seqtrimnext 2.0.57 → 2.0.59

data/History.txt

@@ -1,3 +1,11 @@
+=== 2.0.59 2014-03-03
+
+Fix issue detecting fasta files without quals
+
+=== 2.0.58 2013-12-16
+
+Uses new scbi_fastq with gzip writing
+
 === 2.0.57 2013-07-26
 
 Option to disable reject by vectors in the middle

data/README.rdoc

@@ -128,7 +128,7 @@ The same way you can modify any of the parameters. You can find all parameters a
 
 == REQUIREMENTS:
 
-* Ruby 1.9.2
+* Ruby 1.9.2 or greater
 * CD-HIT 4.5.3 or greater
 * Blast plus 2.24 or greater (prior versions have bugs that produces bad results)
 * [Optional] - GnuPlot version 4.4.2 or greater (prior versions may produce wrong graphs)
@@ -167,13 +167,9 @@ Download latest certificates (maybe you don't need them):
   $ export CURL_CA_BUNDLE=`pwd`/cacert.pem # add this to your .bashrc or 
 equivalent
 
-Install RVM:
+Install RVM following the directions from this web:
 
-  $ bash < <(curl -k https://rvm.beginrescueend.com/install/rvm)
-
-Setup environment:  
-  
-  $ echo '[[ -s "$HOME/.rvm/scripts/rvm" ]] && . "$HOME/.rvm/scripts/rvm" # Load RVM function' >> ~/.bash_profile
+  https://rvm.io/rvm/install
   
 Install ruby 1.9.2 (this can take a while):
   

data/Rakefile

@@ -24,7 +24,7 @@ $hoe = Hoe.spec 'seqtrimnext' do
   self.extra_deps << ['scbi_blast','>=0.0.34']
   self.extra_deps << ['scbi_mapreduce','>=0.0.38']
   self.extra_deps << ['scbi_fasta','>=0.1.7']
-  self.extra_deps << ['scbi_fastq','>=0.0.17']
+  self.extra_deps << ['scbi_fastq','>=0.0.18']
   self.extra_deps << ['scbi_plot','>=0.0.6']
   self.extra_deps << ['scbi_math','>=0.0.1']
   self.extra_deps << ['scbi_headers','>=0.0.2']

data/bin/split_fastq.rb

@@ -4,19 +4,25 @@ require 'scbi_fastq'
 
 
 if ARGV.count < 3
-  puts "#{$0} FASTQ OUTPUT_NAME SPLIT_BY"
+  puts "#{$0} FASTQ OUTPUT_NAME SPLIT_BY [-gz]"
   exit
 end
 
-
   
 fastq = ARGV.shift
 output_name = ARGV.shift
 split_by = ARGV.shift.to_i
 
+gz_arg=ARGV.shift
+gz=false
+
+if !gz_arg.nil? and gz_arg.index('-gz')
+	gz='.gz'
+end
+
 
 file_index=1
-out=FastqFile.new("#{output_name}#{file_index}.fastq",'w')
+out=FastqFile.new("#{output_name}#{file_index}.fastq#{gz}","w#{gz}")
 
 fqr=FastqFile.new(fastq)
 
@@ -32,7 +38,7 @@ fqr.each do |seq_name,seq_fasta,seq_qual,comments|
       
     file_index +=1
     out.close
-    out=FastqFile.new("#{output_name}#{file_index}.fastq",'w')
+    out=FastqFile.new("#{output_name}#{file_index}.fastq#{gz}","w#{gz}")
 
   end
 end

data/lib/seqtrimnext/plugins/plugin_low_quality.rb

@@ -119,7 +119,7 @@ class PluginLowQuality < Plugin
 
      if ((self.class.to_s=='PluginLowQuality') && seq.seq_qual.nil? ) 
        $LOG.debug " Quality File haven't been provided. It's impossible to execute " + self.class.to_s     
-     elsif (seq.seq_qual.size>0)
+     elsif ((seq.seq_qual.size>0) && (@params.get_param('use_qual')=='true'))
           
           $LOG.debug "[#{self.class.to_s}, seq: #{seq.seq_name}]: checking low quality of the sequence"
           

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 = '2.0.57'
+   VERSION = '2.0.59'
   
   SEQTRIM_VERSION = VERSION
   

metadata

@@ -1,139 +1,248 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: seqtrimnext
-version: !ruby/object:Gem::Version 
-  version: 2.0.57
+version: !ruby/object:Gem::Version
+  version: 2.0.59
+  prerelease: 
 platform: ruby
-authors: 
+authors:
 - Dario Guerrero & Almudena Bocinos
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2013-07-26 00:00:00 Z
-dependencies: 
-- !ruby/object:Gem::Dependency 
+date: 2014-03-03 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
   name: narray
-  prerelease: false
-  requirement: &id001 !ruby/object:Gem::Requirement 
-    requirements: 
-    - &id002 
-      - ">="
-      - !ruby/object:Gem::Version 
-        version: "0"
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :runtime
-  version_requirements: *id001
-- !ruby/object:Gem::Dependency 
-  name: gnuplot
   prerelease: false
-  requirement: &id003 !ruby/object:Gem::Requirement 
-    requirements: 
-    - *id002
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: gnuplot
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :runtime
-  version_requirements: *id003
-- !ruby/object:Gem::Dependency 
-  name: term-ansicolor
   prerelease: false
-  requirement: &id004 !ruby/object:Gem::Requirement 
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: term-ansicolor
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
         version: 1.0.5
   type: :runtime
-  version_requirements: *id004
-- !ruby/object:Gem::Dependency 
-  name: xml-simple
   prerelease: false
-  requirement: &id005 !ruby/object:Gem::Requirement 
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.5
+- !ruby/object:Gem::Dependency
+  name: xml-simple
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
         version: 1.0.12
   type: :runtime
-  version_requirements: *id005
-- !ruby/object:Gem::Dependency 
-  name: scbi_blast
   prerelease: false
-  requirement: &id006 !ruby/object:Gem::Requirement 
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.12
+- !ruby/object:Gem::Dependency
+  name: scbi_blast
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
         version: 0.0.34
   type: :runtime
-  version_requirements: *id006
-- !ruby/object:Gem::Dependency 
-  name: scbi_mapreduce
   prerelease: false
-  requirement: &id007 !ruby/object:Gem::Requirement 
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.0.34
+- !ruby/object:Gem::Dependency
+  name: scbi_mapreduce
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
         version: 0.0.38
   type: :runtime
-  version_requirements: *id007
-- !ruby/object:Gem::Dependency 
-  name: scbi_fasta
   prerelease: false
-  requirement: &id008 !ruby/object:Gem::Requirement 
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.0.38
+- !ruby/object:Gem::Dependency
+  name: scbi_fasta
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
         version: 0.1.7
   type: :runtime
-  version_requirements: *id008
-- !ruby/object:Gem::Dependency 
-  name: scbi_fastq
   prerelease: false
-  requirement: &id009 !ruby/object:Gem::Requirement 
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        version: 0.0.17
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.1.7
+- !ruby/object:Gem::Dependency
+  name: scbi_fastq
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.0.18
   type: :runtime
-  version_requirements: *id009
-- !ruby/object:Gem::Dependency 
-  name: scbi_plot
   prerelease: false
-  requirement: &id010 !ruby/object:Gem::Requirement 
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.0.18
+- !ruby/object:Gem::Dependency
+  name: scbi_plot
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
         version: 0.0.6
   type: :runtime
-  version_requirements: *id010
-- !ruby/object:Gem::Dependency 
-  name: scbi_math
   prerelease: false
-  requirement: &id011 !ruby/object:Gem::Requirement 
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.0.6
+- !ruby/object:Gem::Dependency
+  name: scbi_math
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
         version: 0.0.1
   type: :runtime
-  version_requirements: *id011
-- !ruby/object:Gem::Dependency 
-  name: scbi_headers
   prerelease: false
-  requirement: &id012 !ruby/object:Gem::Requirement 
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.0.1
+- !ruby/object:Gem::Dependency
+  name: scbi_headers
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
         version: 0.0.2
   type: :runtime
-  version_requirements: *id012
-- !ruby/object:Gem::Dependency 
-  name: hoe
   prerelease: false
-  requirement: &id013 !ruby/object:Gem::Requirement 
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        version: 2.8.0
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.0.2
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '4.0'
   type: :development
-  version_requirements: *id013
-description: SeqtrimNEXT is a customizable and distributed pre-processing software for NGS (Next Generation Sequencing) biological data. It makes use of scbi_mapreduce gem to be able to run in parallel and distributed environments. It is specially suited for Roche 454 (normal and paired-end) & Ilumina datasets, although it could be easyly adapted to any other situation.
-email: 
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '4.0'
+- !ruby/object:Gem::Dependency
+  name: newgem
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.5.3
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.5.3
+- !ruby/object:Gem::Dependency
+  name: hoe
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.7'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.7'
+description: SeqtrimNEXT is a customizable and distributed pre-processing software
+  for NGS (Next Generation Sequencing) biological data. It makes use of scbi_mapreduce
+  gem to be able to run in parallel and distributed environments. It is specially
+  suited for Roche 454 (normal and paired-end) & Ilumina datasets, although it could
+  be easyly adapted to any other situation.
+email:
 - dariogf@gmail.com & alkoke@gmail.com
-executables: 
+executables:
 - create_graphs.rb
 - extract_seqs.rb
 - extract_seqs_from_fasta.rb
@@ -158,8 +267,7 @@ executables:
 - split_ilumina_paired.rb
 - split_paired.rb
 extensions: []
-
-extra_rdoc_files: 
+extra_rdoc_files:
 - History.txt
 - lib/seqtrimnext/templates/amplicons.txt
 - lib/seqtrimnext/templates/sanger.txt
@@ -173,7 +281,8 @@ extra_rdoc_files:
 - lib/seqtrimnext/templates/transcriptomics_454_plants.txt
 - Manifest.txt
 - PostInstall.txt
-files: 
+- README.rdoc
+files:
 - bin/create_graphs.rb
 - bin/extract_seqs.rb
 - bin/extract_seqs_from_fasta.rb
@@ -299,30 +408,35 @@ files:
 - script/generate
 - test/test_helper.rb
 - test/test_seqtrimnext.rb
+- .gemtest
 homepage: http://www.scbi.uma.es/downloads
-licenses: []
-
-metadata: {}
-
+licenses:
+- MIT
 post_install_message: PostInstall.txt
-rdoc_options: 
+rdoc_options:
 - --main
 - README.rdoc
-require_paths: 
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
-  requirements: 
-  - *id002
-required_rubygems_version: !ruby/object:Gem::Requirement 
-  requirements: 
-  - *id002
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
 rubyforge_project: seqtrimnext
-rubygems_version: 2.0.3
+rubygems_version: 1.8.23
 signing_key: 
-specification_version: 4
-summary: SeqtrimNEXT is a customizable and distributed pre-processing software for NGS (Next Generation Sequencing) biological data
-test_files: 
-- test/test_helper.rb
+specification_version: 3
+summary: SeqtrimNEXT is a customizable and distributed pre-processing software for
+  NGS (Next Generation Sequencing) biological data
+test_files:
 - test/test_seqtrimnext.rb
+- test/test_helper.rb

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@@ -1,7 +0,0 @@
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