Racon, Miniasm and Minimap added

circlator/assemble.py

@@ -19,7 +19,7 @@ def __init__(self,
       spades_use_first_success=False,
       assembler='spades',
       genomeSize=100000, # only matters for Canu if correcting reads (which we're not)
-      data_type='pacbio-corrected',
+      data_type='pacbio-raw',
     ):
         self.outdir = os.path.abspath(outdir)
         self.reads = os.path.abspath(reads)
@@ -41,6 +41,9 @@ def __init__(self,
             self.canu = external_progs.make_and_check_prog('canu', verbose=self.verbose, required=True)
             self.genomeSize=genomeSize
             self.data_type = data_type
+        elif self.assembler == 'racon':
+            self.racon = external_progs.make_and_check_prog('racon', verbose=self.verbose, required=True)
+            self.data_type = data_type
         else:
             raise Error('Unknown assembler: "' + self.assembler + '". cannot continue')
 
@@ -170,11 +173,119 @@ def run_canu(self):
         renamed_gfa = os.path.join(self.outdir, 'contigs.gfa')
         os.rename(original_gfa, renamed_gfa)
 
+    def run_racon(self):
+        '''Runs minimap, miniasm, racon instead of spades'''
+
+        if self.data_type.split('-')[0] == 'pacbio':
+            overlapRaadsType = 'ava-pb' # PacBio
+        else:
+            overlapReadsType = 'ava-ont' # Nanopore
+
+        # minimap2
+        cmd = [
+            self.minimap2.exe(),
+            '-t', self.threads,
+            '-x', overlapReadsType, self.reads, self.reads,
+            '>', os.path.join(self.outdir, 'output.paf')
+        ]
+
+        ok, errs = common.syscall(' '.join(cmd), verbose=self.verbose, allow_fail=False)
+        if not ok:
+            raise Error('Error running minimap2.')
+
+        # miniasm
+        cmd = [
+            self.miniasm.exe(),
+            '-Rc2', '-f', self.reads, os.path.join(self.outdir, 'output.paf'),
+            '>', os.path.join(self.outdir, 'output.gfa')
+        ]
+
+        ok, errs = common.syscall(' '.join(cmd), verbose=self.verbose, allow_fail=False)
+        if not ok:
+            raise Error('Error running miniasm.')
+
+        # gfa2fasta
+        cmd = [
+            self.awk.exe(),
+            '/^S/{print ">"$2"\n"$3}', os.path.join(self.outdir, 'output.gfa'),
+            '|', 'fold ' '>',  os.path.join(self.outdir, 'output.gfa.fasta')
+
+        ]
+
+        ok, errs = common.syscall(' '.join(cmd), verbose=self.verbose, allow_fail=False)
+        if not ok:
+            raise Error('Error running awk.')
+
+        if self.data_type.split('-')[0] == 'pacbio':
+            mapRaadsType = 'map-pb' # PacBio
+        else:
+            mapReadsType = 'map-ont' # Nanopore
+
+
+        # Correction 1
+        # minimap2
+        cmd = [
+            self.minimap2.exe(),
+            '-t', self.threads,
+            '-ax', mapRaadsType, os.path.join(self.outdir, 'output.gfa.fasta'), self.reads,
+            '>', os.path.join(self.outdir, 'output.gfa1.sam')
+        ]
+
+        ok, errs = common.syscall(' '.join(cmd), verbose=self.verbose, allow_fail=False)
+        if not ok:
+            raise Error('Error running minimap2 correction step #1.')
+
+        # Racon 1
+        cmd = [
+            self.racon.exe(),
+            '-t', self.threads, self.reads, os.path.join(self.outdir, 'output.gfa1.sam'),
+            os.path.join(self.outdir, 'output.gfa.fasta'),
+            '>', os.path.join(self.outdir, 'output.racon1.fasta')
+        ]
+
+        ok, errs = common.syscall(' '.join(cmd), verbose=self.verbose, allow_fail=False)
+        if not ok:
+            raise Error('Error running racon correction step #1.')
+
+
+        # Correction 2
+        # minimap2 2
+        cmd = [
+            self.minimap2.exe(),
+            '-t', self.threads,
+            '-ax map-pb', os.path.join(self.outdir, 'output.racon1.fasta'), self.reads,
+            '>', os.path.join(self.outdir, 'output.gfa2.sam')
+        ]
+
+        ok, errs = common.syscall(' '.join(cmd), verbose=self.verbose, allow_fail=False)
+        if not ok:
+            raise Error('Error running minimap2 correction step #2.')
+
+        # Racon 2
+        cmd = [
+            self.racon.exe(),
+            '-t', self.threads, self.reads, os.path.join(self.outdir, 'output.gfa2.sam'),
+            os.path.join(self.outdir, 'output.racon1.fasta'),
+            '>', os.path.join(self.outdir, 'output.racon2.fasta')
+        ]
+
+        ok, errs = common.syscall(' '.join(cmd), verbose=self.verbose, allow_fail=False)
+        if not ok:
+            raise Error('Error running racon correction step #2.')
+
+        original_gfa = os.path.join(self.outdir, 'output.gfa')
+        renamed_gfa = os.path.join(self.outdir, 'contigs.gfa')
+        os.rename(original_gfa, renamed_gfa)
+        original_contigs = os.path.join(self.outdir, 'output.racon2.fasta')
+        renamed_contigs = os.path.join(self.outdir, 'contigs.fasta')
+        os.rename(original_contigs, renamed_contigs)
 
     def run(self):
         if self.assembler == 'spades':
             self.run_spades(stop_at_first_success=self.spades_use_first_success)
         elif self.assembler == 'canu':
             self.run_canu()
+        elif self.assembler == 'racon':
+            self.run_racon()
         else:
             raise Error('Unknown assembler: "' + self.assembler + '". cannot continue')

circlator/assembly.py

@@ -64,6 +64,9 @@ def _set_filenames(self):
         elif self.assembler == 'canu':
             if self.contigs_fasta is None or self.contigs_gfa is None:
                 raise Error('Error finding canu contigs fasta and/or gfa file')
+        elif self.assembler == 'racon':
+            if self.contigs_fasta is None or self.contigs_gfa is None:
+                raise Error('Error finding canu contigs fasta and/or gfa file')
         else:
             raise Error('Assembler "' + self.assembler + '" not recognised. Cannot continue')
 
@@ -185,5 +188,7 @@ def circular_contigs(self):
                 return set()
         elif self.assembler == 'canu':
             return self._circular_contigs_from_canu_gfa(self.contigs_gfa)
+        elif self.assembler == 'racon':
+            return self._circular_contigs_from_canu_gfa(self.contigs_gfa)
         else:
             return set()

circlator/common.py

@@ -4,7 +4,7 @@
 
 class Error (Exception): pass
 
-allowed_assemblers = ['canu', 'spades'] 
+allowed_assemblers = ['canu', 'spades', 'racon']
 allowed_data_types = ['pacbio-raw', 'pacbio-corrected', 'nanopore-raw', 'nanopore-corrected']
 
 def syscall(cmd, allow_fail=False, verbose=False):

circlator/external_progs.py

@@ -11,6 +11,7 @@ class Error (Exception): pass
     'samtools': 'CIRCLATOR_SAMTOOLS',
     'spades': 'CIRCLATOR_SPADES',
     'canu': 'CIRCLATOR_CANU',
+    'racon': 'CIRCLATOR_RACON',
 }
 
 prog_to_version_cmd = {
@@ -20,15 +21,21 @@ class Error (Exception): pass
     'samtools': ('', re.compile(r'Version: (\d+\.\d+[\.\d]*)')),
     'spades': ('-v', re.compile(r'v.?([0-9][0-9\.]+)')),
     'canu': ('-version', re.compile(r'^Canu \D*([\d][\d\.]+)')),
+    'minimap2': ('-V', re.compile(r'([0-9\.]+)')),
+    'miniasm': ('-V', re.compile(r'([0-9\.]+)')),
+    'racon': ('--version', re.compile(r'v.?([0-9][0-9\.]+)')),
 }
 
 min_versions = {
     'bwa': '0.7.12',
     'nucmer': '3.1',
     'prodigal': '2.6',
     'samtools': '0.1.19',
-    'spades': '3.6.2', # this is the first version to support python3
+    'spades': '3.11.1', # this is the first version to support python3
     'canu': '0.0',
+    'minimap2': '2.10',
+    'miniasm': '0.2',
+    'racon': '1.2.1',
 }
 
 
@@ -44,9 +51,12 @@ class Error (Exception): pass
     'spades': 'spades.py',
     'samtools': 'samtools',
     'canu': 'canu',
+    'minimap2':'minimap2',
+    'miniasm': 'miniasm',
+    'racon': 'racon'
 }
 
-not_required = {'spades', 'canu'}
+not_required = {'spades', 'canu','racon'}
 
 def handle_error(message, raise_error=True):
     if raise_error:

circlator/merge.py

@@ -1,4 +1,5 @@
 import os
+import os
 import sys
 import copy
 import shutil

circlator/tasks/assemble.py

@@ -5,7 +5,7 @@
 
 def run():
     parser = argparse.ArgumentParser(
-        description = 'Assemble reads using SPAdes/Canu',
+        description = 'Assemble reads using SPAdes/Canu/Racon',
         usage = 'circlator assemble [options] <in.reads.fasta> <out_dir>')
     parser.add_argument('--not_careful', action='store_true', help='Do not use the --careful option with SPAdes (used by default)')
     parser.add_argument('--not_only_assembler', action='store_true', help='Do not use the --assemble-only option with SPAdes (used by default)')
@@ -14,7 +14,7 @@ def run():
     parser.add_argument('--spades_k', help='Comma separated list of kmers to use when running SPAdes. Max kmer is 127 and each kmer should be an odd integer [%(default)s]', default='127,117,107,97,87,77', metavar='k1,k2,k3,...')
     parser.add_argument('--spades_use_first', action='store_true', help='Use the first successful SPAdes assembly. Default is to try all kmers and use the assembly with the largest N50')
     parser.add_argument('--assembler', choices=circlator.common.allowed_assemblers, help='Assembler to use for reassemblies [%(default)s]', default='spades')
-    parser.add_argument('--data_type', choices=circlator.common.allowed_data_types, help='String representing one of the 4 type of data analysed (only used for Canu) [%(default)s]', default='pacbio-corrected')
+    parser.add_argument('--data_type', choices=circlator.common.allowed_data_types, help='String representing one of the 4 type of data analysed (only used for Canu and Racon) [%(default)s]', default='pacbio-raw')
     parser.add_argument('reads', help='Name of input reads FASTA file', metavar='in.reads.fasta')
     parser.add_argument('out_dir', help='Output directory (must not already exist)')
     options = parser.parse_args()

circlator/tasks/merge.py

@@ -18,7 +18,7 @@ def run():
     parser.add_argument('--spades_k', help='Comma separated list of kmers to use when running SPAdes. Max kmer is 127 and each kmer should be an odd integer [%(default)s]', default='127,117,107,97,87,77', metavar='k1,k2,k3,...')
     parser.add_argument('--spades_use_first', action='store_true', help='Use the first successful SPAdes assembly. Default is to try all kmers and use the assembly with the largest N50')
     parser.add_argument('--assembler', choices=circlator.common.allowed_assemblers, help='Assembler to use for reassemblies [%(default)s]', default='spades')
-    parser.add_argument('--data_type', choices=circlator.common.allowed_data_types, help='String representing one of the 4 type of data analysed (only used for Canu) [%(default)s]', default='pacbio-corrected')
+    parser.add_argument('--data_type', choices=circlator.common.allowed_data_types, help='String representing one of the 4 type of data analysed (only used for Canu and Racon) [%(default)s]', default='pacbio-raw')
     parser.add_argument('--b2r_length_cutoff', type=int, help='All reads mapped to contigs shorter than this will be kept [%(default)s]', default=100000, metavar='INT')
     parser.add_argument('--b2r_split_all_reads', action='store_true', help='By default, reads mapped to shorter contigs are left unchanged. This option splits them into two, broken at the middle of the contig to try to force circularization. May help if the assembler does not detect circular contigs (eg canu)')
     parser.add_argument('--ref_end', type=int, help='max distance allowed between nucmer hit and end of input assembly contig [%(default)s]', metavar='INT', default=15000)

install_dependencies.sh

@@ -9,15 +9,21 @@ CANU_VERSION=1.4
 PRODIGAL_VERSION=2.6.2
 SAMTOOLS_VERSION=1.3
 MUMMER_VERSION=3.23
-SPADES_VERSION=3.7.1
+SPADES_VERSION=3.11.1
+
+MINIMAP2_VERSION=2.10
+MINIASM_VERSION=55cf0189e2f7d5bda5868396cebe066eec0a9547
+RACON_VERSION=1.3.0
 
 BWA_DOWNLOAD_URL="http://downloads.sourceforge.net/project/bio-bwa/bwa-${BWA_VERSION}.tar.bz2"
 CANU_DOWNLOAD_URL="https://github.com/marbl/canu/releases/download/v${CANU_VERSION}/canu-${CANU_VERSION}.Linux-amd64.tar.xz"
 PRODIGAL_DOWNLOAD_URL="https://github.com/hyattpd/Prodigal/releases/download/v${PRODIGAL_VERSION}/prodigal.linux"
 SAMTOOLS_DOWNLOAD_URL="https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2"
 MUMMER_DOWNLOAD_URL="http://downloads.sourceforge.net/project/mummer/mummer/${MUMMER_VERSION}/MUMmer${MUMMER_VERSION}.tar.gz"
 SPADES_DOWNLOAD_URL="http://spades.bioinf.spbau.ru/release${SPADES_VERSION}/SPAdes-${SPADES_VERSION}-Linux.tar.gz"
-
+MINIMAP2_DOWNLOAD_URL="https://github.com/lh3/minimap2/archive/v${MINIMAP2_VERSION}.tar.gz"
+MINIASM_DOWNLOAD_URL="https://github.com/lh3/miniasm/archive/${MINIASM_VERSION}.tar.gz"
+RACON_DOWNLOAD_URL="https://github.com/isovic/racon/releases/download/${RACON_VERSION}/racon-v${RACON_VERSION}.tar.gz"
 
 # Make an install location
 if [ ! -d 'build' ]; then
@@ -91,6 +97,36 @@ spades_dir="$build_dir/SPAdes-${SPADES_VERSION}-Linux/bin"
 tar -zxf SPAdes-${SPADES_VERSION}-Linux.tar.gz
 
 
+# --------------- minimap2 -----------------
+cd $build_dir
+download $MINIMAP2_DOWNLOAD_URL "${MINIMAP2_VERSION}.tar.gz"
+minimap2_dir="$build_dir/minimap2-${MINIMAP2_VERSION}/"
+tar -zxf ${MINIMAP2_VERSION}.tar.gz
+cd $minimap2_dir
+make
+
+
+# --------------- miniasm -----------------
+cd $build_dir
+download $MINIASM_DOWNLOAD_URL "${MINIASM_VERSION}.tar.gz"
+miniasm_dir="$build_dir/miniasm-${MINIASM_VERSION}"
+tar -zxf ${MINIASM_VERSION}.tar.gz
+cd $miniasm_dir
+make
+
+# --------------- racon -----------------
+cd $build_dir
+download $RACON_DOWNLOAD_URL "racon-v${RACON_VERSION}.tar.gz"
+racon_dir="$build_dir/racon-v${RACON_VERSION}"
+tar -zxf racon-v${RACON_VERSION}.tar.gz
+cd $racon_dir
+mkdir build
+cd build
+cmake -DCMAKE_BUILD_TYPE=Release ..
+make
+racon_dir="$build_dir/racon-v${RACON_VERSION}/build/bin"
+
+
 cd $start_dir
 
 update_path () {
@@ -106,4 +142,8 @@ update_path ${prodigal_dir}
 update_path ${mummer_dir}
 update_path ${samtools_dir}
 update_path ${spades_dir}
+update_path ${minimap2_dir}
+update_path ${miniasm_dir}
+update_path ${racon_dir}
+
 

setup.py

@@ -7,7 +7,7 @@
 
 setup(
     name='circlator',
-    version='1.5.5',
+    version='1.5.6',
     description='circlator: a tool to circularise genome assemblies',
     packages = find_packages(),
     package_data={'circlator': ['data/*']},