Switch to gawk to read fasta

erikrikarddaniel · Sep 11, 2020 · cbc6b6c · cbc6b6c
1 parent 7eb5336
commit cbc6b6c
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Showing 2 changed files with 4 additions and 3 deletions.
diff --git a/conda/meta.yaml b/conda/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.9.10" %}
+{% set version = "1.9.11" %}
 
 package:
   name: pfitmap-db
@@ -25,3 +25,4 @@ requirements:
     - r-stringr
     - r-feather
     - bioconductor-biostrings
+    - gawk
diff --git a/src/R/pf-classify.r b/src/R/pf-classify.r
@@ -13,7 +13,7 @@ suppressPackageStartupMessages(library(tidyr))
 suppressPackageStartupMessages(library(stringr))
 suppressPackageStartupMessages(library(feather))
 
-SCRIPT_VERSION = "1.9.10"
+SCRIPT_VERSION = "1.9.11"
 ROWS_PER_SEQUENCE_TSV = 1e7
 
 options(warn = 1)
@@ -501,7 +501,7 @@ if ( opt$options$seqfaa != '' ) {
   cmd <- c(
     sprintf("%s %s", ifelse(grepl('\\.gz$', opt$options$seqfaa), 'zcat', 'cat'), opt$options$seqfaa),
     "sed '/^>/s/ .*//'",
-    "awk '/^>/ { printf(\"\\n%s\\n\",$$0); next; } { printf(\"%s\",$$0);} END { printf(\"\\n\");}'",
+    "gawk '/^>/ { printf(\"\\n%s\\n\",$$0); next; } { printf(\"%s\",$$0);} END { printf(\"\\n\");}'",
     "grep -v '^$'", 
     "sed 's/^>//'", 
     "paste - -",