fastq-factory 0.1.14 → 0.1.15

data/VERSION

@@ -1 +1 @@
-0.1.14
+0.1.15

data/fastq-factory.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "fastq-factory"
-  s.version = "0.1.14"
+  s.version = "0.1.15"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Anthony Underwood"]
-  s.date = "2012-10-11"
+  s.date = "2012-10-12"
   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

@@ -34,23 +34,23 @@ def trim_and_correct_fastqs(sample_map, directory, forward_reads_suffix, forward
   # cleanup and rename files
 
   sample_map.each do |sample_file_prefix, sample_name|
-    File.delete("#{sample_file_prefix}#{forward_reads_suffix}.trimmed.#{forward_reads_file_extension}") if File.exists?("#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension}")
-    File.delete("#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.#{reverse_reads_file_extension}") if File.exists?("#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.#{reverse_reads_file_extension}")
-    File.delete("orphaned_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.#{forward_reads_file_extension}") if File.exists?("orphaned_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.#{forward_reads_file_extension}")
-    File.delete("orphaned_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.#{reverse_reads_file_extension}") if File.exists?("orphaned_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.#{reverse_reads_file_extension}")
+    delete_file_with_dependencies("#{sample_file_prefix}#{forward_reads_suffix}.trimmed.#{forward_reads_file_extension}", "#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension}")
+    delete_file_with_dependencies("#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.#{reverse_reads_file_extension}", "#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor.#{reverse_reads_file_extension}")
+    delete_file_with_dependencies("orphaned_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.#{forward_reads_file_extension}")
+    delete_file_with_dependencies("orphaned_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.#{reverse_reads_file_extension}")
     if File.exists?("paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension}")
-      File.delete("paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.#{forward_reads_file_extension}") if File.exists?("paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.#{forward_reads_file_extension}")
-      File.delete("paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.#{reverse_reads_file_extension}") if File.exists?("paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.#{reverse_reads_file_extension}")
-      File.delete("error_model.paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.txt") if File.exists?("error_model.paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.txt")
-      File.delete("error_model.paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.txt") if File.exists?("error_model.paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.txt")
-      File.delete("paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.stats.txt") if File.exists?("paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.stats.txt")
-      File.delete("paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor_single.#{forward_reads_file_extension}") if File.exists?("paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor_single.#{forward_reads_file_extension}")
-      File.delete("paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.stats.txt") if File.exists?("paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.stats.txt")
-      File.delete("paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor_single.#{forward_reads_file_extension}") if File.exists?("paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor_single.#{forward_reads_file_extension}")
-      File.delete("paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension}") if File.exists?("paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension}")
-      File.delete("paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor.#{reverse_reads_file_extension}") if File.exists?("paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor.#{reverse_reads_file_extension}")
-      File.delete("orphaned_paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension}") if File.exists?("orphaned_paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension}")
-      File.delete("orphaned_paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor.#{reverse_reads_file_extension}") if File.exists?("orphaned_paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor.#{reverse_reads_file_extension}")
+      delete_file_with_dependencies("paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.#{forward_reads_file_extension}")
+      delete_file_with_dependencies("paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.#{reverse_reads_file_extension}")
+      delete_file_with_dependencies("error_model.paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.txt")
+      delete_file_with_dependencies("error_model.paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.txt")
+      delete_file_with_dependencies("paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.stats.txt")
+      delete_file_with_dependencies("paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor_single.#{forward_reads_file_extension}")
+      delete_file_with_dependencies("paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.stats.txt")
+      delete_file_with_dependencies("paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor_single.#{forward_reads_file_extension}")
+      delete_file_with_dependencies("paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension}")
+      delete_file_with_dependencies("paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor.#{reverse_reads_file_extension}")
+      delete_file_with_dependencies("orphaned_paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension}")
+      delete_file_with_dependencies("orphaned_paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor.#{reverse_reads_file_extension}")
       File.rename("paired_paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension}", "#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension}") if File.exists?("paired_paired_#{sample_file_prefix}#{forward_reads_suffix}.trimmed.cor.#{forward_reads_file_extension}")
       File.rename("paired_paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor.#{reverse_reads_file_extension}", "#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor.#{reverse_reads_file_extension}") if File.exists?("paired_paired_#{sample_file_prefix}#{reverse_reads_suffix}.trimmed.cor.#{reverse_reads_file_extension}")
     else
@@ -60,6 +60,13 @@ def trim_and_correct_fastqs(sample_map, directory, forward_reads_suffix, forward
   end
 end
 
+def delete_file_with_dependencies(file, *dependencies)
+  dependencies << file
+  if dependencies.all?{|dependency| File.exists?(dependency)} && File.exists?(file)
+    File.delete(file)
+  end
+end
+
 def calculate_read_length(filename)
   read_length = nil
   File.open(filename) do |f|

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: fastq-factory
 version: !ruby/object:Gem::Version
-  version: 0.1.14
+  version: 0.1.15
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-10-11 00:00:00.000000000 Z
+date: 2012-10-12 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: 968500425624435397
+      hash: -59302719065495313
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: