fastq-factory 0.1.6 → 0.1.7

data/VERSION

@@ -1 +1 @@
-0.1.6
+0.1.7

data/fastq-factory.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "fastq-factory"
-  s.version = "0.1.6"
+  s.version = "0.1.7"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Anthony Underwood"]
-  s.date = "2012-08-31"
+  s.date = "2012-09-07"
   s.description = "This tool can process fastq files, using fastq_quality_trimmer and quake to correct fastq files and then provide a quality asssessment of the data"
   s.email = "anthony.underwood@hpa.org.uk"
   s.executables = ["fastq-factory"]

data/lib/trim_and_correct.rb

@@ -2,6 +2,7 @@ def trim_and_correct_fastqs(sample_map, directory, forward_reads_suffix, forward
   Dir.chdir(directory)
   # trimming
   sample_map.each do |sample_file_prefix, sample_name|
+    next if File.exists?("paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.#{forward_reads_file_extension}")
     puts "Trimming files for #{sample_name}"
     #determine read length
     read_length = calculate_read_length("#{directory}/#{sample_file_prefix}#{forward_reads_suffix}.#{forward_reads_file_extension}")
@@ -15,6 +16,7 @@ def trim_and_correct_fastqs(sample_map, directory, forward_reads_suffix, forward
   #  quake correction
   # write file for quake
   sample_map.each do |sample_file_prefix, sample_name|
+    next if File.exists?("#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension}") || File.exists?(("paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor.#{forward_reads_file_extension}"))
     puts "Error correcting files for #{sample_name}"
     output_file = File.open("quake_file_list.txt","w")
     output_file.puts "paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.#{forward_reads_file_extension} paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.#{reverse_reads_file_extension}"
@@ -23,9 +25,9 @@ def trim_and_correct_fastqs(sample_map, directory, forward_reads_suffix, forward
     `#{quake_path} -f quake_file_list.txt -k 15 -q #{quality_scale}`
   end
   sample_map.each do |sample_file_prefix, sample_name|
-    if File.exists?("paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension}")
-      `perl /Volumes/NGS2_DataRAID/projects/MRSA/scripts/fastq-remove-orphans.pl -1 paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension} -2 paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor.#{reverse_reads_file_extension}`
-    end
+    next if File.exists?("#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension}")
+    # remove orphans
+    `perl /tmp/fastq-remove-orphans.pl -1 paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension} -2 paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor.#{reverse_reads_file_extension}`
   end
 
   # cleanup and rename files

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: fastq-factory
 version: !ruby/object:Gem::Version
-  version: 0.1.6
+  version: 0.1.7
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-08-31 00:00:00.000000000 Z
+date: 2012-09-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: trollop
@@ -165,7 +165,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -2993436781626522659
+      hash: -4361859413612648693
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: