bio-rdf 0.0.1 → 0.0.2

data/Rakefile

@@ -20,7 +20,7 @@ Jeweler::Tasks.new do |gem|
   gem.summary = %Q{Bioinformatics triple-store support}
   gem.description = %Q{Store relationships in a triple-store, such as gene enrichment and QTL, and use this information for inference and causality}
   gem.email = "pjotr.public01@thebird.nl"
-  gem.authors = ["Pjotr Prins", "Anurag Priyam"]
+  gem.authors = ["Pjotr Prins"]
   # dependencies defined in Gemfile
 end
 Jeweler::RubygemsDotOrgTasks.new

data/VERSION

@@ -1 +1 @@
-0.0.1
+0.0.2

data/lib/bio-rdf/parsers/gsea/broadgsea.rb

@@ -135,9 +135,12 @@ module BioRdf
           Dir.foreach(input) do |entry| # two step search, because of many dirs
             next if entry == '.' or entry == '..'
             log.info("Parsing directory "+entry)
-            resultfilenames = File.join(input,entry,"*SUMMARY.RESULTS.REPORT.[01].txt")
-            clsfilename = File.join(input,entry,"cls")
+            clsfilename = File.join(input,entry,"*cls")
+            clsfilename = Dir.glob(clsfilename)
+            raise "We need one cls file: #{clsfilename}" if clsfilename.size != 1
+            clsfilename = clsfilename[0]
             # log.info(resultfilenames)
+            resultfilenames = File.join(input,entry,"*SUMMARY.RESULTS.REPORT.[01].txt")
             Dir.glob(resultfilenames) do |fn|
               genotype = "A"
               genotype = "B" if fn =~ /1.txt/

metadata

@@ -1,20 +1,19 @@
 --- !ruby/object:Gem::Specification
 name: bio-rdf
 version: !ruby/object:Gem::Version
-  version: 0.0.1
+  version: 0.0.2
   prerelease: 
 platform: ruby
 authors:
 - Pjotr Prins
-- Anurag Priyam
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-05-01 00:00:00.000000000Z
+date: 2012-05-23 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio-logger
-  requirement: &15565000 !ruby/object:Gem::Requirement
+  requirement: &25421560 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -22,10 +21,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *15565000
+  version_requirements: *25421560
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &15564160 !ruby/object:Gem::Requirement
+  requirement: &25421080 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -33,10 +32,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *15564160
+  version_requirements: *25421080
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &15562720 !ruby/object:Gem::Requirement
+  requirement: &25420540 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -44,10 +43,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *15562720
+  version_requirements: *25420540
 - !ruby/object:Gem::Dependency
   name: cucumber
-  requirement: &15560480 !ruby/object:Gem::Requirement
+  requirement: &25420000 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -55,10 +54,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *15560480
+  version_requirements: *25420000
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &15559440 !ruby/object:Gem::Requirement
+  requirement: &25419480 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -66,10 +65,10 @@ dependencies:
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: *15559440
+  version_requirements: *25419480
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &15558220 !ruby/object:Gem::Requirement
+  requirement: &25418940 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -77,10 +76,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *15558220
+  version_requirements: *25418940
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &15557260 !ruby/object:Gem::Requirement
+  requirement: &25415260 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -88,10 +87,10 @@ dependencies:
         version: 1.8.3
   type: :development
   prerelease: false
-  version_requirements: *15557260
+  version_requirements: *25415260
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &15515240 !ruby/object:Gem::Requirement
+  requirement: &25414540 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -99,10 +98,10 @@ dependencies:
         version: 1.4.2
   type: :development
   prerelease: false
-  version_requirements: *15515240
+  version_requirements: *25414540
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &15514680 !ruby/object:Gem::Requirement
+  requirement: &25413440 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -110,7 +109,7 @@ dependencies:
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: *15514680
+  version_requirements: *25413440
 description: Store relationships in a triple-store, such as gene enrichment and QTL,
   and use this information for inference and causality
 email: pjotr.public01@thebird.nl
@@ -158,7 +157,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 4447990018592781869
+      hash: 4202591751013078134
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: