bio-ngs 0.4.6.alpha.01 → 0.4.6.alpha.02

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-ngs
 version: !ruby/object:Gem::Version
-  version: 0.4.6.alpha.01
+  version: 0.4.6.alpha.02
   prerelease: 6
 platform: ruby
 authors:
@@ -10,11 +10,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-03-21 00:00:00.000000000 Z
+date: 2012-05-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &2166120140 !ruby/object:Gem::Requirement
+  requirement: &2153665000 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -22,10 +22,10 @@ dependencies:
         version: 1.4.2
   type: :runtime
   prerelease: false
-  version_requirements: *2166120140
+  version_requirements: *2153665000
 - !ruby/object:Gem::Dependency
   name: bio-samtools
-  requirement: &2166117920 !ruby/object:Gem::Requirement
+  requirement: &2153664500 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -33,21 +33,21 @@ dependencies:
         version: 0.3.2
   type: :runtime
   prerelease: false
-  version_requirements: *2166117920
+  version_requirements: *2153664500
 - !ruby/object:Gem::Dependency
   name: thor
-  requirement: &2166248820 !ruby/object:Gem::Requirement
+  requirement: &2153795800 !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ! '>='
+    - - =
       - !ruby/object:Gem::Version
         version: 0.14.6
   type: :runtime
   prerelease: false
-  version_requirements: *2166248820
+  version_requirements: *2153795800
 - !ruby/object:Gem::Dependency
   name: rubyvis
-  requirement: &2166247760 !ruby/object:Gem::Requirement
+  requirement: &2153795320 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -55,10 +55,10 @@ dependencies:
         version: 0.5.0
   type: :runtime
   prerelease: false
-  version_requirements: *2166247760
+  version_requirements: *2153795320
 - !ruby/object:Gem::Dependency
   name: daemons
-  requirement: &2166246800 !ruby/object:Gem::Requirement
+  requirement: &2153794840 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -66,10 +66,10 @@ dependencies:
         version: 1.1.0
   type: :runtime
   prerelease: false
-  version_requirements: *2166246800
+  version_requirements: *2153794840
 - !ruby/object:Gem::Dependency
   name: ruby-ensembl-api
-  requirement: &2166245540 !ruby/object:Gem::Requirement
+  requirement: &2153794300 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -77,10 +77,10 @@ dependencies:
         version: 1.0.1
   type: :runtime
   prerelease: false
-  version_requirements: *2166245540
+  version_requirements: *2153794300
 - !ruby/object:Gem::Dependency
   name: activerecord
-  requirement: &2166244540 !ruby/object:Gem::Requirement
+  requirement: &2153793160 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -88,10 +88,10 @@ dependencies:
         version: 3.0.5
   type: :runtime
   prerelease: false
-  version_requirements: *2166244540
+  version_requirements: *2153793160
 - !ruby/object:Gem::Dependency
   name: sqlite3
-  requirement: &2166243560 !ruby/object:Gem::Requirement
+  requirement: &2153791580 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -99,10 +99,10 @@ dependencies:
         version: 1.3.3
   type: :runtime
   prerelease: false
-  version_requirements: *2166243560
+  version_requirements: *2153791580
 - !ruby/object:Gem::Dependency
   name: bio-blastxmlparser
-  requirement: &2166242560 !ruby/object:Gem::Requirement
+  requirement: &2153790980 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -110,10 +110,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *2166242560
+  version_requirements: *2153790980
 - !ruby/object:Gem::Dependency
   name: progressbar
-  requirement: &2166241680 !ruby/object:Gem::Requirement
+  requirement: &2153790500 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -121,10 +121,10 @@ dependencies:
         version: 0.9.0
   type: :runtime
   prerelease: false
-  version_requirements: *2166241680
+  version_requirements: *2153790500
 - !ruby/object:Gem::Dependency
   name: rake
-  requirement: &2166257200 !ruby/object:Gem::Requirement
+  requirement: &2153789980 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - =
@@ -132,10 +132,10 @@ dependencies:
         version: 0.9.2.2
   type: :runtime
   prerelease: false
-  version_requirements: *2166257200
+  version_requirements: *2153789980
 - !ruby/object:Gem::Dependency
   name: json
-  requirement: &2166255420 !ruby/object:Gem::Requirement
+  requirement: &2153789440 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -143,10 +143,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *2166255420
+  version_requirements: *2153789440
 - !ruby/object:Gem::Dependency
   name: parallel
-  requirement: &2166252880 !ruby/object:Gem::Requirement
+  requirement: &2153788960 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -154,10 +154,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *2166252880
+  version_requirements: *2153788960
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &2166375840 !ruby/object:Gem::Requirement
+  requirement: &2153788480 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -165,10 +165,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2166375840
+  version_requirements: *2153788480
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2166373980 !ruby/object:Gem::Requirement
+  requirement: &2153787960 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -176,10 +176,10 @@ dependencies:
         version: 1.1.0
   type: :development
   prerelease: false
-  version_requirements: *2166373980
+  version_requirements: *2153787960
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &2166373320 !ruby/object:Gem::Requirement
+  requirement: &2153846060 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -187,10 +187,10 @@ dependencies:
         version: 1.8.3
   type: :development
   prerelease: false
-  version_requirements: *2166373320
+  version_requirements: *2153846060
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &2166372800 !ruby/object:Gem::Requirement
+  requirement: &2153845580 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -198,10 +198,10 @@ dependencies:
         version: 0.9.11
   type: :development
   prerelease: false
-  version_requirements: *2166372800
+  version_requirements: *2153845580
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &2166379100 !ruby/object:Gem::Requirement
+  requirement: &2153844960 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -209,21 +209,21 @@ dependencies:
         version: 1.4.2
   type: :development
   prerelease: false
-  version_requirements: *2166379100
+  version_requirements: *2153844960
 - !ruby/object:Gem::Dependency
   name: thor
-  requirement: &2166377460 !ruby/object:Gem::Requirement
+  requirement: &2153844140 !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ! '>='
+    - - =
       - !ruby/object:Gem::Version
         version: 0.14.6
   type: :development
   prerelease: false
-  version_requirements: *2166377460
+  version_requirements: *2153844140
 - !ruby/object:Gem::Dependency
   name: ffi
-  requirement: &2166391740 !ruby/object:Gem::Requirement
+  requirement: &2153843400 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -231,10 +231,10 @@ dependencies:
         version: 1.0.6
   type: :development
   prerelease: false
-  version_requirements: *2166391740
+  version_requirements: *2153843400
 - !ruby/object:Gem::Dependency
   name: rubyvis
-  requirement: &2166390020 !ruby/object:Gem::Requirement
+  requirement: &2153842920 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -242,10 +242,10 @@ dependencies:
         version: 0.5.0
   type: :development
   prerelease: false
-  version_requirements: *2166390020
+  version_requirements: *2153842920
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &2166388100 !ruby/object:Gem::Requirement
+  requirement: &2153842440 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -253,10 +253,10 @@ dependencies:
         version: 2.5.0
   type: :development
   prerelease: false
-  version_requirements: *2166388100
+  version_requirements: *2153842440
 - !ruby/object:Gem::Dependency
   name: daemons
-  requirement: &2166386680 !ruby/object:Gem::Requirement
+  requirement: &2153841880 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -264,10 +264,10 @@ dependencies:
         version: 1.1.0
   type: :development
   prerelease: false
-  version_requirements: *2166386680
+  version_requirements: *2153841880
 - !ruby/object:Gem::Dependency
   name: bio-samtools
-  requirement: &2166386000 !ruby/object:Gem::Requirement
+  requirement: &2153841380 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -275,10 +275,10 @@ dependencies:
         version: 0.3.2
   type: :development
   prerelease: false
-  version_requirements: *2166386000
+  version_requirements: *2153841380
 - !ruby/object:Gem::Dependency
   name: ruby-ensembl-api
-  requirement: &2166385360 !ruby/object:Gem::Requirement
+  requirement: &2153840900 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -286,10 +286,10 @@ dependencies:
         version: 1.0.1
   type: :development
   prerelease: false
-  version_requirements: *2166385360
+  version_requirements: *2153840900
 - !ruby/object:Gem::Dependency
   name: activerecord
-  requirement: &2166400500 !ruby/object:Gem::Requirement
+  requirement: &2153840400 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -297,10 +297,10 @@ dependencies:
         version: 3.0.5
   type: :development
   prerelease: false
-  version_requirements: *2166400500
+  version_requirements: *2153840400
 - !ruby/object:Gem::Dependency
   name: sqlite3
-  requirement: &2166399280 !ruby/object:Gem::Requirement
+  requirement: &2153839920 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -308,10 +308,10 @@ dependencies:
         version: 1.3.3
   type: :development
   prerelease: false
-  version_requirements: *2166399280
+  version_requirements: *2153839920
 - !ruby/object:Gem::Dependency
   name: bio-blastxmlparser
-  requirement: &2166397820 !ruby/object:Gem::Requirement
+  requirement: &2153839360 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -319,10 +319,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2166397820
+  version_requirements: *2153839360
 - !ruby/object:Gem::Dependency
   name: progressbar
-  requirement: &2166397040 !ruby/object:Gem::Requirement
+  requirement: &2153838840 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -330,10 +330,10 @@ dependencies:
         version: 0.9.0
   type: :development
   prerelease: false
-  version_requirements: *2166397040
+  version_requirements: *2153838840
 - !ruby/object:Gem::Dependency
   name: json
-  requirement: &2166396420 !ruby/object:Gem::Requirement
+  requirement: &2153838360 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -341,10 +341,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2166396420
+  version_requirements: *2153838360
 - !ruby/object:Gem::Dependency
   name: rake
-  requirement: &2166395200 !ruby/object:Gem::Requirement
+  requirement: &2153897220 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - =
@@ -352,10 +352,10 @@ dependencies:
         version: 0.9.2.2
   type: :development
   prerelease: false
-  version_requirements: *2166395200
+  version_requirements: *2153897220
 - !ruby/object:Gem::Dependency
   name: parallel
-  requirement: &2166394460 !ruby/object:Gem::Requirement
+  requirement: &2153896700 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -363,7 +363,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2166394460
+  version_requirements: *2153896700
 description: bio-ngs provides a framework for handling NGS data with BioRuby
 email: francesco.strozzi@gmail.com
 executables:
@@ -384,6 +384,11 @@ files:
 - bin/biongs
 - bio-ngs.gemspec
 - ext/mkrf_conf.rb
+- features/cufflinks_gtf_parser.feature
+- features/cufflinks_gtf_parser_indexing.feature
+- features/step_definitions/cufflinks_gtf.rb
+- features/step_definitions/cufflinks_gtf_parser_indexing.rb
+- features/support/env.rb
 - lib/bio-ngs.rb
 - lib/bio/appl/ngs/bcftools.rb
 - lib/bio/appl/ngs/bcl2qseq.rb
@@ -391,6 +396,9 @@ files:
 - lib/bio/appl/ngs/bowtie-inspect.rb
 - lib/bio/appl/ngs/bwa.rb
 - lib/bio/appl/ngs/cufflinks.rb
+- lib/bio/appl/ngs/cufflinks/gtf/gtf.rb
+- lib/bio/appl/ngs/cufflinks/gtf/gtf_parser.rb
+- lib/bio/appl/ngs/cufflinks/gtf/transcript.rb
 - lib/bio/appl/ngs/cufflinks/iterators.rb
 - lib/bio/appl/ngs/fastx.rb
 - lib/bio/appl/ngs/samtools.rb
@@ -412,8 +420,13 @@ files:
 - lib/bio/ngs/ext/bin/linux/samtools
 - lib/bio/ngs/ext/bin/osx/samtools
 - lib/bio/ngs/ext/versions.yaml
+- lib/bio/ngs/fs.rb
 - lib/bio/ngs/graphics.rb
 - lib/bio/ngs/homology.rb
+- lib/bio/ngs/illumina/fastq.rb
+- lib/bio/ngs/illumina/illumina.rb
+- lib/bio/ngs/illumina/project.rb
+- lib/bio/ngs/illumina/sample.rb
 - lib/bio/ngs/ontology.rb
 - lib/bio/ngs/quality.rb
 - lib/bio/ngs/record.rb
@@ -421,6 +434,7 @@ files:
 - lib/bio/ngs/utils.rb
 - lib/development_tasks.rb
 - lib/enumerable.rb
+- lib/meta.rb
 - lib/tasks/bwa.thor
 - lib/tasks/convert.thor
 - lib/tasks/filter.thor
@@ -435,8 +449,22 @@ files:
 - lib/templates/README.tt
 - lib/templates/db.tt
 - lib/wrapper.rb
+- spec/bio/ngs/fs_spec.rb
+- spec/bio/ngs/illumina/fastq_spec.rb
+- spec/bio/ngs/illumina/illumina_spec.rb
+- spec/bio/ngs/illumina/project_spec.rb
+- spec/bio/ngs/illumina/sample_spec.rb
+- spec/bio/ngs/illumina/samples_spec.rb
 - spec/converter_qseq_spec.rb
+- spec/filter_spec.rb
 - spec/fixture/s_1_1_1108_qseq.txt
+- spec/fixture/table_filter_list.txt
+- spec/fixture/table_filter_list_first_column.txt
+- spec/fixture/table_filter_source.tsv
+- spec/fixture/test-filtered-reference.fastq.gz
+- spec/fixture/test-merged-reference.fastq.gz
+- spec/fixture/test.fastq.gz
+- spec/meta_spec.rb
 - spec/quality_spec.rb
 - spec/sff_extract_spec.rb
 - spec/spec_helper.rb
@@ -469,7 +497,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -1654016565511947688
+      hash: -1070352367343550027
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: