RubyGems - seqtrimnext - Versions diffs - 2.0.57 → 2.0.59 - Mend

seqtrimnext 2.0.57 → 2.0.59

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (9) hide show

data/.gemtest +0 -0
data/History.txt +8 -0
data/README.rdoc +3 -7
data/Rakefile +1 -1
data/bin/split_fastq.rb +10 -4
data/lib/seqtrimnext/plugins/plugin_low_quality.rb +1 -1
data/lib/seqtrimnext.rb +1 -1
metadata +232 -118
checksums.yaml +0 -7

data/.gemtest ADDED Viewed

File without changes

data/History.txt CHANGED Viewed

@@ -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 CHANGED Viewed

@@ -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 CHANGED Viewed

@@ -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 CHANGED Viewed

@@ -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 CHANGED Viewed

@@ -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 CHANGED Viewed

@@ -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 CHANGED Viewed

@@ -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

checksums.yaml DELETED Viewed

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