seqtrimnext 2.0.59 → 2.0.60

metadata

@@ -1,247 +1,205 @@
 --- !ruby/object:Gem::Specification
 name: seqtrimnext
 version: !ruby/object:Gem::Version
-  version: 2.0.59
-  prerelease: 
+  version: 2.0.60
 platform: ruby
 authors:
-- Dario Guerrero & Almudena Bocinos
+- Dario Guerrero
+- Almudena Bocinos
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-03-03 00:00:00.000000000 Z
+date: 2015-07-23 00:00:00.000000000 Z
 dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.7'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.7'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
 - !ruby/object:Gem::Dependency
   name: narray
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   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
   prerelease: false
   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
   prerelease: false
   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
   prerelease: false
   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
   prerelease: false
   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
   prerelease: false
   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
   prerelease: false
   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
   prerelease: false
   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
   prerelease: false
   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
   prerelease: false
   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
   prerelease: false
   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
-  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.
+description: Seqtrimnext is a plugin based system to preprocess and clean sequences
+  from multiple NGS sequencing platforms
 email:
-- dariogf@gmail.com & alkoke@gmail.com
+- dariogf@gmail.com
+- |-
+  alkoke@gmail.com
+  t
 executables:
 - create_graphs.rb
 - extract_seqs.rb
@@ -262,27 +220,18 @@ executables:
 - resume_rejected.rb
 - reverse_paired.rb
 - seqtrimnext
-- split_fastq.rb
 - split_fasta.rb
+- split_fastq.rb
 - split_ilumina_paired.rb
 - split_paired.rb
 extensions: []
-extra_rdoc_files:
-- History.txt
-- lib/seqtrimnext/templates/amplicons.txt
-- lib/seqtrimnext/templates/sanger.txt
-- lib/seqtrimnext/templates/only_quality.txt
-- lib/seqtrimnext/templates/genomics_454.txt
-- lib/seqtrimnext/templates/genomics_454_with_paired.txt
-- lib/seqtrimnext/templates/genomics_short_reads.txt
-- lib/seqtrimnext/templates/genomics_short_reads_2.txt
-- lib/seqtrimnext/templates/transcriptomics_454.txt
-- lib/seqtrimnext/templates/transcriptomics_short_reads.txt
-- lib/seqtrimnext/templates/transcriptomics_454_plants.txt
-- Manifest.txt
-- PostInstall.txt
-- README.rdoc
+extra_rdoc_files: []
 files:
+- ".gitignore"
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
 - bin/create_graphs.rb
 - bin/extract_seqs.rb
 - bin/extract_seqs_from_fasta.rb
@@ -302,17 +251,14 @@ files:
 - bin/resume_rejected.rb
 - bin/reverse_paired.rb
 - bin/seqtrimnext
-- bin/split_fastq.rb
 - bin/split_fasta.rb
+- bin/split_fastq.rb
 - bin/split_ilumina_paired.rb
 - bin/split_paired.rb
-- History.txt
+- lib/seqtrimnext.rb
 - lib/seqtrimnext/actions/action_ab_adapter.rb
 - lib/seqtrimnext/actions/action_ab_far_adapter.rb
 - lib/seqtrimnext/actions/action_ab_left_adapter.rb
-- lib/seqtrimnext/actions/action_sanger_left_adapter.rb
-- lib/seqtrimnext/actions/action_sanger_right_adapter.rb
-- lib/seqtrimnext/actions/action_user_contaminant.rb
 - lib/seqtrimnext/actions/action_empty_insert.rb
 - lib/seqtrimnext/actions/action_ignore_repeated.rb
 - lib/seqtrimnext/actions/action_indetermination.rb
@@ -335,9 +281,12 @@ files:
 - lib/seqtrimnext/actions/action_rem_adit_artifacts.rb
 - lib/seqtrimnext/actions/action_right_adapter.rb
 - lib/seqtrimnext/actions/action_right_primer.rb
+- lib/seqtrimnext/actions/action_sanger_left_adapter.rb
+- lib/seqtrimnext/actions/action_sanger_right_adapter.rb
 - lib/seqtrimnext/actions/action_short_insert.rb
 - lib/seqtrimnext/actions/action_unexpected_poly_t.rb
 - lib/seqtrimnext/actions/action_unexpected_vector.rb
+- lib/seqtrimnext/actions/action_user_contaminant.rb
 - lib/seqtrimnext/actions/action_vectors.rb
 - lib/seqtrimnext/actions/seqtrim_action.rb
 - lib/seqtrimnext/classes/action_manager.rb
@@ -360,13 +309,12 @@ files:
 - lib/seqtrimnext/classes/sequence.rb
 - lib/seqtrimnext/classes/sequence_group.rb
 - lib/seqtrimnext/classes/sequence_with_action.rb
+- lib/seqtrimnext/plugins/.DS_Store
 - lib/seqtrimnext/plugins/plugin.rb
 - lib/seqtrimnext/plugins/plugin_ab_adapters.rb
-- lib/seqtrimnext/plugins/plugin_sanger_adapters.rb
 - lib/seqtrimnext/plugins/plugin_adapters.rb
 - lib/seqtrimnext/plugins/plugin_amplicons.rb
 - lib/seqtrimnext/plugins/plugin_contaminants.rb
-- lib/seqtrimnext/plugins/plugin_user_contaminants.rb
 - lib/seqtrimnext/plugins/plugin_extract_inserts.rb
 - lib/seqtrimnext/plugins/plugin_find_poly_at.rb
 - lib/seqtrimnext/plugins/plugin_ignore_repeated.rb
@@ -377,18 +325,24 @@ files:
 - lib/seqtrimnext/plugins/plugin_low_high_size.rb
 - lib/seqtrimnext/plugins/plugin_low_quality.rb
 - lib/seqtrimnext/plugins/plugin_mids.rb
+- lib/seqtrimnext/plugins/plugin_sanger_adapters.rb
 - lib/seqtrimnext/plugins/plugin_short_insert.rb
+- lib/seqtrimnext/plugins/plugin_user_contaminants.rb
 - lib/seqtrimnext/plugins/plugin_vectors.rb
+- lib/seqtrimnext/plugins_old/.DS_Store
+- lib/seqtrimnext/plugins_old/plugin_adapters_old.rb
+- lib/seqtrimnext/plugins_old/plugin_low_quality_old.rb
+- lib/seqtrimnext/plugins_old/plugin_rem_adit_artifacts.rb
 - lib/seqtrimnext/templates/amplicons.txt
-- lib/seqtrimnext/templates/sanger.txt
-- lib/seqtrimnext/templates/only_quality.txt
 - lib/seqtrimnext/templates/genomics_454.txt
 - lib/seqtrimnext/templates/genomics_454_with_paired.txt
 - lib/seqtrimnext/templates/genomics_short_reads.txt
 - lib/seqtrimnext/templates/genomics_short_reads_2.txt
+- lib/seqtrimnext/templates/only_quality.txt
+- lib/seqtrimnext/templates/sanger.txt
 - lib/seqtrimnext/templates/transcriptomics_454.txt
-- lib/seqtrimnext/templates/transcriptomics_short_reads.txt
 - lib/seqtrimnext/templates/transcriptomics_454_plants.txt
+- lib/seqtrimnext/templates/transcriptomics_short_reads.txt
 - lib/seqtrimnext/utils/extract_samples.rb
 - lib/seqtrimnext/utils/fasta2xml.rb
 - lib/seqtrimnext/utils/global_match.rb
@@ -398,45 +352,30 @@ files:
 - lib/seqtrimnext/utils/load_qual_in_hash.rb
 - lib/seqtrimnext/utils/recover_mid.rb
 - lib/seqtrimnext/utils/string_utils.rb
-- lib/seqtrimnext.rb
-- Manifest.txt
-- PostInstall.txt
-- Rakefile
-- README.rdoc
-- script/console
-- script/destroy
-- script/generate
-- test/test_helper.rb
-- test/test_seqtrimnext.rb
-- .gemtest
-homepage: http://www.scbi.uma.es/downloads
+- lib/seqtrimnext/version.rb
+- seqtrimnext.gemspec
+homepage: ''
 licenses:
 - MIT
-post_install_message: PostInstall.txt
-rdoc_options:
-- --main
-- README.rdoc
+metadata: {}
+post_install_message: 
+rdoc_options: []
 require_paths:
 - lib
 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: 1.8.23
+rubyforge_project: 
+rubygems_version: 2.4.8
 signing_key: 
-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
+specification_version: 4
+summary: Sequences preprocessing and cleaning software
+test_files: []

data/History.txt

@@ -1,130 +0,0 @@
-=== 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
-
-=== 2.0.56 2013-07-25
-
-added split_fasta.rb script
-
-=== 2.0.55 2013-07-23
-
-Sanger adapters plugin. Option to disable reject by indeterminations in the middle of a sequence.
-
-=== 2.0.54 2012-09-07
-
-* Flag to write fastq files as fastq.gz
-
-=== 2.0.53 2012-07-24
-
-* Added illumina adapters
-* Gzipped fastq files can be used with SeqtrimNext
-
-=== 2.0.52 2012-06-26
-
-* Added new plugin for user contaminants.
-* Sequences contaminated with user contaminants are stored in separate files.
-* Processing of both illumina fastq paired-end files in the same execution.
-* Template reorganization.
-
-=== 2.0.51 2012-06-20
-
-Added cont_viruses database
-
-=== 2.0.50 2012-06-13
-
-Added classification plugin
-
-=== 2.0.49 2012-05-24
-
-Updated gem dependencies
-
-=== 2.0.48 2012-05-16
-
-Select biggest sequence on cluster 
-
-=== 2.0.47 2012-05-14
-
-Added option for illumina qualities based on phred+64 scores
-
-=== 2.0.46 2012-04-13
-
-Checkpointing activated. Jobs can be restarted where stopped.
-
-=== 2.0.45 2012-03-05
-
-Improved LowComplexity plugin to ignore low complexity regions inside low qual regions
-
-=== 2.0.44 2012-02-23
-
-Skip output
-
-=== 2.0.43 2012-02-22
-
-Lower logger levels
-
-=== 2.0.42 2012-02-01
-
-Added custom cd-hit cmd parameters
-
-=== 2.0.41 2011-11-04
-
-Added extra adapters plugin for transcriptomics
-
-=== 2.0.40 2011-10-27
-
--Support Relative paths in user DB
--Can mix relative and absolute paths in user DB
--Custom linkers database
-
-=== 2.0.39 2011-07-07
-
-Fixed database list option
-
-=== 2.0.38 2011-07-07
-
-Optional Initial Stats generation in templates
-
-=== 2.0.37 2011-07-07
-
-Added option to skip initial stats
-
-=== 2.0.36 2011-06-24
-
-Added clustered installation documentation
-
-=== 2.0.35 2011-06-22
-
-FarAdapters improvement
-
-=== 2.0.34 2011-06-21
-
-Added some additional FAR AB_ADAPTER restrictions
-
-=== 2.0.33 2011-06-17
-
-Added SEQTRIMNEXT_INIT environment variable
-
-=== 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
-
-=== 2.0.30 2011-06-14
-
-Removed gnuplot as a prerequisite
-
-=== 2.0.29 2011-06-06
-
-* Initial public release on rubygems
-