Fixed tests; release

pjotrp · May 16, 2014 · cbb6d8a · cbb6d8a
1 parent 75321bf
commit cbb6d8a
Show file tree

Hide file tree

Showing 11 changed files with 96 additions and 62 deletions.
diff --git a/Gemfile b/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
diff --git a/Gemfile.lock b/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
diff --git a/LICENSE.txt b/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

diff --git a/README.md b/README.md
@@ -250,5 +250,5 @@ 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.
 
diff --git a/Rakefile b/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') : ""
 

diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-0.1.5
+0.1.6
diff --git a/bin/getorf b/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

diff --git a/bin/nt2aa.rb b/bin/nt2aa.rb
@@ -1,4 +1,4 @@
-#! /usr/bin/ruby
+#! /usr/bin/env ruby
 #
 # Translate nucleotide sequences into aminoacids sequences in all 
 # reading frames.

diff --git a/spec/emitter_spec.rb b/spec/emitter_spec.rb
@@ -10,7 +10,7 @@
 
   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 @@
   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 @@
   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 @@
     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 @@
 
     # 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 @@
 
     # 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 @@
   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 @@
     #     ......---===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 @@
     #     ......---===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 @@
     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 @@
   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 @@
     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"

diff --git a/test/performance/translate_with_biolib.rb b/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.

diff --git a/test/performance/translate_with_bioruby.rb b/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.