bio-kmer_counter 0.0.3 → 0.0.4

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Files changed (4) hide show
  1. data/VERSION +1 -1
  2. data/bin/kmer_counter.rb +1 -0
  3. data/test/test_bio-kmer_counter.rb +10 -0
  4. metadata +22 -67
data/VERSION CHANGED
@@ -1 +1 @@
1
- 0.0.3
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+ 0.0.4
data/bin/kmer_counter.rb CHANGED
@@ -120,6 +120,7 @@ process_window = lambda do |window,kmer,sequence_name,contig_name|
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  window.window_search(options[:kmer],1) do |tetranucleotide|
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  str = tetranucleotide.to_s
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+ str.upcase!
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  next unless str.gsub(/[ATGC]+/,'') == ''
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  num_kmers_counted += 1
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  counts[str]+=1
data/test/test_bio-kmer_counter.rb CHANGED
@@ -102,4 +102,14 @@ class TestBioKmerCounter < Test::Unit::TestCase
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  assert stderr.readlines[0].match(/^Usage: kmer_counter/)
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  end
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  end
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+
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+ should 'work with lowercase' do
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+ Tempfile.open('one') do |tempfile|
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+ tempfile.puts '>one'
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+ tempfile.puts 'acagt'
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+ tempfile.close
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+
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+ assert_equal "ID\tA\tC\none_0\t0.6\t0.4\n", `#{script_path} -w 5 -k 1 #{tempfile.path}`
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+ end
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+ end
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  end
metadata CHANGED
@@ -1,7 +1,7 @@
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  --- !ruby/object:Gem::Specification
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  name: bio-kmer_counter
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  version: !ruby/object:Gem::Version
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- version: 0.0.3
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+ version: 0.0.4
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  prerelease:
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  platform: ruby
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  authors:
@@ -9,11 +9,11 @@ authors:
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2012-07-09 00:00:00.000000000 Z
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+ date: 2012-08-09 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: bio
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- requirement: !ruby/object:Gem::Requirement
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+ requirement: &79074710 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -21,15 +21,10 @@ dependencies:
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  version: 1.4.2
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  type: :runtime
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  prerelease: false
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- version_requirements: !ruby/object:Gem::Requirement
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- none: false
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- requirements:
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- - - ! '>='
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- - !ruby/object:Gem::Version
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- version: 1.4.2
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+ version_requirements: *79074710
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  - !ruby/object:Gem::Dependency
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  name: progressbar
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- requirement: !ruby/object:Gem::Requirement
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+ requirement: &79238200 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -37,15 +32,10 @@ dependencies:
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  version: 0.11.0
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  type: :runtime
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  prerelease: false
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- version_requirements: !ruby/object:Gem::Requirement
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- none: false
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- requirements:
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- - - ! '>='
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- - !ruby/object:Gem::Version
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- version: 0.11.0
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+ version_requirements: *79238200
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  - !ruby/object:Gem::Dependency
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  name: parallel
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- requirement: !ruby/object:Gem::Requirement
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+ requirement: &79249880 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -53,15 +43,10 @@ dependencies:
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  version: 0.5.17
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  type: :runtime
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  prerelease: false
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- version_requirements: !ruby/object:Gem::Requirement
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- none: false
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- requirements:
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- - - ! '>='
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- - !ruby/object:Gem::Version
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- version: 0.5.17
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+ version_requirements: *79249880
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  - !ruby/object:Gem::Dependency
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  name: bio-logger
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- requirement: !ruby/object:Gem::Requirement
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+ requirement: &79249150 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -69,15 +54,10 @@ dependencies:
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  version: 1.0.1
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  type: :runtime
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  prerelease: false
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- version_requirements: !ruby/object:Gem::Requirement
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- none: false
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- requirements:
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- - - ! '>='
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- - !ruby/object:Gem::Version
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- version: 1.0.1
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+ version_requirements: *79249150
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  - !ruby/object:Gem::Dependency
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  name: shoulda
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- requirement: !ruby/object:Gem::Requirement
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+ requirement: &79246850 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -85,15 +65,10 @@ dependencies:
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  version: '0'
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  type: :development
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  prerelease: false
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- version_requirements: !ruby/object:Gem::Requirement
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- none: false
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- requirements:
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- - - ! '>='
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- - !ruby/object:Gem::Version
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- version: '0'
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+ version_requirements: *79246850
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  - !ruby/object:Gem::Dependency
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  name: rdoc
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- requirement: !ruby/object:Gem::Requirement
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+ requirement: &79245070 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -101,15 +76,10 @@ dependencies:
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  version: '3.12'
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  type: :development
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  prerelease: false
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- version_requirements: !ruby/object:Gem::Requirement
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- none: false
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- requirements:
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- - - ~>
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- - !ruby/object:Gem::Version
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- version: '3.12'
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+ version_requirements: *79245070
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  - !ruby/object:Gem::Dependency
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  name: jeweler
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- requirement: !ruby/object:Gem::Requirement
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+ requirement: &79286630 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -117,15 +87,10 @@ dependencies:
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  version: 1.8.3
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  type: :development
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  prerelease: false
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- version_requirements: !ruby/object:Gem::Requirement
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- none: false
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- requirements:
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- - - ~>
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- - !ruby/object:Gem::Version
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- version: 1.8.3
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+ version_requirements: *79286630
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  - !ruby/object:Gem::Dependency
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  name: bundler
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- requirement: !ruby/object:Gem::Requirement
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+ requirement: &79285430 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -133,15 +98,10 @@ dependencies:
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  version: 1.0.21
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  type: :development
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  prerelease: false
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- version_requirements: !ruby/object:Gem::Requirement
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- none: false
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- requirements:
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- - - ! '>='
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- - !ruby/object:Gem::Version
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- version: 1.0.21
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+ version_requirements: *79285430
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  - !ruby/object:Gem::Dependency
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  name: rdoc
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- requirement: !ruby/object:Gem::Requirement
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+ requirement: &79284460 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -149,12 +109,7 @@ dependencies:
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  version: '3.12'
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  type: :development
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  prerelease: false
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- version_requirements: !ruby/object:Gem::Requirement
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- none: false
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- requirements:
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- - - ~>
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- - !ruby/object:Gem::Version
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- version: '3.12'
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+ version_requirements: *79284460
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  description: A biogem for counting small kmers for fingerprinting nucleotide sequences.
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  See README for details.
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  email: gmail.com after donttrustben
@@ -192,7 +147,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
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  version: '0'
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  segments:
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  - 0
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- hash: -309263761
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+ hash: -548048899
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  required_rubygems_version: !ruby/object:Gem::Requirement
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  none: false
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  requirements:
@@ -201,7 +156,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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  version: '0'
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  requirements: []
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  rubyforge_project:
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- rubygems_version: 1.8.24
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+ rubygems_version: 1.8.17
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  signing_key:
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  specification_version: 3
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  summary: A biogem for counting small kmers for fingerprinting nucleotide sequences