seqtrimnext 2.0.31 → 2.0.32

data/History.txt

@@ -1,3 +1,7 @@
+=== 2.0.32 2011-06-15
+
+Minor adjustements to work with INGEBIOL
+
 === 2.0.31 2011-06-14
 
 Added option to not fail without gnuplot

data/Manifest.txt

@@ -12,7 +12,7 @@ bin/parse_amplicons.rb
 bin/parse_json_results.rb
 bin/parse_params.rb
 bin/resume_clusters.rb
-bin/resume_rejected.sh
+bin/resume_rejected.rb
 bin/reverse_paired.rb
 bin/seqtrimnext
 bin/split_fastq.rb

data/bin/parse_params.rb

@@ -24,6 +24,7 @@ end
 params={}
 
 params['vector_db_field']='vectors_db'
+params['primers_db_field']='primers_db'
 params['contaminants_db_field']='contaminants_db'
 params['species_field']='genus'
 params['min_insert_size_field']='min_insert_size_trimmed'

data/bin/resume_rejected.rb

@@ -0,0 +1,32 @@
+#!/usr/bin/env ruby
+
+if ARGV.count!=1
+  puts "You must specify a file with seqtrim's rejected sequences"
+	puts "Usage $0 rejected_seqtrim_file";
+	exit(-1);
+end
+
+
+rejected_file=ARGV.shift
+
+if !File.exists?(rejected_file)
+  puts "File #{rejected_file} doesn't exists"
+	puts "Usage $0 rejected_seqtrim_file";
+	exit(-1);
+end
+
+
+res={}
+
+File.open(rejected_file).each do |line|
+  
+  cols=line.split(' ')
+  cols.shift
+  
+  res[cols.join(' ')] = 0 if !res[cols.join(' ')]
+  res[cols.join(' ')] += 1
+end
+
+res.each do |k,v|
+  puts "#{v} #{k}"
+end

data/lib/seqtrimnext.rb

@@ -30,7 +30,7 @@ module Seqtrimnext
   # SEQTRIM_VERSION_STAGE = 'b'
   # SEQTRIM_VERSION = "2.0.0#{SEQTRIM_VERSION_STAGE}#{SEQTRIM_VERSION_REVISION}"
   
-   VERSION = '2.0.31'
+   VERSION = '2.0.32'
   
   SEQTRIM_VERSION = VERSION
   

metadata

@@ -2,7 +2,7 @@
 name: seqtrimnext
 version: !ruby/object:Gem::Version 
   prerelease: 
-  version: 2.0.31
+  version: 2.0.32
 platform: ruby
 authors: 
 - Dario Guerrero & Almudena Bocinos
@@ -10,7 +10,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-06-14 00:00:00 Z
+date: 2011-06-15 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: narray
@@ -151,7 +151,7 @@ executables:
 - parse_json_results.rb
 - parse_params.rb
 - resume_clusters.rb
-- resume_rejected.sh
+- resume_rejected.rb
 - reverse_paired.rb
 - seqtrimnext
 - split_fastq.rb
@@ -185,7 +185,7 @@ files:
 - bin/parse_json_results.rb
 - bin/parse_params.rb
 - bin/resume_clusters.rb
-- bin/resume_rejected.sh
+- bin/resume_rejected.rb
 - bin/reverse_paired.rb
 - bin/seqtrimnext
 - bin/split_fastq.rb

data/bin/resume_rejected.sh

@@ -1,9 +0,0 @@
-#!/usr/bin/env bash
-
-if [ ! -f $1 ]; then
-	echo "You must specify a file with seqtrim's rejected sequences"
-	echo "Usage $0 rejected_seqtrim_file";
-	exit;
-fi
-
-cat $1 | cut -d ' ' -f 2-20 | sort | uniq -c;