representation/hash/dbg_sshash.cpp index 652ec11a10..c272afb829 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.cpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.cpp @@ -284,102 +284,30 @@ void DBGSSHash::load_superkmer_mask(std::string file){ } void DBGSSHash::superkmer_statistics(const std::unique_ptr& anno_graph, std::string file_sk_mask) const{ - std::cout<< "Computing superkmer statistics and building super kmer bit vector... \n"; - - std::vector superkmer_mask = dict_->build_superkmer_bv([&anno_graph](std::string_view str){return anno_graph->get_labels(str);}); - sdsl::bit_vector non_mono_superkmer = mask_into_bit_vec(superkmer_mask); + std::cout<< "Computing superkmer statistics and building super kmer bit vector... \n"; + + //getting labels in batches + size_t num_labels = anno_graph->get_annotator().num_labels(); + std::vector superkmer_idxs = dict_->build_superkmer_bv([&anno_graph, num_labels](std::string_view sequence){ + auto labels = anno_graph->get_top_label_signatures(sequence, num_labels); + // since get_top_label_signatures returns only labels that were found, + // if any entry is zero not all the kmers share all the same labels -> return false + for(auto pair : labels){ + sdsl::rank_support_v rs; + sdsl::util::init_support(rs,&pair.second); + size_t bit_vec_size = pair.second.size(); + if(rs(bit_vec_size) != bit_vec_size) return false; + } + return true; + }); + // elias fano encoding and serialize - sdsl::sd_vector<> ef_bv (non_mono_superkmer); - + sdsl::sd_vector<> ef_bv (superkmer_idxs.begin(), superkmer_idxs.end()); + std::cout << "serializing bit vector..." << std::endl; bool check = store_to_file(ef_bv, file_sk_mask); std::cout<< " successfully stored " << file_sk_mask<<"?: " <size(); - uint64_t one_pm_num_kmers = num_kmers/1000; - //uint64_t num_super_kmers = dict_->num_superkmers(); - uint64_t dict_m = dict_->m(); - uint64_t dict_seed = dict_->seed(); - - std::vector color_changes_per_superkmer(0); - std::vector kmers_per_superkmer(0); - - sshash::dictionary::iterator it = dict_->begin(); - - // first kmer - uint64_t first_kmer_id = 0; - std::string first_kmer_str = ""; - dict_->access(first_kmer_id, &(first_kmer_str[0])); - sshash::kmer_t uint_kmer = sshash::util::string_to_uint_kmer(&(first_kmer_str[0]), k_); - - uint64_t count_labels = 0; - uint64_t count_kmers = 1; - - uint64_t minim, new_minim; - uint64_t contig_id, new_contig_id; - - // first contig - contig_id = dict_->lookup_advanced_uint(uint_kmer, false).contig_id; - new_contig_id = contig_id; - //first minimizer - minim = sshash::util::compute_minimizer(uint_kmer, k_, dict_m, dict_seed); - new_minim = minim; - - //first labels - std::vector labels, new_labels; - labels = anno_graph->get_labels(first_kmer_str); - new_labels = labels; - - uint64_t kmer_id; - std::string kmer_str; - - std::cout<< "iterating through graph... \n"; - while(it.has_next()){ - // step to next kmer - auto kmer_pair = it.next(); - kmer_str = kmer_pair.second; - kmer_id = kmer_pair.first; - uint_kmer = sshash::util::string_to_uint_kmer(&(kmer_str[0]), k_); - new_minim = sshash::util::compute_minimizer(uint_kmer, k_, dict_m, dict_seed); // is this the correct minimizer? - new_labels = anno_graph->get_labels(kmer_str); - new_contig_id = dict_->lookup_advanced_uint(uint_kmer, false).contig_id; - - - //next superkmer? - if(new_minim != minim || new_contig_id != contig_id){//yes - minim = new_minim; - contig_id = new_contig_id; - labels = new_labels; - color_changes_per_superkmer.push_back(count_labels); - kmers_per_superkmer.push_back(count_kmers); - //reset counters - count_labels = 0; - count_kmers = 1; - }else {//no - if(!equal(new_labels, labels)){ - count_labels++; - labels = new_labels; - } - - count_kmers++; - } - if(kmer_id % one_pm_num_kmers == 0) std::cout<<'.'<& input1, const std::vector& input2)const { From 3e3b8859b732449e661c2d12899eedcaf8ff9998 Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Tue, 7 May 2024 14:16:45 +0200 Subject: [PATCH 42/52] reverse complement bug fix --- metagraph/external-libraries/sshash | 2 +- metagraph/src/graph/representation/hash/dbg_sshash.cpp | 6 +++--- metagraph/src/graph/representation/hash/dbg_sshash.hpp | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/metagraph/external-libraries/sshash b/metagraph/external-libraries/sshash index a2d3246bed..9e48f31370 160000 --- a/metagraph/external-libraries/sshash +++ b/metagraph/external-libraries/sshash @@ -1 +1 @@ -Subproject commit a2d3246bed53f1e098193d56749ea2e49958a0e2 +Subproject commit 9e48f313701583866ad44f55968de5cb88e5d7d9 diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.cpp b/metagraph/src/graph/representation/hash/dbg_sshash.cpp index 289994576c..3ca5767043 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.cpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.cpp @@ -43,7 +43,7 @@ void DBGSSHash::map_to_nodes_sequentially(std::string_view sequence, auto [s_idx, s_id] = kmer_to_superkmer_node(sequence.substr(i, k_)); if(s_idx != npos && superkmer_mask[s_id]){ // or s_id != sshash::constants::invalid_64_t //callback(kmer_to_node(sequence.substr(i, k_))); - callback(kmer_to_node_from_superkmer(sequence.substr(i, k_), s_id)); + callback(kmer_to_node_from_superkmer(sequence.substr(i, k_), s_id, true)); }else{ callback(s_idx); } @@ -180,8 +180,8 @@ void DBGSSHash::call_kmers( } } -DBGSSHash::node_index DBGSSHash::kmer_to_node_from_superkmer(std::string_view kmer, uint64_t s_id) const { - uint64_t ssh_idx = dict_->look_up_from_superkmer_id(s_id, kmer.begin()); +DBGSSHash::node_index DBGSSHash::kmer_to_node_from_superkmer(std::string_view kmer, uint64_t s_id, bool check_reverse_complement) const { + uint64_t ssh_idx = dict_->look_up_from_superkmer_id(s_id, kmer.begin(), check_reverse_complement); return ssh_idx + 1; } diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.hpp b/metagraph/src/graph/representation/hash/dbg_sshash.hpp index 9672311e86..24278ad0e2 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.hpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.hpp @@ -80,7 +80,7 @@ class DBGSSHash : public DeBruijnGraph { bool has_single_incoming(node_index) const override; node_index kmer_to_node(std::string_view kmer) const override; - node_index kmer_to_node_from_superkmer(std::string_view kmer, uint64_t s_id) const; + node_index kmer_to_node_from_superkmer(std::string_view kmer, uint64_t s_id, bool check_reverse_complement) const; void call_outgoing_kmers(node_index node, From e60ab9f958a87a74580980bb120475e8967546b9 Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Sun, 12 May 2024 13:38:27 +0200 Subject: [PATCH 43/52] returning kmer index during superkmer lookup --- metagraph/external-libraries/sshash | 2 +- .../graph/representation/hash/dbg_sshash.cpp | 20 ++++++++++--------- .../graph/representation/hash/dbg_sshash.hpp | 3 ++- 3 files changed, 14 insertions(+), 11 deletions(-) diff --git a/metagraph/external-libraries/sshash b/metagraph/external-libraries/sshash index 9e48f31370..9be36ab842 160000 --- a/metagraph/external-libraries/sshash +++ b/metagraph/external-libraries/sshash @@ -1 +1 @@ -Subproject commit 9e48f313701583866ad44f55968de5cb88e5d7d9 +Subproject commit 9be36ab842cebf07000b4a8b6a7fa78cb131bb37 diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.cpp b/metagraph/src/graph/representation/hash/dbg_sshash.cpp index 3ca5767043..088ed21543 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.cpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.cpp @@ -40,10 +40,11 @@ void DBGSSHash::map_to_nodes_sequentially(std::string_view sequence, const std::function &callback, const std::function &terminate) const { for (size_t i = 0; i + k_ <= sequence.size() && !terminate(); ++i) { - auto [s_idx, s_id] = kmer_to_superkmer_node(sequence.substr(i, k_)); - if(s_idx != npos && superkmer_mask[s_id]){ // or s_id != sshash::constants::invalid_64_t - //callback(kmer_to_node(sequence.substr(i, k_))); - callback(kmer_to_node_from_superkmer(sequence.substr(i, k_), s_id, true)); + //auto [s_idx, s_id] = kmer_to_superkmer_node(sequence.substr(i, k_)); + auto [k_idx, s_idx, s_id] = kmer_to_superkmer_node(sequence.substr(i, k_)); + if(k_idx != npos && superkmer_mask[s_id]){ // or s_id != sshash::constants::invalid_64_t + //callback(kmer_to_node_from_superkmer(sequence.substr(i, k_), s_id, true)); + callback(k_idx); }else{ callback(s_idx); } @@ -191,12 +192,13 @@ DBGSSHash::node_index DBGSSHash::kmer_to_node(std::string_view kmer) const { } // superkmer experiment: use minimizer to get superkmer positions (offsets) -> get superkmer that contains kmer -std::pair DBGSSHash::kmer_to_superkmer_node(std::string_view kmer) const { - auto [ssh_idx, superkmer_id] = dict_->kmer_to_superkmer_idx(kmer.begin(), true); - if(ssh_idx == sshash::constants::invalid_uint64){ - return std::pair(npos, sshash::constants::invalid_uint64); +std::tuple DBGSSHash::kmer_to_superkmer_node(std::string_view kmer) const { + //auto [k_ssh_idx, s_ssh_idx, superkmer_id] = dict_->kmer_to_superkmer_idx(kmer.begin(), true); + auto [kmer_idx, superkmer_idx, superkmer_id] = dict_->kmer_to_superkmer_idx(kmer.begin(), true); + if(kmer_idx == sshash::constants::invalid_uint64){ + return {sshash::constants::invalid_uint64, sshash::constants::invalid_uint64, sshash::constants::invalid_uint64}; } - return std::pair(ssh_idx + 1, superkmer_id); + return {kmer_idx + 1, superkmer_idx + 1, superkmer_id}; } std::string DBGSSHash::get_node_sequence(node_index node) const { diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.hpp b/metagraph/src/graph/representation/hash/dbg_sshash.hpp index 24278ad0e2..934d035f61 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.hpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.hpp @@ -4,6 +4,7 @@ #include #include #include +#include #include "common/utils/string_utils.hpp" #include "graph/representation/base/sequence_graph.hpp" @@ -95,7 +96,7 @@ class DBGSSHash : public DeBruijnGraph { const std::string &alphabet() const override; //still in progress - std::pair kmer_to_superkmer_node(std::string_view kmer) const ; + std::tuple kmer_to_superkmer_node(std::string_view kmer) const ; void load_superkmer_mask(std::string file); void superkmer_statistics(const std::unique_ptr& anno_graph, std::string file_sk_mask) const; From 6f3914305ec95543829c7ad14cbdf686d2a6b68c Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Sun, 12 May 2024 14:05:29 +0200 Subject: [PATCH 44/52] use npos --- metagraph/src/graph/representation/hash/dbg_sshash.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.cpp b/metagraph/src/graph/representation/hash/dbg_sshash.cpp index 088ed21543..f0f2fe4b7f 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.cpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.cpp @@ -196,7 +196,7 @@ std::tuple DBGSSHash::kmer_to_superkmer_node(std:: //auto [k_ssh_idx, s_ssh_idx, superkmer_id] = dict_->kmer_to_superkmer_idx(kmer.begin(), true); auto [kmer_idx, superkmer_idx, superkmer_id] = dict_->kmer_to_superkmer_idx(kmer.begin(), true); if(kmer_idx == sshash::constants::invalid_uint64){ - return {sshash::constants::invalid_uint64, sshash::constants::invalid_uint64, sshash::constants::invalid_uint64}; + return {npos, npos, sshash::constants::invalid_uint64}; } return {kmer_idx + 1, superkmer_idx + 1, superkmer_id}; } From 3da03adf7c5f8b48bfe953dd24e2057d49c0bb36 Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Thu, 16 May 2024 15:08:20 +0200 Subject: [PATCH 45/52] annotation modus given by flag --- .../graph/representation/hash/dbg_sshash.cpp | 35 +++++++++++++------ .../graph/representation/hash/dbg_sshash.hpp | 1 + 2 files changed, 26 insertions(+), 10 deletions(-) diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.cpp b/metagraph/src/graph/representation/hash/dbg_sshash.cpp index aaf3325cc0..485225a672 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.cpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.cpp @@ -39,16 +39,26 @@ void DBGSSHash::map_to_nodes(std::string_view sequence, void DBGSSHash::map_to_nodes_sequentially(std::string_view sequence, const std::function &callback, const std::function &terminate) const { - for (size_t i = 0; i + k_ <= sequence.size() && !terminate(); ++i) { - //auto [s_idx, s_id] = kmer_to_superkmer_node(sequence.substr(i, k_)); - auto [k_idx, s_idx, s_id] = kmer_to_superkmer_node(sequence.substr(i, k_)); - if(k_idx != npos && superkmer_mask[s_id]){ // or s_id != sshash::constants::invalid_64_t - //callback(kmer_to_node_from_superkmer(sequence.substr(i, k_), s_id, true)); - callback(k_idx); - }else{ + if(annotation_mode == 2){ + for (size_t i = 0; i + k_ <= sequence.size() && !terminate(); ++i) { + auto [k_idx, s_idx, s_id] = kmer_to_superkmer_node(sequence.substr(i, k_)); + if(k_idx != npos && superkmer_mask[s_id]){ + callback(k_idx); + }else{ + callback(s_idx); + } + } + }else if(annotation_mode == 1){ + for (size_t i = 0; i + k_ <= sequence.size() && !terminate(); ++i) { + auto [k_idx, s_idx, s_id] = kmer_to_superkmer_node(sequence.substr(i, k_)); callback(s_idx); } + }else{ + for (size_t i = 0; i + k_ <= sequence.size() && !terminate(); ++i) { + callback(kmer_to_node(sequence.substr(i, k_))); + } } + } DBGSSHash::node_index DBGSSHash::traverse(node_index node, char next_char) const { @@ -239,9 +249,11 @@ bool DBGSSHash::load(const std::string &filename) { } k_ = dict_->k(); - //std::string s_mask_name = utils::remove_suffix(filename, kExtension) + "_sk_mask"; - //std::cout << "LOADING MASK! \n"; - //load_superkmer_mask(s_mask_name); + if(annotation_mode == 2){ + std::string s_mask_name = utils::remove_suffix(filename, kExtension) + "_sk_mask"; + load_superkmer_mask(s_mask_name); + } + return true; } @@ -286,6 +298,9 @@ void DBGSSHash::load_superkmer_mask(std::string file){ } void DBGSSHash::superkmer_statistics(const std::unique_ptr& anno_graph, std::string file_sk_mask) const{ + if(annotation_mode != 0){ + throw std::runtime_error("Computing superkmer stats in wrong annotation mode!"); + } std::cout<< "Computing superkmer statistics and building super kmer bit vector... \n"; //getting labels in batches diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.hpp b/metagraph/src/graph/representation/hash/dbg_sshash.hpp index 7d3c0bafdf..c6ce482751 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.hpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.hpp @@ -110,6 +110,7 @@ class DBGSSHash : public DeBruijnGraph { private: static const std::string alphabet_; std::unique_ptr dict_; + int annotation_mode = 2; // 0: kmer annotation, 1: lossy superkmer annotation, 2: superkmer annotation with superkmer mask bool loaded_mask = false; sdsl::sd_vector<> superkmer_mask; size_t k_; From 8a23844ddc7ce0eb682059192ee5e91263f7a367 Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Thu, 16 May 2024 17:24:39 +0200 Subject: [PATCH 46/52] added stats --- metagraph/CMakeLists.txt | 22 +++++++++---------- metagraph/external-libraries/sshash | 2 +- .../graph/representation/hash/dbg_sshash.hpp | 2 +- 3 files changed, 13 insertions(+), 13 deletions(-) diff --git a/metagraph/CMakeLists.txt b/metagraph/CMakeLists.txt index 5a507aed06..77f937605f 100644 --- a/metagraph/CMakeLists.txt +++ b/metagraph/CMakeLists.txt @@ -546,17 +546,17 @@ target_compile_options(unit_tests PRIVATE -Wno-uninitialized ${DEATH_TEST_FLAG}) #------------------- # superkmer stats #------------------- -#add_executable(superkmer_stats scripts/run_superkmer_stats.cpp) -#target_include_directories(superkmer_stats PRIVATE src/graph/representation/hash -# src/graph/ -# src/annotation/representation/base/ -# src/cli/config -# src/cli/load -# src/common/utils/ -# ) - -#target_link_libraries(superkmer_stats PRIVATE metagraph-core metagraph-cli ${METALIBS}) -#target_compile_options(superkmer_stats PRIVATE -Wno-unused-parameter) +add_executable(superkmer_stats scripts/run_superkmer_stats.cpp) +target_include_directories(superkmer_stats PRIVATE src/graph/representation/hash + src/graph/ + src/annotation/representation/base/ + src/cli/config + src/cli/load + src/common/utils/ + ) + +target_link_libraries(superkmer_stats PRIVATE metagraph-core metagraph-cli ${METALIBS}) +target_compile_options(superkmer_stats PRIVATE -Wno-unused-parameter) #------------------- # Benchmarks diff --git a/metagraph/external-libraries/sshash b/metagraph/external-libraries/sshash index 9be36ab842..dd9684fd8d 160000 --- a/metagraph/external-libraries/sshash +++ b/metagraph/external-libraries/sshash @@ -1 +1 @@ -Subproject commit 9be36ab842cebf07000b4a8b6a7fa78cb131bb37 +Subproject commit dd9684fd8d9d9c8d95bf991ce82a48edd82cf109 diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.hpp b/metagraph/src/graph/representation/hash/dbg_sshash.hpp index c6ce482751..83f3b34f0c 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.hpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.hpp @@ -110,7 +110,7 @@ class DBGSSHash : public DeBruijnGraph { private: static const std::string alphabet_; std::unique_ptr dict_; - int annotation_mode = 2; // 0: kmer annotation, 1: lossy superkmer annotation, 2: superkmer annotation with superkmer mask + int annotation_mode = 0; // 0: kmer annotation, 1: lossy superkmer annotation, 2: superkmer annotation with superkmer mask bool loaded_mask = false; sdsl::sd_vector<> superkmer_mask; size_t k_; From 719530063523ae246415ce2613aa9548e916dbc0 Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Fri, 24 May 2024 13:14:08 +0200 Subject: [PATCH 47/52] clean-up --- metagraph/CMakeLists.txt | 2 +- metagraph/external-libraries/sshash | 2 +- metagraph/scripts/run_superkmer_stats.cpp | 34 ++-------- .../graph/representation/hash/dbg_sshash.cpp | 65 +++++-------------- .../graph/representation/hash/dbg_sshash.hpp | 10 +-- 5 files changed, 26 insertions(+), 87 deletions(-) diff --git a/metagraph/CMakeLists.txt b/metagraph/CMakeLists.txt index 77f937605f..52446760fd 100644 --- a/metagraph/CMakeLists.txt +++ b/metagraph/CMakeLists.txt @@ -544,7 +544,7 @@ target_link_libraries(unit_tests gtest_main gtest gmock metagraph-core metagraph target_compile_options(unit_tests PRIVATE -Wno-uninitialized ${DEATH_TEST_FLAG}) #------------------- -# superkmer stats +# superkmer bit vector #------------------- add_executable(superkmer_stats scripts/run_superkmer_stats.cpp) target_include_directories(superkmer_stats PRIVATE src/graph/representation/hash diff --git a/metagraph/external-libraries/sshash b/metagraph/external-libraries/sshash index dd9684fd8d..e156b27fc6 160000 --- a/metagraph/external-libraries/sshash +++ b/metagraph/external-libraries/sshash @@ -1 +1 @@ -Subproject commit dd9684fd8d9d9c8d95bf991ce82a48edd82cf109 +Subproject commit e156b27fc6f604c466b90e7f26a7c4e9279cc18d diff --git a/metagraph/scripts/run_superkmer_stats.cpp b/metagraph/scripts/run_superkmer_stats.cpp index aa04a15051..573581fea6 100644 --- a/metagraph/scripts/run_superkmer_stats.cpp +++ b/metagraph/scripts/run_superkmer_stats.cpp @@ -19,12 +19,12 @@ int main (int argc, char *argv[]){ using namespace mtg::cli; if(argc <3){ - std::cerr<<"missing input files!\n" ;//<< "graph path, annotation path, superkmer mask path\n"; + std::cerr<<"missing input files!\n" ;//<< "graph path, annotation path\n"; return EXIT_FAILURE; } std::string graph_path = argv[1]; std::string anno_path = argv[2]; - //std::string sk_mask_path = argv[3]; + std::shared_ptr graph_ptr = std::make_shared(31); graph_ptr->load(graph_path); @@ -32,36 +32,14 @@ int main (int argc, char *argv[]){ Config::AnnotationType config = parse_annotation_type(anno_path); - /* - Types of annotations: - ColumnCompressed = 1, - RowCompressed, - BRWT, - BinRelWT, - RowDiff, - RowDiffBRWT, - RowDiffRowFlat, - RowDiffRowSparse, - RowDiffDisk, - RowFlat, - RowSparse, - RBFish, - RbBRWT, - IntBRWT, - IntRowDiffBRWT, - IntRowDiffDisk, - ColumnCoord, - BRWTCoord, - RowDiffCoord, - RowDiffBRWTCoord, - RowDiffDiskCoord, - */ assert(config == Config::AnnotationType::RowFlat); - //std::unique_ptr> anno_ptr = std::make_unique> (); + std::unique_ptr anno_ptr = std::make_unique(); anno_ptr->load(anno_path); std::unique_ptr anno_graph = std::make_unique(graph_ptr, std::move(anno_ptr), false); - graph_ptr->superkmer_statistics(anno_graph, sk_mask_path); + + //graph_ptr->superkmer_stats(anno_graph); + graph_ptr->superkmer_bv(anno_graph, sk_mask_path); return 0; } diff --git a/metagraph/src/graph/representation/hash/dbg_sshash.cpp b/metagraph/src/graph/representation/hash/dbg_sshash.cpp index 485225a672..c8cb1d1d8a 100644 --- a/metagraph/src/graph/representation/hash/dbg_sshash.cpp +++ b/metagraph/src/graph/representation/hash/dbg_sshash.cpp @@ -12,7 +12,7 @@ DBGSSHash::DBGSSHash(size_t k):k_(k) { DBGSSHash::DBGSSHash(std::string const& input_filename, size_t k):k_(k){ sshash::build_configuration build_config; - build_config.k = k;// + build_config.k = k; // quick fix for value of m... k/2 but odd build_config.m = (k_+1)/2; if(build_config.m % 2 == 0) build_config.m++; @@ -25,7 +25,6 @@ DBGSSHash::DBGSSHash(std::string const& input_filename, size_t k):k_(k){ void DBGSSHash::add_sequence(std::string_view sequence, const std::function &on_insertion) { - // TODO: throw exception? :) throw std::runtime_error("adding sequences not implemented"); } @@ -151,7 +150,7 @@ void DBGSSHash ::call_incoming_kmers(node_index node, size_t DBGSSHash::outdegree(node_index node) const { std::string kmer = DBGSSHash::get_node_sequence(node); sshash::neighbourhood nb = dict_->kmer_forward_neighbours(&kmer[0]); - size_t out_deg = bool(nb.forward_A.kmer_id + 1) // change to loop? + size_t out_deg = bool(nb.forward_A.kmer_id + 1) + bool(nb.forward_C.kmer_id + 1) + bool(nb.forward_G.kmer_id + 1) + bool(nb.forward_T.kmer_id + 1); @@ -169,7 +168,7 @@ bool DBGSSHash::has_multiple_outgoing(node_index node) const { size_t DBGSSHash::indegree(node_index node) const { std::string kmer = DBGSSHash::get_node_sequence(node); sshash::neighbourhood nb = dict_->kmer_backward_neighbours(&kmer[0]); - size_t in_deg = bool(nb.backward_A.kmer_id + 1) // change to loop? + size_t in_deg = bool(nb.backward_A.kmer_id + 1) + bool(nb.backward_C.kmer_id + 1) + bool(nb.backward_G.kmer_id + 1) + bool(nb.backward_T.kmer_id + 1); @@ -201,13 +200,12 @@ DBGSSHash::node_index DBGSSHash::kmer_to_node(std::string_view kmer) const { return ssh_idx + 1; } -// superkmer experiment: use minimizer to get superkmer positions (offsets) -> get superkmer that contains kmer std::tuple DBGSSHash::kmer_to_superkmer_node(std::string_view kmer) const { - //auto [k_ssh_idx, s_ssh_idx, superkmer_id] = dict_->kmer_to_superkmer_idx(kmer.begin(), true); auto [kmer_idx, superkmer_idx, superkmer_id] = dict_->kmer_to_superkmer_idx(kmer.begin(), true); if(kmer_idx == sshash::constants::invalid_uint64){ return {npos, npos, sshash::constants::invalid_uint64}; } + // switch to DBG index return {kmer_idx + 1, superkmer_idx + 1, superkmer_id}; } @@ -268,22 +266,7 @@ const std::string &DBGSSHash::alphabet() const { } uint64_t DBGSSHash::num_nodes() const { return dict_->size(); } -void write_stats_to_file(const std::vector& km_skmer, const std::vector& cc_skmer){ - std::ofstream output_file_kmers("./superkmer_stats_kmers.txt"); - output_file_kmers << "kmers_per_superkmer: "<<'\n'; - for(auto const& x : km_skmer){ - output_file_kmers << x << '\n'; - } - output_file_kmers.close(); - - std::ofstream output_file_colors("./superkmer_stats_color.txt"); - output_file_colors << "color_changes_per_superkmer: "<<'\n'; - for(auto const& y : cc_skmer){ - output_file_colors << y << '\n'; - } - output_file_colors.close(); -} sdsl::bit_vector mask_into_bit_vec(const std::vector& mask){ sdsl::bit_vector bv (mask.size()); for(size_t idx = 0; idx < mask.size(); idx++){ @@ -297,12 +280,18 @@ void DBGSSHash::load_superkmer_mask(std::string file){ std::cout<< " successfully loaded " << file<<"?: " <& anno_graph, std::string file_sk_mask) const{ +void DBGSSHash::superkmer_stats(const std::unique_ptr& anno_graph) const{ if(annotation_mode != 0){ - throw std::runtime_error("Computing superkmer stats in wrong annotation mode!"); + throw std::runtime_error("Computing super-k-mer stats in wrong annotation mode!"); } - std::cout<< "Computing superkmer statistics and building super kmer bit vector... \n"; - + std::cout<< "Computing super-k-mer statistics ... \n"; + dict_->make_superkmer_stats(([&anno_graph](std::string_view str){return anno_graph->get_labels(str);})); +} +void DBGSSHash::superkmer_bv(const std::unique_ptr& anno_graph, std::string file_sk_mask) const{ + if(annotation_mode != 0){ + throw std::runtime_error("Building super-k-mer bit vector in wrong annotation mode!"); + } + std::cout<< "Building super-k-mer bit vector... \n"; //getting labels in batches size_t num_labels = anno_graph->get_annotator().num_labels(); std::vector superkmer_idxs = dict_->build_superkmer_bv([&anno_graph, num_labels](std::string_view sequence){ @@ -318,7 +307,7 @@ void DBGSSHash::superkmer_statistics(const std::unique_ptr& anno_g return true; }); - // elias fano encoding and serialize + // elias fano encoding sdsl::sd_vector<> ef_bv (superkmer_idxs.begin(), superkmer_idxs.end()); std::cout << "serializing bit vector..." << std::endl; @@ -326,29 +315,5 @@ void DBGSSHash::superkmer_statistics(const std::unique_ptr& anno_g std::cout<< " successfully stored " << file_sk_mask<<"?: " <& input1, const std::vector& input2)const { - if(input1.size() != input2.size()){ - return false; - } - for(size_t i = 0; i < input1.size(); i++){ - if(input1.at(i) != input2.at(i)){ - return false; - } - } - return true; -} - -void DBGSSHash::sanity_check_1(const std::vector& cc_skmer, const std::vector& km_skmer, uint64_t num_super_kmers)const { - std::cout << "length of color changes vector: "<& km_skmer, uint64_t num_kmers)const{ - uint64_t sum = std::accumulate(km_skmer.begin(), km_skmer.end(),0); - std::cout << "sum of kmers in superkmers vector: "< kmer_to_superkmer_node(std::string_view kmer) const ; void load_superkmer_mask(std::string file); - void superkmer_statistics(const std::unique_ptr& anno_graph, std::string file_sk_mask) const; - bool equal(const std::vector& input1, const std::vector& input2) const; + void superkmer_bv(const std::unique_ptr& anno_graph, std::string file_sk_mask) const; + void superkmer_stats(const std::unique_ptr& anno_graph) const; - void sanity_check_1(const std::vector& cc_skmer, const std::vector& km_skmer, uint64_t num_super_kmers) const; - void sanity_check_2(const std::vector& km_skmer, uint64_t num_kmers) const; - private: static const std::string alphabet_; std::unique_ptr dict_; From 5b251ad33f5dcc3a6d3064b78ae15a3aedbdddd1 Mon Sep 17 00:00:00 2001 From: Marianna Marzetta Date: Sat, 25 May 2024 00:32:56 +0200 Subject: [PATCH 48/52] plotting and stats scripts updated --- metagraph/scripts/plot_file_sizes.ipynb | 162 +++++++++++ metagraph/scripts/plot_query_bench.ipynb | 252 ++++++++++++++++++ .../plot_query_bench_by_anno_mode.ipynb | 191 +++++++++++++ .../scripts/plot_superkmer_stats_colors.py | 45 ---- .../scripts/plot_superkmer_stats_kmers.py | 45 ---- metagraph/scripts/superkmer_stats.ipynb | 204 ++++++++++++++ 6 files changed, 809 insertions(+), 90 deletions(-) create mode 100644 metagraph/scripts/plot_file_sizes.ipynb create mode 100644 metagraph/scripts/plot_query_bench.ipynb create mode 100644 metagraph/scripts/plot_query_bench_by_anno_mode.ipynb delete mode 100644 metagraph/scripts/plot_superkmer_stats_colors.py delete mode 100644 metagraph/scripts/plot_superkmer_stats_kmers.py create mode 100644 metagraph/scripts/superkmer_stats.ipynb diff --git a/metagraph/scripts/plot_file_sizes.ipynb b/metagraph/scripts/plot_file_sizes.ipynb new file mode 100644 index 0000000000..ae12e263cd --- /dev/null +++ b/metagraph/scripts/plot_file_sizes.ipynb @@ -0,0 +1,162 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 4, + "id": "00becd8f", + "metadata": {}, + "outputs": [], + "source": [ + "import pandas as pd" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "id": "3cf1eb23", + "metadata": {}, + "outputs": [], + "source": [ + "anno_sizes_path = \"/cluster/work/grlab/projects/metagenome/data/BIGSI/subsets/sshash/brwt_annotation_sizes.txt\"\n", + "graph_sizes_path = \"/cluster/work/grlab/projects/metagenome/data/BIGSI/subsets/sshash/graph_sizes.txt\"" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "id": "ea1c847e", + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/scratch/slurm-job.4695059/ipykernel_663185/4000796926.py:1: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n", + " df_anno = pd.read_csv(anno_sizes_path, sep=', ')\n", + "/scratch/slurm-job.4695059/ipykernel_663185/4000796926.py:2: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.\n", + " df_graph = pd.read_csv(graph_sizes_path, sep=', ')\n" + ] + } + ], + "source": [ + "df_anno = pd.read_csv(anno_sizes_path, sep=', ')\n", + "df_graph = pd.read_csv(graph_sizes_path, sep=', ')" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "id": "bc3b0948", + "metadata": {}, + "outputs": [], + "source": [ + "anno_max = df_anno.max().max()\n", + "graph_max = df_graph.max().max()\n", + "y_max = max([anno_max, graph_max])" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "id": "98b46833", + "metadata": {}, + "outputs": [], + "source": [ + "color_dict = {\"SSHash kmers\":'tab:blue',\"SSHash pure superkmers\":'red',\n", + " \"SSHash superkmers\":'tab:green',\"superkmer bit vector\":'darkgreen',\n", + " \"succinct\":'tab:orange',\n", + " \"SSHash\":'tab:blue',\"succinct\":'tab:orange'}" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "id": "fb507a4c", + "metadata": {}, + "outputs": [ + { + "data": { + "image/png": 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\n", 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\n", + "text/plain": [ + "
" + ] + }, + "metadata": { + "needs_background": "light" + }, + "output_type": "display_data" + } + ], + "source": [ + "cols = df_anno.columns[1:]\n", + "anno_fig = df_anno.plot(x=df_anno.columns[0],y=cols,ylim=(0, 1.1*y_max),\n", + " xlabel=\"subset\",ylabel=\"annotation size [bytes]\",title=\"annotation sizes (BRWT)\",\n", + " color=[color_dict.get(x, '#333333') for x in cols], grid=True, marker='+').get_figure()\n", + "graph_fig = df_graph.plot(x=df_graph.columns[0],y=[df_graph.columns[1],df_graph.columns[2]],\n", + " ylim=(0, 1.1*y_max),xlabel=\"subset\",ylabel=\"graph size [bytes]\",\n", + " title=\"graph sizes\",\n", + " color=[color_dict.get(x, '#333333') for x in df_graph.columns[1:]], grid=True, marker='+').get_figure()" + ] + }, + { + "cell_type": "code", + "execution_count": 21, + "id": "c3b224a1", + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "The PostScript backend does not support transparency; partially transparent artists will be rendered opaque.\n" + ] + } + ], + "source": [ + "anno_fig.savefig(\"brwt_anno_size_plot.eps\",format='eps')\n", + "graph_fig.savefig(\"brwt_graph_size_plot.eps\",format='eps')" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "7f58312d", + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.2" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/metagraph/scripts/plot_query_bench.ipynb b/metagraph/scripts/plot_query_bench.ipynb new file mode 100644 index 0000000000..e149923534 --- /dev/null +++ b/metagraph/scripts/plot_query_bench.ipynb @@ -0,0 +1,252 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 6, + "id": "2ae1b6bc", + "metadata": {}, + "outputs": [], + "source": [ + "import matplotlib.pyplot as plt\n", + "import numpy as np\n", + "\n", + "from datetime import timedelta" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "id": "90adf34a", + "metadata": {}, + "outputs": [], + "source": [ + "# Open the files for reading\n", + "with open('/cluster/work/grlab/projects/metagenome/data/BIGSI/subsets/sshash/bench/brwt/res_kmers/all_times.txt', 'r') as file:\n", + " sshash_lines = file.readlines()\n", + "with open('/cluster/work/grlab/projects/metagenome/data/BIGSI/subsets/sshash/bench/brwt/res_superkmers/all_times.txt', 'r') as file:\n", + " sk_lines = file.readlines()\n", + "with open('/cluster/work/grlab/projects/metagenome/data/BIGSI/subsets/sshash/bench/brwt/res_pure_superkmers/all_times.txt', 'r') as file:\n", + " psk_lines = file.readlines()\n", + "with open('/cluster/work/grlab/projects/metagenome/data/BIGSI/subsets/sshash/bench/brwt/res_succ/all_times.txt', 'r') as file:\n", + " succ_lines = file.readlines()\n", + " \n", + "# Stop if there are not 7*N measurements\n", + "if len(sshash_lines) % 8 != 0:\n", + " print(\"Number of lines (in sshash_lines file) is not multiple of 8! Stopping\")\n", + "if len(sk_lines) % 8 != 0:\n", + " print(\"Number of lines (in sk_lines file) is not multiple of 8! Stopping\")\n", + "if len(psk_lines) % 8 != 0:\n", + " print(\"Number of lines (in psk_lines file) is not multiple of 8! Stopping\")" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "id": "27aa78b8", + "metadata": {}, + "outputs": [], + "source": [ + "def time_to_seconds(time_str):\n", + " # Split the time string into hours, minutes, and seconds\n", + " parts = time_str.split(':')\n", + " \n", + " # If the time format is h:mm:ss\n", + " if len(parts) == 3:\n", + " hours, minutes, seconds = map(float, parts)\n", + " total_seconds = hours * 3600 + minutes * 60 + seconds\n", + " # If the time format is m:ss\n", + " elif len(parts) == 2:\n", + " minutes, seconds = map(float, parts)\n", + " total_seconds = minutes * 60 + seconds\n", + " else:\n", + " print(parts)\n", + " raise ValueError(\"Invalid time format\")\n", + " \n", + " return total_seconds\n", + "\n", + "def compute_avg_time(sizes, times, lines, idx):\n", + " #first line is subset size\n", + " size = lines[idx]\n", + " time = 0\n", + " \n", + " # lines[1:3] are warm-up runs\n", + " for j in range(3,8):\n", + " time_str = lines[idx+j].strip().split(\"Elapsed (wall clock) time (h:mm:ss or m:ss): \",1)[-1]\n", + " time = time + time_to_seconds(time_str)\n", + " avg_time = time / 5\n", + " sizes.append(size)\n", + " times.append(avg_time)" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "id": "97c35b26", + "metadata": {}, + "outputs": [], + "source": [ + "# Initialize lists to store times for each series\n", + "sshash_times = []\n", + "sshash_sizes = []\n", + "sk_times = []\n", + "sk_sizes = []\n", + "psk_times = []\n", + "psk_sizes = []\n", + "\n", + "succ_times = []\n", + "succ_sizes = []\n", + "\n", + "for i in range(0,len(sshash_lines),8):\n", + " compute_avg_time(sshash_sizes,sshash_times,sshash_lines,i)\n", + "for i in range(0,len(sk_lines),8):\n", + " compute_avg_time(sk_sizes,sk_times,sk_lines,i)\n", + "for i in range(0,len(psk_lines),8):\n", + " compute_avg_time(psk_sizes,psk_times,psk_lines,i)\n", + "\n", + "for i in range(0,len(succ_lines),8):\n", + " compute_avg_time(succ_sizes,succ_times,succ_lines,i)" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "id": "52bcd95e", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Times for superkmer:\n", + "1.3519999999999999\n", + "3.2920000000000003\n", + "5.388\n", + "7.564000000000002\n", + "8.3\n", + "9.408000000000001\n", + "12.404\n", + "12.474\n", + "13.907999999999998\n", + "\n", + "Times for pure superkmer:\n", + "1.418\n", + "3.246\n", + "4.912\n", + "6.697999999999999\n", + "7.948\n", + "9.582\n", + "10.088\n", + "12.09\n", + "12.916\n", + "\n", + "Times for kmer:\n", + "1.518\n", + "4.176\n", + "6.7620000000000005\n", + "8.842\n", + "9.591999999999999\n", + "13.916\n", + "15.209999999999999\n", + "16.564\n", + "16.9\n", + "\n", + "Times for succ:\n", + "4.061999999999999\n", + "8.280000000000001\n", + "11.778\n", + "14.936000000000002\n", + "18.2\n", + "19.886000000000003\n", + "22.749999999999996\n", + "26.308000000000003\n", + "28.6\n" + ] + } + ], + "source": [ + "print(\"Times for superkmer:\")\n", + "for time in sk_times:\n", + " print(time)\n", + "print(\"\\nTimes for pure superkmer:\")\n", + "for time in psk_times:\n", + " print(time)\n", + "print(\"\\nTimes for kmer:\")\n", + "for time in sshash_times:\n", + " print(time)\n", + "print(\"\\nTimes for succ:\")\n", + "for time in succ_times:\n", + " print(time)" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "id": "d2cf37fa", + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "The PostScript backend does not support transparency; partially transparent artists will be rendered opaque.\n" + ] + }, + { + "data": { + "image/png": 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\n", + "text/plain": [ + "
" + ] + }, + "metadata": { + "needs_background": "light" + }, + "output_type": "display_data" + } + ], + "source": [ + "# Plot the two series\n", + "plt.plot(np.asarray(succ_sizes,dtype=np.int32), np.asarray(succ_times), label='succinct', marker='x', color='tab:orange')\n", + "plt.plot(np.asarray(sshash_sizes,dtype=np.int32), np.asarray(sshash_times), label='SSHash kmers', marker='x', color='tab:blue')\n", + "plt.plot(np.asarray(psk_sizes,dtype=np.int32), np.asarray(psk_times), label='SSHash pure superkmers', marker='x', color='tab:red')\n", + "plt.plot(np.asarray(sk_sizes,dtype=np.int32), np.asarray(sk_times), label='SSHash superkmers', marker='x', color='tab:green')\n", + "plt.xlabel('Subset Size')\n", + "plt.ylabel('Time[s]')\n", + "plt.grid()\n", + "plt.title('Benchmark Query Time (BRWT)')\n", + "plt.legend()\n", + "plt.savefig(\"plot_query_bench_sshash_versions_brwt.eps\",format='eps')\n", + "plt.show()\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "37cb2462", + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.2" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/metagraph/scripts/plot_query_bench_by_anno_mode.ipynb b/metagraph/scripts/plot_query_bench_by_anno_mode.ipynb new file mode 100644 index 0000000000..9e4973f39a --- /dev/null +++ b/metagraph/scripts/plot_query_bench_by_anno_mode.ipynb @@ -0,0 +1,191 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 2, + "id": "2ae1b6bc", + "metadata": {}, + "outputs": [], + "source": [ + "import matplotlib.pyplot as plt\n", + "import numpy as np\n", + "\n", + "from datetime import timedelta\n" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "id": "27aa78b8", + "metadata": {}, + "outputs": [], + "source": [ + "def time_to_seconds(time_str):\n", + " # Split the time string into hours, minutes, and seconds\n", + " parts = time_str.split(':')\n", + " \n", + " # If the time format is h:mm:ss\n", + " if len(parts) == 3:\n", + " hours, minutes, seconds = map(float, parts)\n", + " total_seconds = hours * 3600 + minutes * 60 + seconds\n", + " # If the time format is m:ss\n", + " elif len(parts) == 2:\n", + " minutes, seconds = map(float, parts)\n", + " total_seconds = minutes * 60 + seconds\n", + " else:\n", + " print(parts)\n", + " raise ValueError(\"Invalid time format\")\n", + " \n", + " return total_seconds\n", + "\n", + "def compute_avg_time(sizes, times, lines, idx):\n", + " #first line is subset size\n", + " size = lines[idx]\n", + " time = 0\n", + " \n", + " # lines[1:3] are warm-up runs\n", + " for j in range(3,8):\n", + " time_str = lines[idx+j].strip().split(\"Elapsed (wall clock) time (h:mm:ss or m:ss): \",1)[-1]\n", + " time = time + time_to_seconds(time_str)\n", + " avg_time = time / 5\n", + " sizes.append(size)\n", + " times.append(avg_time)" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "id": "90adf34a", + "metadata": {}, + "outputs": [], + "source": [ + "# Open the files for reading\n", + "with open('/cluster/work/grlab/projects/metagenome/data/BIGSI/subsets/sshash/bench/brwt/res_pure_superkmers/all_times.txt', 'r') as file:\n", + " brwt_lines = file.readlines()\n", + "with open('/cluster/work/grlab/projects/metagenome/data/BIGSI/subsets/sshash/bench/flat/res_pure_superkmers/all_times.txt', 'r') as file:\n", + " flat_lines = file.readlines()\n", + "with open('/cluster/work/grlab/projects/metagenome/data/BIGSI/subsets/sshash/bench/res_pure_superkmers/all_times.txt', 'r') as file:\n", + " column_lines = file.readlines()\n", + "\n", + "# Stop if there are not 7*N measurements\n", + "if len(brwt_lines) % 8 != 0:\n", + " print(\"Number of lines (in sshash file) is not multiple of 8! Stopping\")\n", + "if len(flat_lines) % 8 != 0:\n", + " print(\"Number of lines (in sshash file) is not multiple of 8! Stopping\")\n", + "if len(column_lines) % 8 != 0:\n", + " print(\"Number of lines (in sshash file) is not multiple of 8! Stopping\")" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "id": "97c35b26", + "metadata": {}, + "outputs": [], + "source": [ + "# Initialize lists to store times for each series\n", + "brwt_times = []\n", + "brwt_sizes = []\n", + "flat_times = []\n", + "flat_sizes = []\n", + "\n", + "col_times = []\n", + "col_sizes = []\n", + "\n", + "for i in range(0,len(brwt_lines),8):\n", + " compute_avg_time(brwt_sizes,brwt_times,brwt_lines,i)\n", + "for i in range(0,len(flat_lines),8):\n", + " compute_avg_time(flat_sizes,flat_times,flat_lines,i)\n", + "for i in range(0,len(column_lines),8):\n", + " compute_avg_time(col_sizes,col_times,column_lines,i)\n" + ] + }, + { + "cell_type": "code", + "execution_count": 40, + "id": "d2cf37fa", + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "The PostScript backend does not support transparency; partially transparent artists will be rendered opaque.\n" + ] + }, + { + "data": { + "image/png": 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\n", + "text/plain": [ + "
" + ] + }, + "metadata": { + "needs_background": "light" + }, + "output_type": "display_data" + } + ], + "source": [ + "# Plot the two series\n", + "plt.plot(np.asarray(col_sizes,dtype=np.int32), np.asarray(col_times), label='column-major', marker='x', color='#1F00FF')\n", + "plt.plot(np.asarray(flat_sizes,dtype=np.int32), np.asarray(flat_times), label='row-flat', marker='x', color='#9F00FF')\n", + "plt.plot(np.asarray(brwt_sizes,dtype=np.int32), np.asarray(brwt_times), label='BRWT', marker='x', color='#FF00FF')\n", + "plt.xlabel('Subset Size')\n", + "plt.ylabel('Time[s]')\n", + "plt.grid()\n", + "plt.title('Benchmark Query Time (SSHash pure super-k-mer Annotation)')\n", + "plt.legend()\n", + "plt.savefig(\"plot_query_bench_anno_versions_pure_superkmer.eps\",format='eps')\n", + "plt.show()\n" + ] + }, + { + "cell_type": "code", + "execution_count": 20, + "id": "5719dab1", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "
" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "7b16fa3d", + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.2" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/metagraph/scripts/plot_superkmer_stats_colors.py b/metagraph/scripts/plot_superkmer_stats_colors.py deleted file mode 100644 index 76da92e58d..0000000000 --- a/metagraph/scripts/plot_superkmer_stats_colors.py +++ /dev/null @@ -1,45 +0,0 @@ -#!/usr/bin/env python -# coding: utf-8 - -# In[1]: - - -import pandas as pd -import numpy as np -import matplotlib.pyplot as plt - - -# In[2]: - - -path = "/cluster/home/mmarzett/superkmer_stats_color.txt" - - -# In[3]: - - -file = open(path, "r") -colors_array = np.loadtxt(path, dtype=int, skiprows=1) - - -# In[4]: - - -colors_array - - -# In[5]: - - -plt.hist(colors_array,bins=np.arange(min(colors_array), max(colors_array)+1, step=1)) -plt.title("#color changes per superkmer") -plt.xlabel("#color changes") -plt.savefig("colors_hist_10000") -plt.show() - - -# In[ ]: - - - - diff --git a/metagraph/scripts/plot_superkmer_stats_kmers.py b/metagraph/scripts/plot_superkmer_stats_kmers.py deleted file mode 100644 index ddae06d24a..0000000000 --- a/metagraph/scripts/plot_superkmer_stats_kmers.py +++ /dev/null @@ -1,45 +0,0 @@ -#!/usr/bin/env python -# coding: utf-8 - -# In[1]: - - -import pandas as pd -import numpy as np -import matplotlib.pyplot as plt - - -# In[2]: - - -path = "/cluster/home/mmarzett/superkmer_stats_kmers.txt" - - -# In[10]: - - -file = open(path, "r") -kmers_array = np.loadtxt(path, dtype=int, skiprows=1) - - -# In[11]: - - -kmers_array - - -# In[12]: - - -plt.hist(kmers_array,bins=np.arange(min(kmers_array), max(kmers_array)+1, step=1)) -plt.title("#kmers per superkmer") -plt.xlabel("#kmers") -plt.savefig("kmers_hist") -plt.show() - - -# In[ ]: - - - - diff --git a/metagraph/scripts/superkmer_stats.ipynb b/metagraph/scripts/superkmer_stats.ipynb new file mode 100644 index 0000000000..19d75a0e0d --- /dev/null +++ b/metagraph/scripts/superkmer_stats.ipynb @@ -0,0 +1,204 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 2, + "id": "96ca58d1", + "metadata": {}, + "outputs": [], + "source": [ + "import pandas as pd\n", + "import numpy as np\n", + "import matplotlib.pyplot as plt" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "id": "0573db7c", + "metadata": {}, + "outputs": [], + "source": [ + "path = \"/cluster/work/grlab/projects/metagenome/data/BIGSI/subsets/sshash/final_color_stats.txt\"\n", + "file = open(path, \"r\")\n", + "colors_array = np.loadtxt(path, dtype=int)" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "id": "04ef5e10", + "metadata": {}, + "outputs": [], + "source": [ + "path = \"/cluster/work/grlab/projects/metagenome/data/BIGSI/subsets/sshash/final_kmer_stats.txt\"\n", + "file = open(path, \"r\")\n", + "kmers_array = np.loadtxt(path, dtype=int)" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "id": "e98810cd", + "metadata": {}, + "outputs": [ + { + "data": { + "image/png": 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\n", + "text/plain": [ + "
" + ] + }, + "metadata": { + "needs_background": "light" + }, + "output_type": "display_data" + } + ], + "source": [ + "number_bins = max(colors_array)+2\n", + "plt.hist(colors_array,bins=np.arange(0,number_bins))\n", + "plt.xticks(range(number_bins))\n", + "plt.title(\"#color changes per super-k-mer\")\n", + "plt.xlabel(\"#color changes\")\n", + "plt.yscale('log')\n", + "plt.savefig(\"final_colors_hist.eps\",format='eps')\n", + "plt.show()" + ] + }, + { + "cell_type": "code", + "execution_count": 70, + "id": "5eecf991", + "metadata": {}, + "outputs": [ + { + "data": { + "image/png": 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igR4RUYjMh/4c0fT86pA51iNKkyP0iIhCJNAjIgqRQI+IKEQCPSKiEAn0iIhCJNAjIgqRQI+IKEQCPSKiEAn0iIhCJNAjIgqRQI+IKETmctmANT0/TOaGiRhbOUKPiChEAj0iohAdBbqkGZLukLRE0nFDtHuvJEvqba6LERHRibaBLmkccBpwADAdmCVp+gDtXgh8DLim6U5GRER7nRyh7wEssX2X7aeB84CZA7T7PHAq8FSD/YuIiA51EugTgeUt6yvq6/5M0q7AZNtDnjYhabakhZIWrl69etidjYiIwXX9pqik5wFfAT7Zrq3tObZ7bff29PR0u+uIiGjRSaCvBCa3rE+qr+vzQmAn4ApJy4A9gXl5YzQiYt3q5INF1wHbSppGFeSHAv+zb6PtR4EJfeuSrgA+ZXths12N9V0+qBQxttoeodteAxwFLABuB863vVjSyZIOHu0ORkREZzr66L/t+cD8ftedMEjbfbrvVkREDFc+KRoRUYgEekREIRLoERGFSKBHRBQi86HHeiunQUYMT47QIyIKkUCPiChEAj0iohAJ9IiIQiTQIyIKkbNcYoPR9FkzkDNnYv2SI/SIiEIk0CMiCpFAj4goRAI9IqIQeVM0oguZniDWJzlCj4goRAI9IqIQCfSIiEJ0NIYuaQbwdWAccKbtU/pt/wRwJLAGWA38o+27G+5rRPEyJh/daHuELmkccBpwADAdmCVper9mNwK9tl8HXAB8qemORkTE0DoZctkDWGL7LttPA+cBM1sb2L7c9pP16tXApGa7GRER7XQS6BOB5S3rK+rrBnME8OOBNkiaLWmhpIWrV6/uvJcREdFWo+ehS3o/0AvsPdB223OAOQC9vb1uct8RsbZMSLZh6STQVwKTW9Yn1df9FUn7A8cDe9v+YzPdi4iITnUy5HIdsK2kaZI2Bg4F5rU2kLQL8E3gYNurmu9mRES00/YI3fYaSUcBC6hOWzzb9mJJJwMLbc8Dvgy8APiBJIB7bB88iv2OiDGSUyvXXx2NodueD8zvd90JLcv7N9yviIgYpnxSNCKiEJltMSLGVIZwmpMj9IiIQuQIPSKKMhrn3j9X5Ag9IqIQCfSIiEIk0CMiCpFAj4goRAI9IqIQCfSIiEIk0CMiCpFAj4goRAI9IqIQCfSIiEIk0CMiCpFAj4goRAI9IqIQCfSIiEIk0CMiCtFRoEuaIekOSUskHTfA9udL+n69/RpJUxvvaUREDKltoEsaB5wGHABMB2ZJmt6v2RHAw7ZfDXwVOLXpjkZExNA6OULfA1hi+y7bTwPnATP7tZkJfLtevgDYT5Ka62ZERLTTyVfQTQSWt6yvAN4wWBvbayQ9CrwE+F1rI0mzgdn16hOS7hhJp4EJ/Ws3oOma63u90ai5odUbjZrre73RqLmh1UOndlVzm8E2rNPvFLU9B5jTbR1JC233NtClUau5vtcbjZobWr3RqLm+1xuNmhtavdGqCZ0NuawEJresT6qvG7CNpPHAlsCDTXQwIiI600mgXwdsK2mapI2BQ4F5/drMA/6+Xn4f8DPbbq6bERHRTtshl3pM/ChgATAOONv2YkknAwttzwPOAs6RtAR4iCr0R1PXwzbroOb6Xm80am5o9Uaj5vpebzRqbmj1RqsmyoF0REQZ8knRiIhCJNAjIgrxnAp0SWdLWiVpUUP1Jku6XNJtkhZL+lgDNTeRdK2km+ua/9JQX8dJulHSJQ3UWibpVkk3SVrYQL2tJF0g6TeSbpf0xi7rbV/3re/ymKRjuqz58frxWCTpXEmbdFnvY3WtxSPt20DPZ0kvlvQTSb+tf76oy3qH1H18VtKwTpMbpN6X68f5FkkXS9qqgZqfr+vdJOkySa/opl7Ltk9KsqQJXfbvJEkrW56PB3Zab6g+Sjq6vi8XS/rScGoOyvZz5gK8FdgVWNRQva2BXevlFwJ3AtO7rCngBfXyRsA1wJ4N9PUTwPeASxqotQyY0ODj8m3gyHp5Y2CrBmuPA+4HtumixkRgKbBpvX4+cHgX9XYCFgGbUZ1Y8FPg1SOos9bzGfgScFy9fBxwapf1dgS2B64Aehvo39uB8fXyqcPp3xA1t2hZ/mfgjG7q1ddPpjqR4+7hPNcH6d9JwKe6eL4MVHPf+nnz/Hr9pSOt33p5Th2h276S6iyapurdZ/uGevlx4HaqP/5uatr2E/XqRvWlq3eeJU0C3gmc2U2d0SBpS6on7FkAtp+2/UiDu9gP+H+27+6yznhg0/pzEpsB93ZRa0fgGttP2l4D/Bx4z3CLDPJ8bp1G49vAu7qpZ/t22yP6RPYg9S6rf2eAq6k+l9JtzcdaVjdnGH8vQ2TCV4H/NZxabeqN2CA1PwKcYvuPdZtVTezrORXoo6meIXIXqiPqbmuNk3QTsAr4ie1ua36N6sn5bJd1+hi4TNL19XQM3ZgGrAb+sx4SOlPS5t138c8OBc7tpoDtlcD/Bu4B7gMetX1ZFyUXAXtJeomkzYAD+esP33XjZbbvq5fvB17WUN3R8I/Aj5soJOmLkpYDhwEndFlrJrDS9s1N9K12VD0sdPZwhsGGsB3Vc+gaST+XtHsDNRPoAJJeAFwIHNPvaGFEbP/J9s5URy97SNqpi74dBKyyfX23/WrxFtu7Us2g+VFJb+2i1niql5On294F+D3VUEHX6g+yHQz8oMs6L6I68p0GvALYXNL7R1rP9u1Uww2XAf8XuAn4Uzd9HGQ/pstXd6NF0vHAGuC7TdSzfbztyXW9o7ro12bAZ+nyn0I/pwOvAnamOiD49wZqjgdeDOwJHAucL3U/oeEGH+iSNqIK8+/avqjJ2vXQw+XAjC7KvBk4WNIyqpku/0bSd7rs18r65yrgYqoZNUdqBbCi5VXIBVQB34QDgBtsP9Blnf2BpbZX234GuAh4UzcFbZ9lezfbbwUepnr/pQkPSNoaoP7ZyEvxJkk6HDgIOKz+p9Ok7wLv7eL2r6L6x31z/TczCbhB0stHWtD2A/VB2rPAt+ju76XPCuCieoj2WqpX3x2/eTuYDTrQ6/+IZwG32/5KQzV7+t75l7Qp8DbgNyOtZ/sztifZnko1/PAz2yM+upS0uaQX9i1Tvck14rOGbN8PLJe0fX3VfsBtI63Xzyy6HG6p3QPsKWmz+jHfj+r9khGT9NL65xSq8fPvdd3LSus0Gn8P/Kihuo2QNINq+O9g2082VHPbltWZdPf3cqvtl9qeWv/NrKA68eH+Lvq3dcvqu+ni76XFD6neGEXSdlQnE3Q/o2MT76yuqwvVH/d9wDNUD9QRXdZ7C9VL2luoXjbfBBzYZc3XATfWNRcBJzT4++9Dl2e5AK8Ebq4vi4HjG+jXzsDC+nf+IfCiBmpuTjXB25YN3Xf/QhUUi4BzqM8u6KLeL6j+cd0M7DfCGms9n6mmnf5v4LdUZ0G8uMt6766X/wg8ACzost4Sqqmy+/5eOj4jZYiaF9aPyy3A/wEmdlOv3/ZlDO8sl4H6dw5wa92/ecDWDfzOGwPfqX/vG4C/aeJ5no/+R0QUYoMecomIKEkCPSKiEAn0iIhCJNAjIgqRQI+IKEQCPYok6d8k7SvpXZI+U193xXBnHIx4LkmgR6neQDV51N7Aletih/XEXxFjJoEeRann674F2B34NXAkcLqkE1raPE/SXElfqNefqG+3WNJPJe1RH83fJengus24us119SRN/1Rfv4+kX0iaB9xWfxL3UlXz4S+S9Hfr/E6IDVYCPYpi+1iqT+LNpQr1W2y/zvbJdZPxVPOF/Nb25+rrNqeaUuE1wOPAF6imbHg30He7I6hmady9rvshSdPqbbsCH7O9HdW8Pffafr3tnagm74pYJxLoUaJdqT6SvwNrz9nyTaovGvhiy3VP85fgvRX4uatJvG4FptbXvx34YD0t8jVUH9Hvm4PkWttLW27/NkmnStrL9qON/VYRbWTML4ohaWeqI/NJVBMdbVZdrZuAvq/FuwrYV9K/236qvu4Z/2UOjGep5j3B9rMt4+ICjra9oN8+96GaMpj6NndK2pVqjvQvSPrvllcHEaMqR+hRDNs3uZqH/k5gOvAz4B22d7b9h7rZWcB8qvmnh3NAswD4SD3dMpK2G+iLPFR9H+aTtr8DfJnmphKOaCtH6FEUST3Aw/XR9Q6215rK1/ZX6q/OO0fSYR2WPpNq+OWGegre1Qz89XCvBb4s6Vmq2fU+MoJfI2JEMttiREQhMuQSEVGIBHpERCES6BERhUigR0QUIoEeEVGIBHpERCES6BERhfj/UpLe1FomdlMAAAAASUVORK5CYII=\n", + "text/plain": [ + "
" + ] + }, + "metadata": { + "needs_background": "light" + }, + "output_type": "display_data" + } + ], + "source": [ + "number_bins = max(kmers_array)+2\n", + "plt.hist(kmers_array,bins=np.arange(1,number_bins))\n", + "plt.xticks(range(1,number_bins))\n", + "plt.title(\"#kmers per super-k-mer\")\n", + "plt.xlabel(\"#kmers\")\n", + "plt.savefig(\"final_kmers_hist.eps\",format='eps')\n", + "plt.show()" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "id": "1a61bec6", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Average #k-mers per super-k-mer: 7.1757712022432845\n" + ] + } + ], + "source": [ + "print(\"Average #k-mers per super-k-mer: \", np.mean(kmers_array))" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "id": "d3859df4", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "ratio of polychromatic super-k-mers: 0.07684760258167535\n" + ] + } + ], + "source": [ + "print(\"ratio of polychromatic super-k-mers: \", np.sum(colors_array>0)/len(kmers_array))" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "id": "3494d258", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "#sparsified rows: 436177187\n", + "fraction of sparsified rows: num_sparsified_rows/num_kmers = 0.8606421565270391\n" + ] + } + ], + "source": [ + "# rows that are empty with lossy super-k-mer annotation\n", + "tot_num_kmers=(np.sum(kmers_array))\n", + "num_sparsified_rows = tot_num_kmers - len(kmers_array)\n", + "print(\"#sparsified rows: \", num_sparsified_rows)\n", + "print(\"fraction of sparsified rows: num_sparsified_rows/num_kmers = \", num_sparsified_rows/tot_num_kmers)" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "id": "6c1348ab", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "#sparsified rows: 384836802\n", + "fraction of sparsified rows: num_sparsified/num_kmers = 0.75933997709112\n" + ] + } + ], + "source": [ + "# rows that are empty with lossless super-k-mer annotation\n", + "sparsified_rows = (kmers_array - 1)*(colors_array==0)\n", + "tot_num_kmers=(np.sum(kmers_array))\n", + "tot_sparsified_rows = np.sum(sparsified_rows)\n", + "\n", + "print(\"#sparsified rows: \", tot_sparsified_rows)\n", + "print(\"fraction of sparsified rows: num_sparsified/num_kmers = \", tot_sparsified_rows/tot_num_kmers)" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.2" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} From efce431fedd2a7c159eb216356e4c28a6b4033d6 Mon Sep 17 00:00:00 2001 From: Oleksandr Kulkov Date: Thu, 25 Jul 2024 16:59:51 +0200 Subject: [PATCH 49/52] Don't disable tests for sshash --- metagraph/tests/graph/all/test_dbg_basic.cpp | 8 ----- .../tests/graph/all/test_dbg_contigs.cpp | 30 ------------------- .../tests/graph/all/test_dbg_node_degree.cpp | 16 ---------- metagraph/tests/graph/all/test_dbg_search.cpp | 4 --- 4 files changed, 58 deletions(-) diff --git a/metagraph/tests/graph/all/test_dbg_basic.cpp b/metagraph/tests/graph/all/test_dbg_basic.cpp index c2d39ad78c..4049a73aa9 100644 --- a/metagraph/tests/graph/all/test_dbg_basic.cpp +++ b/metagraph/tests/graph/all/test_dbg_basic.cpp @@ -278,10 +278,6 @@ TYPED_TEST(DeBruijnGraphTest, TestNonASCIIStrings) { } TYPED_TEST(DeBruijnGraphTest, AddSequences) { - if constexpr(std::is_same_v) { - common::logger->warn("Test case disabled for DBGSSHash"); - return; - } { std::vector sequences { "AAAC", "CAAC" }; EXPECT_EQ(2u, build_graph(4, sequences)->num_nodes()); @@ -331,10 +327,6 @@ TYPED_TEST(DeBruijnGraphTest, CallKmersEmptyGraph) { } TYPED_TEST(DeBruijnGraphTest, CallKmersTwoLoops) { - if constexpr(std::is_same_v) { - common::logger->warn("Test case disabled for DBGSSHash"); - return; - } for (size_t k = 2; k <= max_test_k(); ++k) { auto graph = build_graph(k, { std::string(2 * k, 'A') }); diff --git a/metagraph/tests/graph/all/test_dbg_contigs.cpp b/metagraph/tests/graph/all/test_dbg_contigs.cpp index df226f7d69..60b7f55028 100644 --- a/metagraph/tests/graph/all/test_dbg_contigs.cpp +++ b/metagraph/tests/graph/all/test_dbg_contigs.cpp @@ -66,10 +66,6 @@ TYPED_TEST(DeBruijnGraphTest, CallUnitigsEmptyGraph) { } TYPED_TEST(DeBruijnGraphTest, CallPathsOneSelfLoop) { - if constexpr(std::is_same_v) { - common::logger->warn("Test case disabled for DBGSSHash"); - return; - } for (size_t num_threads : { 1, 4 }) { for (size_t k = 2; k <= max_test_k(); ++k) { std::vector sequences { std::string(2 * k, 'A') }; @@ -97,10 +93,6 @@ TYPED_TEST(DeBruijnGraphTest, CallPathsOneSelfLoop) { } TYPED_TEST(DeBruijnGraphTest, CallUnitigsOneSelfLoop) { - if constexpr(std::is_same_v) { - common::logger->warn("Test case disabled for DBGSSHash"); - return; - } for (size_t num_threads : { 1, 4 }) { for (size_t k = 2; k <= max_test_k(); ++k) { std::vector sequences { std::string(2 * k, 'A') }; @@ -466,17 +458,6 @@ TYPED_TEST(DeBruijnGraphTest, CallPaths) { std::vector({ "AAACTCGTAGC", "AAATGCGTAGC" }), std::vector({ "AAACT", "AAATG" }), std::vector({ "ATGCAGTACTCAG", "ATGCAGTAGTCAG", "GGGGGGGGGGGGG" }) }) { - - if constexpr(std::is_same_v) { - if(k > sequences[0].size()){ - common::logger->warn("Test case disabled for DBGSSHash"); - continue; - } - if(sequences[0] == "AAACTCGTAGC" && k == 10 ){ - common::logger->warn("Test case disabled for DBGSSHash"); - continue; - } - } auto graph = build_graph_batch(k, sequences); // in stable graphs the order of input sequences @@ -511,17 +492,6 @@ TYPED_TEST(DeBruijnGraphTest, CallUnitigs) { std::vector({ "AAACTCGTAGC", "AAATGCGTAGC" }), std::vector({ "AAACT", "AAATG" }), std::vector({ "ATGCAGTACTCAG", "ATGCAGTAGTCAG", "GGGGGGGGGGGGG" }) }) { - - if constexpr(std::is_same_v) { - if(k > sequences[0].size()){ - common::logger->warn("Test case disabled for DBGSSHash"); - continue; - } - if(sequences[0] == "AAACTCGTAGC" && k == 10 ){ - common::logger->warn("Test case disabled for DBGSSHash"); - continue; - } - } auto graph = build_graph_batch(k, sequences); // in stable graphs the order of input sequences diff --git a/metagraph/tests/graph/all/test_dbg_node_degree.cpp b/metagraph/tests/graph/all/test_dbg_node_degree.cpp index 54944b8f89..79f04e6583 100644 --- a/metagraph/tests/graph/all/test_dbg_node_degree.cpp +++ b/metagraph/tests/graph/all/test_dbg_node_degree.cpp @@ -16,10 +16,6 @@ TYPED_TEST_SUITE(DeBruijnGraphTest, GraphTypes); TYPED_TEST(DeBruijnGraphTest, get_outdegree_single_node) { - if constexpr(std::is_same_v) { - common::logger->warn("Test case disabled for DBGSSHash"); - return; - } for (size_t k = 2; k < 10; ++k) { auto graph = build_graph(k, { std::string(k - 1, 'A') + 'C' }); EXPECT_EQ(1ull, graph->num_nodes()); @@ -28,10 +24,6 @@ TYPED_TEST(DeBruijnGraphTest, get_outdegree_single_node) { } TYPED_TEST(DeBruijnGraphTest, get_maximum_outdegree) { - if constexpr(std::is_same_v) { - common::logger->warn("Test case disabled for DBGSSHash"); - return; - } for (size_t k = 2; k < 10; ++k) { auto graph = build_graph(k, { std::string(k - 1, 'A') + 'A', @@ -111,10 +103,6 @@ TYPED_TEST(DeBruijnGraphTest, get_outdegree_loop) { } TYPED_TEST(DeBruijnGraphTest, get_indegree_single_node) { - if constexpr(std::is_same_v) { - common::logger->warn("Test case disabled for DBGSSHash"); - return; - } for (size_t k = 2; k < 10; ++k) { auto graph = build_graph(k, { std::string(k - 1, 'A') + 'C' }); @@ -305,10 +293,6 @@ TYPED_TEST(DeBruijnGraphTest, indegree_identity_traverse_back_incoming) { } TYPED_TEST(DeBruijnGraphTest, is_single_outgoing_simple) { - if constexpr(std::is_same_v) { - common::logger->warn("Test case disabled for DBGSSHash"); - return; - } size_t k = 4; std::string reference = "CATC"; diff --git a/metagraph/tests/graph/all/test_dbg_search.cpp b/metagraph/tests/graph/all/test_dbg_search.cpp index 2f2b7c8538..1fe3969712 100644 --- a/metagraph/tests/graph/all/test_dbg_search.cpp +++ b/metagraph/tests/graph/all/test_dbg_search.cpp @@ -16,10 +16,6 @@ TYPED_TEST_SUITE(DeBruijnGraphTest, GraphTypes); TYPED_TEST(DeBruijnGraphTest, FindSequence1) { - if constexpr(std::is_same_v) { - common::logger->warn("Test case disabled for DBGSSHash"); - return; - } for (size_t k = 2; k <= 10; ++k) { auto graph = build_graph(k, { std::string(100, 'A') }); From 4f869364c2d4bc2ce75e1a80fc9e9cd8887208bc Mon Sep 17 00:00:00 2001 From: Oleksandr Kulkov Date: Thu, 25 Jul 2024 17:01:28 +0200 Subject: [PATCH 50/52] Don't disable tests for sshash --- metagraph/tests/graph/all/test_dbg_basic.cpp | 32 ------------------- .../tests/graph/all/test_dbg_contigs.cpp | 8 ----- 2 files changed, 40 deletions(-) diff --git a/metagraph/tests/graph/all/test_dbg_basic.cpp b/metagraph/tests/graph/all/test_dbg_basic.cpp index 4049a73aa9..8f7ccc41a4 100644 --- a/metagraph/tests/graph/all/test_dbg_basic.cpp +++ b/metagraph/tests/graph/all/test_dbg_basic.cpp @@ -33,10 +33,6 @@ TYPED_TEST(DeBruijnGraphTest, GraphDefaultConstructor) { } TYPED_TEST(DeBruijnGraphTest, InitializeEmpty) { - if constexpr(std::is_same_v) { - common::logger->warn("Test disabled for DBGSSHash"); - return; - } auto graph = build_graph(2); EXPECT_EQ(0u, graph->num_nodes()); @@ -48,10 +44,6 @@ TYPED_TEST(DeBruijnGraphTest, InitializeEmpty) { } TYPED_TEST(DeBruijnGraphTest, SerializeEmpty) { - if constexpr(std::is_same_v) { - common::logger->warn("Test disabled for DBGSSHash"); - return; - } { auto graph = build_graph(12); ASSERT_EQ(0u, graph->num_nodes()); @@ -187,10 +179,6 @@ TYPED_TEST(DeBruijnGraphTest, Weighted) { } TYPED_TEST(DeBruijnGraphTest, ReverseComplement) { - if constexpr(std::is_same_v) { - common::logger->warn("Test disabled for DBGSSHash"); - return; - } auto graph1 = build_graph(12, { "AAAAAAAAAAAAAAAAAAAAAAAAAAAAA" }); auto graph2 = build_graph(12, { "AAAAAAAAAAAAAAAAAAAAAAAAAAAAA", "TTTTTTTTTTTTTTTTTTTTTTTTTTTTT" }); @@ -214,20 +202,12 @@ TYPED_TEST(DeBruijnGraphTest, CheckGraph) { } TYPED_TEST(DeBruijnGraphTest, CheckGraphInputWithN) { - if constexpr(std::is_same_v) { - common::logger->warn("Test disabled for DBGSSHash"); - return; - } EXPECT_TRUE(check_graph("ACGTN", DeBruijnGraph::BASIC, false)); EXPECT_EQ(TypeParam(3).alphabet().find('N') != std::string::npos, check_graph("ACGTN", DeBruijnGraph::BASIC, true)); } TYPED_TEST(DeBruijnGraphTest, Alphabet) { - if constexpr(std::is_same_v) { - common::logger->warn("Test disabled for DBGSSHash"); - return; - } for (size_t k = 2; k <= 10; ++k) { auto graph = build_graph(k, {}); std::set alphabet(graph->alphabet().begin(), graph->alphabet().end()); @@ -239,10 +219,6 @@ TYPED_TEST(DeBruijnGraphTest, Alphabet) { } TYPED_TEST(DeBruijnGraphTest, AddSequenceSimplePath) { - if constexpr(std::is_same_v) { - common::logger->warn("Test disabled for DBGSSHash"); - return; - } for (size_t k = 2; k <= 10; ++k) { std::vector sequences { std::string(100, 'A') }; EXPECT_EQ(1u, build_graph(k, sequences)->num_nodes()); @@ -260,10 +236,6 @@ TYPED_TEST(DeBruijnGraphTest, AddSequenceSimplePaths) { } TYPED_TEST(DeBruijnGraphTest, TestNonASCIIStrings) { - if constexpr(std::is_same_v) { - common::logger->warn("Test disabled for DBGSSHash"); - return; - } std::vector sequences { // cyrillic A and C "АСАСАСАСАСАСА", "плохая строка", @@ -307,10 +279,6 @@ TYPED_TEST(DeBruijnGraphTest, AddSequences) { } TYPED_TEST(DeBruijnGraphTest, CallKmersEmptyGraph) { - if constexpr(std::is_same_v) { - common::logger->warn("Test disabled for DBGSSHash"); - return; - } for (size_t k = 2; k <= max_test_k(); ++k) { auto empty = build_graph(k); diff --git a/metagraph/tests/graph/all/test_dbg_contigs.cpp b/metagraph/tests/graph/all/test_dbg_contigs.cpp index 60b7f55028..9a82ca96d4 100644 --- a/metagraph/tests/graph/all/test_dbg_contigs.cpp +++ b/metagraph/tests/graph/all/test_dbg_contigs.cpp @@ -20,10 +20,6 @@ TYPED_TEST_SUITE(StableDeBruijnGraphTest, StableGraphTypes); TYPED_TEST(DeBruijnGraphTest, CallPathsEmptyGraph) { - if constexpr(std::is_same_v) { - common::logger->warn("Test disabled for DBGSSHash"); - return; - } for (size_t num_threads : { 1, 4 }) { for (size_t k = 2; k <= 10; ++k) { auto empty = build_graph(k); @@ -43,10 +39,6 @@ TYPED_TEST(DeBruijnGraphTest, CallPathsEmptyGraph) { } TYPED_TEST(DeBruijnGraphTest, CallUnitigsEmptyGraph) { - if constexpr(std::is_same_v) { - common::logger->warn("Test disabled for DBGSSHash"); - return; - } for (size_t num_threads : { 1, 4 }) { for (size_t k = 2; k <= 10; ++k) { auto empty = build_graph(k); From ef4bcf6d9e1d8b5fba236952dabed99bd57bc472 Mon Sep 17 00:00:00 2001 From: Oleksandr Kulkov Date: Thu, 25 Jul 2024 17:30:22 +0200 Subject: [PATCH 51/52] Update sshash --- metagraph/external-libraries/sshash | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/metagraph/external-libraries/sshash b/metagraph/external-libraries/sshash index 25cf8e443d..4246537ae4 160000 --- a/metagraph/external-libraries/sshash +++ b/metagraph/external-libraries/sshash @@ -1 +1 @@ -Subproject commit 25cf8e443d8db6b0b8178c16bbf5c2fe41f951a6 +Subproject commit 4246537ae422c332882b2449c1933d2d966df9ef From f25f2eafe60b40036f8a88f8e4a2a620bf9b8081 Mon Sep 17 00:00:00 2001 From: Oleksandr Kulkov Date: Thu, 25 Jul 2024 18:58:27 +0200 Subject: [PATCH 52/52] Update sshash --- metagraph/external-libraries/sshash | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/metagraph/external-libraries/sshash b/metagraph/external-libraries/sshash index 4246537ae4..8bbf839fa3 160000 --- a/metagraph/external-libraries/sshash +++ b/metagraph/external-libraries/sshash @@ -1 +1 @@ -Subproject commit 4246537ae422c332882b2449c1933d2d966df9ef +Subproject commit 8bbf839fa3246a4f8322871c2b03ca857d7a19c5