bio-bigbio 0.1.5 → 0.1.6

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 358cea2b69da2db20774ab98b4c0dfaa561b32c6
+  data.tar.gz: 1e1baca80f0aa0fd26d579e158aa88e0361493e9
+SHA512:
+  metadata.gz: ac532f773fd025ee927bfff89a96d142b2d9b9ca28f14a2bd368553a164026bd2530d4f4f95e2addcc30ae323d6b58ed5c30111335927c2e66630933ee16f75c
+  data.tar.gz: b228c3d346a4cf87f9fec71392336d9e66be1c721f8dae167553ecac5a92b689cd9420a0206ef31fee4dd4e9df43ea5a97472474a07cb4ed1da0bd553a013473

data/Gemfile

@@ -1,15 +1,11 @@
 source "http://rubygems.org"
-# Add dependencies required to use your gem here.
-# Example:
-#   gem "activesupport", ">= 2.3.5"
 gem "bio", ">= 1.4.1"
-gem "bio-logger", ">= 0.9.0"
+gem "bio-logger"
 
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.
 group :development do
-  gem "rspec", "~> 2.3.0"
-  gem "bundler", "~> 1.0.0"
-  gem "jeweler", "~> 1.5.2"
-  gem "rcov", ">= 0"
+  gem "rspec"
+  gem "bundler"
+  gem "jeweler"
 end

data/Gemfile.lock

@@ -1,34 +1,72 @@
 GEM
   remote: http://rubygems.org/
   specs:
-    bio (1.4.1)
-    bio-logger (0.9.0)
+    addressable (2.3.6)
+    bio (1.4.3)
+    bio-logger (1.0.1)
       log4r (>= 1.1.9)
-    diff-lcs (1.1.2)
-    git (1.2.5)
-    jeweler (1.5.2)
-      bundler (~> 1.0.0)
+    builder (3.2.2)
+    descendants_tracker (0.0.4)
+      thread_safe (~> 0.3, >= 0.3.1)
+    diff-lcs (1.1.3)
+    faraday (0.9.0)
+      multipart-post (>= 1.2, < 3)
+    git (1.2.6)
+    github_api (0.11.3)
+      addressable (~> 2.3)
+      descendants_tracker (~> 0.0.1)
+      faraday (~> 0.8, < 0.10)
+      hashie (>= 1.2)
+      multi_json (>= 1.7.5, < 2.0)
+      nokogiri (~> 1.6.0)
+      oauth2
+    hashie (2.1.1)
+    highline (1.6.21)
+    jeweler (2.0.1)
+      builder
+      bundler (>= 1.0)
       git (>= 1.2.5)
+      github_api
+      highline (>= 1.6.15)
+      nokogiri (>= 1.5.10)
       rake
-    log4r (1.1.9)
-    rake (0.8.7)
-    rcov (0.9.9)
-    rspec (2.3.0)
-      rspec-core (~> 2.3.0)
-      rspec-expectations (~> 2.3.0)
-      rspec-mocks (~> 2.3.0)
-    rspec-core (2.3.1)
-    rspec-expectations (2.3.0)
-      diff-lcs (~> 1.1.2)
-    rspec-mocks (2.3.0)
+      rdoc
+    json (1.8.1)
+    jwt (0.1.11)
+      multi_json (>= 1.5)
+    log4r (1.1.10)
+    mini_portile (0.5.3)
+    multi_json (1.9.3)
+    multi_xml (0.5.5)
+    multipart-post (2.0.0)
+    nokogiri (1.6.1)
+      mini_portile (~> 0.5.0)
+    oauth2 (0.9.3)
+      faraday (>= 0.8, < 0.10)
+      jwt (~> 0.1.8)
+      multi_json (~> 1.3)
+      multi_xml (~> 0.5)
+      rack (~> 1.2)
+    rack (1.5.2)
+    rake (10.3.1)
+    rdoc (4.1.1)
+      json (~> 1.4)
+    rspec (2.10.0)
+      rspec-core (~> 2.10.0)
+      rspec-expectations (~> 2.10.0)
+      rspec-mocks (~> 2.10.0)
+    rspec-core (2.10.1)
+    rspec-expectations (2.10.0)
+      diff-lcs (~> 1.1.3)
+    rspec-mocks (2.10.1)
+    thread_safe (0.3.3)
 
 PLATFORMS
   ruby
 
 DEPENDENCIES
   bio (>= 1.4.1)
-  bio-logger (>= 0.9.0)
-  bundler (~> 1.0.0)
-  jeweler (~> 1.5.2)
-  rcov
-  rspec (~> 2.3.0)
+  bio-logger
+  bundler
+  jeweler
+  rspec

data/LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright (c) 2011-2013 Pjotr Prins
+Copyright (c) 2011-2014 Pjotr Prins
 
 Permission is hereby granted, free of charge, to any person obtaining
 a copy of this software and associated documentation files (the

data/README.md

@@ -79,6 +79,12 @@ so to skip every other record
 fasta_filter.rb --filter "num % 2 == 0" 
 ```
 
+Find all sequences that contain a stop codon in the sequence
+
+```sh
+fasta_filter.rb --filter 'rec.seq =~ /\*./' aa.fa
+```
+
 Rewrite all sequences to lower case, you can use the useful rewrite
 option
 
@@ -86,7 +92,20 @@ option
 fasta_filter.rb --rewrite 'rec.seq = rec.seq.downcase'
 ```
 
-Filters and rewrites can be combined. The rest is up to your imagination!
+Rewrite the FASTA descriptors
+
+```sh
+fasta_filter.rb --rewrite 'rec.descr =~ /gene=(\S+)/; rec.descr = $1' test.fa
+```
+
+Filters and rewrites can be combined. The rest is up to your
+imagination! One final example to remove low quality sequences from an
+amino acid file (one amino acid dominates):
+
+```sh
+fasta_filter.rb --filter "count = {} ; rec.seq.each_char { |c| count[c] ||= 1 ; count[c] += 1 }; count.values.max.to_f/rec.seq.size < 0.30" < aa.fa > aa1.fa
+```
+
 
 # API Examples
 
@@ -227,9 +246,9 @@ If you use this software, please cite one of
 
 # Biogems.info
 
-This Biogem is published at [#bio-table](http://biogems.info/index.html)
+This Biogem is published on [biogems.info](http://biogems.info/index.html#bigbio)
 
 # Copyright
 
-Copyright (c) 2011-2013 Pjotr Prins. See LICENSE for further details.
+Copyright (c) 2011-2014 Pjotr Prins. See LICENSE for further details.
 

data/Rakefile

@@ -40,7 +40,7 @@ end
 task :test => :spec
 task :default => :spec
 
-require 'rake/rdoctask'
+require 'rdoc/task'
 Rake::RDocTask.new do |rdoc|
   version = File.exist?('VERSION') ? File.read('VERSION') : ""
 

data/VERSION

@@ -1 +1 @@
-0.1.5
+0.1.6

data/bin/fasta_filter.rb

@@ -60,6 +60,8 @@ class OptParser
       opts.separator "  fasta_filter.rb --filter \"rec.descr =~ /C. elegans/\" test/data/fasta/nt.fa"
       opts.separator "  fasta_filter.rb --filter \"num % 2 == 0\" test/data/fasta/nt.fa"
       opts.separator "  fasta_filter.rb test/data/fasta/nt.fa --rewrite 'rec.seq.downcase!'"
+      opts.separator "  fasta_filter.rb --rewrite 'rec.descr =~ /gene=(\S+)/; rec.descr = $1' test.fa"
+      opts.separator "  fasta_filter.rb --filter 'rec.seq =~ /\*./' aa.fa"
       opts.separator ""
       opts.separator "Other options:"
       opts.separator ""

data/bin/getorf

@@ -1,4 +1,4 @@
-#! /usr/bin/ruby
+#! /usr/bin/env ruby
 #
 # Predict ORF's from nucleotide sequences using the BigBio predictors. 
 # The input is a fasta file, the output consists of

data/bin/nt2aa.rb

@@ -1,4 +1,4 @@
-#! /usr/bin/ruby
+#! /usr/bin/env ruby
 #
 # Translate nucleotide sequences into aminoacids sequences in all 
 # reading frames.

data/bio-bigbio.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "bio-bigbio"
-  s.version = "0.1.5"
+  s.version = "0.1.6"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Pjotr Prins"]
-  s.date = "2013-05-03"
+  s.date = "2014-05-16"
   s.description = "Fasta reader, ORF emitter, sequence translation"
   s.email = "pjotr.public01@thebird.nl"
   s.executables = ["fasta_filter.rb", "fasta_sort.rb", "getorf", "nt2aa.rb"]
@@ -63,44 +63,31 @@ Gem::Specification.new do |s|
   s.homepage = "http://github.com/pjotrp/bigbio"
   s.licenses = ["MIT"]
   s.require_paths = ["lib"]
-  s.rubygems_version = "1.8.10"
+  s.rubygems_version = "1.8.23"
   s.summary = "Low memory sequence emitters"
-  s.test_files = [
-    "spec/emitter_spec.rb",
-    "spec/predictorf_spec.rb",
-    "test/doctest/test_fasta.rb",
-    "test/doctest/test_frames.rb",
-    "test/doctest/test_getorf.rb",
-    "test/doctest/test_paired.rb",
-    "test/performance/translate_with_biolib.rb",
-    "test/performance/translate_with_bioruby.rb"
-  ]
 
   if s.respond_to? :specification_version then
     s.specification_version = 3
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<bio>, [">= 1.4.1"])
-      s.add_runtime_dependency(%q<bio-logger>, [">= 0.9.0"])
-      s.add_development_dependency(%q<rspec>, ["~> 2.3.0"])
-      s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
-      s.add_development_dependency(%q<jeweler>, ["~> 1.5.2"])
-      s.add_development_dependency(%q<rcov>, [">= 0"])
+      s.add_runtime_dependency(%q<bio-logger>, [">= 0"])
+      s.add_development_dependency(%q<rspec>, [">= 0"])
+      s.add_development_dependency(%q<bundler>, [">= 0"])
+      s.add_development_dependency(%q<jeweler>, [">= 0"])
     else
       s.add_dependency(%q<bio>, [">= 1.4.1"])
-      s.add_dependency(%q<bio-logger>, [">= 0.9.0"])
-      s.add_dependency(%q<rspec>, ["~> 2.3.0"])
-      s.add_dependency(%q<bundler>, ["~> 1.0.0"])
-      s.add_dependency(%q<jeweler>, ["~> 1.5.2"])
-      s.add_dependency(%q<rcov>, [">= 0"])
+      s.add_dependency(%q<bio-logger>, [">= 0"])
+      s.add_dependency(%q<rspec>, [">= 0"])
+      s.add_dependency(%q<bundler>, [">= 0"])
+      s.add_dependency(%q<jeweler>, [">= 0"])
     end
   else
     s.add_dependency(%q<bio>, [">= 1.4.1"])
-    s.add_dependency(%q<bio-logger>, [">= 0.9.0"])
-    s.add_dependency(%q<rspec>, ["~> 2.3.0"])
-    s.add_dependency(%q<bundler>, ["~> 1.0.0"])
-    s.add_dependency(%q<jeweler>, ["~> 1.5.2"])
-    s.add_dependency(%q<rcov>, [">= 0"])
+    s.add_dependency(%q<bio-logger>, [">= 0"])
+    s.add_dependency(%q<rspec>, [">= 0"])
+    s.add_dependency(%q<bundler>, [">= 0"])
+    s.add_dependency(%q<jeweler>, [">= 0"])
   end
 end
 

data/lib/bigbio.rb

@@ -22,7 +22,7 @@ begin
   Bio::Big::Environment.instance.biolib = true
 rescue LoadError
   log.outputters = Bio::Log::Outputter.stderr
-  log.warn "BioLib functionality not loaded"
+  log.debug "BioLib functionality not loaded"
 end
 
 require 'bio'

data/spec/emitter_spec.rb

@@ -10,7 +10,7 @@ describe Bio::Big::FastaEmitter, "when using the emitter" do
 
   it "should emit small parts" do
     s = ""
-    FastaEmitter.new("test/data/fasta/nt.fa",10).emit_seq do | part, index, tag, seq |
+    Bio::Big::FastaEmitter.new("test/data/fasta/nt.fa",10).emit_seq do | part, index, tag, seq |
       # p [index, part, tag, seq]
       s += seq
       if index == 95 and part == :tail
@@ -38,7 +38,7 @@ describe Bio::Big::FastaEmitter, "when using the emitter" do
   end
 
   it "should emit large parts" do 
-    FastaEmitter.new("test/data/fasta/nt.fa").emit_seq do | part, index, tag, seq |
+    Bio::Big::FastaEmitter.new("test/data/fasta/nt.fa").emit_seq do | part, index, tag, seq |
       # p [index, part, tag, seq]
       if index == 95
         seq.should == "ATCATTAGCAACACCAGCTTCCTCTCTCTCGCTTCAAAGTTCACTACTCGTGGATCTCGTCTTCAGTGTACAGTATCAAGGGCTCGATCTGCGGTGGATGAGACATCAGATTCAGGAGCTTTTCAAAGAACTGCATCGACATCCGTAACTTCGTTTCAAAAGATTCCAATTCTCAGTTTCAGCTGAATCTGGTAGATACCATCTTTACATATCGTATGCTTGTCATGGGCTTCTAGATGCCTTTCATACTTAAAGATCAAAGGACTTGACGATGCAATAAGCTTCTCGTCTGTAAAACCC"
@@ -47,12 +47,12 @@ describe Bio::Big::FastaEmitter, "when using the emitter" do
   end
 end
 
-describe Bio::Big::ShortFrameState, "when using the ShortFrameState" do
+describe Bio::Big::ShortFrameState, "when using the Bio::Big::ShortFrameState" do
 
   include Bio::Big
   
   it "should find an ORF" do
-    fr = ShortFrameState.new "atggattaaatgtaatggatttaatgtaaa",0,0
+    fr = Bio::Big::ShortFrameState.new "atggattaaatgtaatggatttaatgtaaa",0,0
     orfs = fr.get_stopstop_orfs
     orfs.map{ | orf | orf.pos }.should == [ 3, 5 ]
     orfs.map{ | orf | orf.to_seq }.should == ["ATGTAA", "TGGATTTAA"]
@@ -61,14 +61,14 @@ describe Bio::Big::ShortFrameState, "when using the ShortFrameState" do
     orfs.map{ | orf | orf.to_seq }.should == ["ATGGATTAA","ATGTAA"]
   end
   it "should handle min_size" do
-    fr = ShortFrameState.new "atggattaaatgtaatggatttaatgtaaa",0,9
+    fr = Bio::Big::ShortFrameState.new "atggattaaatgtaatggatttaatgtaaa",0,9
     orfs = fr.get_stopstop_orfs
     orfs.map{ | orf | orf.to_seq }.should == [ "TGGATTTAA"]
     orfs.map{ | orf | orf.pos }.should == [ 5 ]
     fr.get_startstop_orfs.should == []
   end
   it "should find ORFs in" do
-    fr = ShortFrameState.new "atgttttaaatgtaatgttgttaaatgttttaaatgtaatgttgttaa",0,0
+    fr = Bio::Big::ShortFrameState.new "atgttttaaatgtaatgttgttaaatgttttaaatgtaatgttgttaa",0,0
     orfs = fr.get_stopstop_orfs
     orfs.map{ | orf | orf.to_seq }.should ==  ["ATGTAA", "TGTTGTTAA", "ATGTTTTAA", "ATGTAA", "TGTTGTTAA"]
     orfs.map{ | orf | orf.pos }.should == [3, 5, 8, 11, 13]
@@ -108,17 +108,17 @@ describe Bio::Big::ShortFrameState, "when using the ShortFrameState" do
 
     # Frame 0
     minsize = 0
-    fr = ShortFrameState.new s,0,minsize
+    fr = Bio::Big::ShortFrameState.new s,0,minsize
     orfs = fr.get_stopstop_orfs
     orfs.map{ | orf | orf.to_seq }.should == []
 
     # Frame 1
-    fr = ShortFrameState.new s[1..-1],0,minsize
+    fr = Bio::Big::ShortFrameState.new s[1..-1],0,minsize
     os = fr.get_stopstop_orfs
     os.map{ | orf | orf.to_seq }.should == ["TTNCGCGTGCCGCCTTCTTTCTCCTTTTTCTCTTTTACTTCTTCATCATCATCTTCTTCTTCTTCCTCTTCGATATTCGTCAGTGTGTGTATTTTGGGGAAAACTTTGTGA"]
     orfs += os
     # Frame 2
-    fr = ShortFrameState.new s[2..-1],0,minsize
+    fr = Bio::Big::ShortFrameState.new s[2..-1],0,minsize
     os = fr.get_stopstop_orfs
     os.map{ | orf | orf.to_seq }.should == ["GCGGANCGGTAA", "GAAAATCGCGGATGTGGCTTTCAAAGCTTCAAGGACTATCGATTGGGATGGTATGGCTAA", "GGTCCTTGTCACAGATGA", "GGCTCGTAG"]
     orfs += os
@@ -132,14 +132,14 @@ describe Bio::Big::ShortFrameState, "when using the ShortFrameState" do
 
     # Frame 0
     minsize = 0
-    fr = ShortFrameState.new s,0,minsize
+    fr = Bio::Big::ShortFrameState.new s,0,minsize
     orfs = fr.get_startstop_orfs
 
     # Frame 1
-    fr = ShortFrameState.new s[1..-1],0,minsize
+    fr = Bio::Big::ShortFrameState.new s[1..-1],0,minsize
     orfs += fr.get_startstop_orfs
     # Frame 2
-    fr = ShortFrameState.new s[2..-1],0,minsize
+    fr = Bio::Big::ShortFrameState.new s[2..-1],0,minsize
     orfs += fr.get_startstop_orfs
     orfs.map{ | orf | orf.to_seq }.should == []
     orfs.size.should == 0
@@ -151,11 +151,11 @@ describe Bio::Big::ShortFrameState, "when combining frames" do
   it "should combine a forward frame" do
     s1 = "atggattaaatgtaata"
     s2 = "atggatttaatgtaaa"
-    fr = ShortFrameState.new s1,0,0
+    fr = Bio::Big::ShortFrameState.new s1,0,0
     fr.ntseq_pos.should == 0
     orfs = fr.get_stopstop_orfs
     orfs.size == 1 # in codons
-    fr3 = FrameCodonHelpers::CreateShortFrame.create_right(fr,orfs,s2)
+    fr3 = Bio::Big::FrameCodonHelpers::CreateShortFrame.create_right(fr,orfs,s2)
     fr3.ntseq_pos.should == 15
     fr3.codons.to_seq.should == "TAATGGATTTAATGTAAA"
     norfs = fr3.get_stopstop_orfs
@@ -169,11 +169,11 @@ describe Bio::Big::ShortFrameState, "when combining frames" do
     #     ......---===xx
     s2 = "atggatttaattattataaa"
     #     x======xxx======xxx.
-    fr = ShortFrameState.new s1,0,0
+    fr = Bio::Big::ShortFrameState.new s1,0,0
     fr.ntseq_pos.should == 0
     orfs = fr.get_stopstop_orfs
     orfs.size == 0 # in codons
-    fr3 = FrameCodonHelpers::CreateShortFrame.create_right(fr,orfs,s2)
+    fr3 = Bio::Big::FrameCodonHelpers::CreateShortFrame.create_right(fr,orfs,s2)
     fr3.ntseq_pos.should == 0
     fr3.codons.to_seq.should == "ATGGATTAAATGTAATGGATTTAATTATTATAA"
     norfs = fr3.get_stopstop_orfs
@@ -187,11 +187,11 @@ describe Bio::Big::ShortFrameState, "when combining frames" do
     #     ......---===xx
     s2 = "atggatttaatgtaaa"
     #     x======xxx
-    fr = ShortFrameState.new s1,0,0
+    fr = Bio::Big::ShortFrameState.new s1,0,0
     fr.ntseq_pos.should == 0
     orfs = fr.get_stopstop_orfs
     orfs.size == 0 # in codons
-    fr3 = FrameCodonHelpers::CreateShortFrame.create_right(fr,orfs,s2)
+    fr3 = Bio::Big::FrameCodonHelpers::CreateShortFrame.create_right(fr,orfs,s2)
     # p fr3
     fr3.ntseq_pos.should == 0 # on the combined sequences
     fr3.codons.to_seq.should == "ATGGATTAAATGTAATGGATTTAATGTAAA"
@@ -221,14 +221,14 @@ describe Bio::Big::ShortFrameState, "when combining frames" do
     s1 = "atggattaaatgta"
     #     ......xxx=====
     # now move the other way, as sequences get emitted on the left
-    fr = ShortReversedFrameState.new s2,0,0
+    fr = Bio::Big::ShortReversedFrameState.new s2,0,0
     # p fr
     fr.codons.to_seq.should == "ATTTAAATGGATTTAATGTAAATT"
     fr.ntseq_pos.should == 0
     orfs = fr.get_stopstop_orfs
     orfs.map{ | orf | orf.to_seq }.should == ["ATGGATTTAATGTAA"]
     orfs.first.pos.should == 2 # in codons
-    fr3 = FrameCodonHelpers::CreateShortFrame.create_left(fr,orfs,s1)
+    fr3 = Bio::Big::FrameCodonHelpers::CreateShortFrame.create_left(fr,orfs,s1)
     fr3.ntseq_pos.should == 18 # 6 codons
     fr3.codons.to_seq.should == "ATGGATTAAATGTATATTTAA"
     norfs = fr3.get_stopstop_orfs
@@ -244,9 +244,9 @@ describe Bio::Big::OrfEmitter, "when using the ORF emitter" do
   include Bio::Big
 
   it "should emit STOP-STOP ORFs in all frames" do
-    f = FastaEmitter.new("test/data/fasta/nt.fa")
+    f = Bio::Big::FastaEmitter.new("test/data/fasta/nt.fa")
     seqs = []
-    OrfEmitter.new(f,:stopstop)::emit_seq do | frame, index, tag, pos, seq |
+    Bio::Big::OrfEmitter.new(f,:stopstop)::emit_seq do | frame, index, tag, pos, seq |
       break if index != 0
       if frame == 0 and index == 0 and pos == 39
         seq.should == "TTNCGCGTGCCGCCTTCTTTCTCCTTTTTCTCTTTTACTTCTTCATCATCATCTTCTTCTTCTTCCTCTTCGATATTCGTCAGTGTGTGTATTTTGGGGAAAACTTTGTGA"
@@ -259,9 +259,9 @@ describe Bio::Big::OrfEmitter, "when using the ORF emitter" do
     seqs.join(';')[50..350].should == "TNCGCGTGCCGCCTTCTTTCTCCTTTTTCTCTTTTACTTCTTCATCATCATCTTCTTCTTCTTCCTCTTCGATATTCGTCAGTGTGTGTATTTTGGGGAAAACTTTGTGA;GCAAAGAGCGAGAAAATGAGCGGANCGGTAAGAAAATCGCGGATGTGGCTTTCAAAGCTTCAAGGACTATCGATTGGGATGGTATGGCTAAGGTCCTTGTCACAGATGAGGCTCGTAGAGAGTTCTCTAACCTTCGTCGTGCTTTCGATGAGGTTAACACACAGCTCCAGACCAAATTTAGTCAGGACCT"
   end
   it "should emit STOP-STOP ORFs in all frames using a shorter emitter" do
-    f = FastaEmitter.new("test/data/fasta/nt.fa",150)
+    f = Bio::Big::FastaEmitter.new("test/data/fasta/nt.fa",150)
     seqs = []
-    OrfEmitter.new(f,:stopstop)::emit_seq do | frame, index, tag, pos, seq |
+    Bio::Big::OrfEmitter.new(f,:stopstop)::emit_seq do | frame, index, tag, pos, seq |
       break if index != 0
       if frame == 0 and index == 0 and pos == 39
         seq.should == "TTNCGCGTGCCGCCTTCTTTCTCCTTTTTCTCTTTTACTTCTTCATCATCATCTTCTTCTTCTTCCTCTTCGATATTCGTCAGTGTGTGTATTTTGGGGAAAACTTTGTGA"

data/test/performance/translate_with_biolib.rb

@@ -1,4 +1,4 @@
-#! /usr/bin/ruby
+#! /usr/bin/env ruby
 #
 # Performance testing routing for translating a FASTA file into six
 # reading frames using the Biolib (EMBOSS) routines.

data/test/performance/translate_with_bioruby.rb

@@ -1,4 +1,4 @@
-#! /usr/bin/ruby
+#! /usr/bin/env ruby
 #
 # Performance testing routing for translating a FASTA file into six
 # reading frames using the Bioruby routines.

metadata

@@ -1,82 +1,85 @@
 --- !ruby/object:Gem::Specification
 name: bio-bigbio
 version: !ruby/object:Gem::Version
-  version: 0.1.5
-  prerelease: 
+  version: 0.1.6
 platform: ruby
 authors:
 - Pjotr Prins
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-05-03 00:00:00.000000000Z
+date: 2014-05-16 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &27203900 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.4.1
   type: :runtime
   prerelease: false
-  version_requirements: *27203900
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.4.1
 - !ruby/object:Gem::Dependency
   name: bio-logger
-  requirement: &27203120 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
-        version: 0.9.0
+        version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *27203120
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &27202300 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version
-        version: 2.3.0
+        version: '0'
   type: :development
   prerelease: false
-  version_requirements: *27202300
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &27201380 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version
-        version: 1.0.0
+        version: '0'
   type: :development
   prerelease: false
-  version_requirements: *27201380
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &27200760 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version
-        version: 1.5.2
+        version: '0'
   type: :development
   prerelease: false
-  version_requirements: *27200760
-- !ruby/object:Gem::Dependency
-  name: rcov
-  requirement: &27199840 !ruby/object:Gem::Requirement
-    none: false
+  version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: *27199840
 description: Fasta reader, ORF emitter, sequence translation
 email: pjotr.public01@thebird.nl
 executables:
@@ -89,7 +92,7 @@ extra_rdoc_files:
 - LICENSE.txt
 - README.md
 files:
-- .travis.yml
+- ".travis.yml"
 - Gemfile
 - Gemfile.lock
 - LICENSE.txt
@@ -133,37 +136,26 @@ files:
 homepage: http://github.com/pjotrp/bigbio
 licenses:
 - MIT
+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'
-      segments:
-      - 0
-      hash: 2941883289909211187
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.10
+rubygems_version: 2.0.3
 signing_key: 
 specification_version: 3
 summary: Low memory sequence emitters
-test_files:
-- spec/emitter_spec.rb
-- spec/predictorf_spec.rb
-- test/doctest/test_fasta.rb
-- test/doctest/test_frames.rb
-- test/doctest/test_getorf.rb
-- test/doctest/test_paired.rb
-- test/performance/translate_with_biolib.rb
-- test/performance/translate_with_bioruby.rb
+test_files: []
+has_rdoc: