dna 0.0.9 → 0.0.10

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Files changed (7) hide show
  1. data/.rspec +1 -0
  2. data/.rvmrc +1 -0
  3. data/Gemfile +2 -0
  4. data/bin/dna +16 -0
  5. data/dna.gemspec +19 -0
  6. data/readme.md +26 -0
  7. metadata +25 -14
data/.rspec ADDED
@@ -0,0 +1 @@
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+ --color
data/.rvmrc ADDED
@@ -0,0 +1 @@
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+ rvm use --create 1.8.7@dna
data/Gemfile ADDED
@@ -0,0 +1,2 @@
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+ source :rubygems
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+ gem 'rspec'
data/bin/dna ADDED
@@ -0,0 +1,16 @@
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+ #!/usr/bin/env ruby
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+
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+ require File.expand_path(File.join(File.dirname(__FILE__), '..', 'lib', 'dna'))
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+
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+ input, regexp = [File.open(ARGV[0]), ARGV[1]]
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+
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+ fail 'usage: dna input regexp > output' if regexp.nil?
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+
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+ records = Dna.new input
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+ regexp = Regexp.new(regexp)
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+
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+ records.each do |record|
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+ puts record if record.name =~ regexp
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+ end
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+
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+ input.close
data/dna.gemspec ADDED
@@ -0,0 +1,19 @@
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+ Gem::Specification.new do |s|
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+ s.name = 'dna'
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+ s.version = '0.0.10'
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+ s.date = '2012-05-21'
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+
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+ s.summary = 'DNA sequence parser'
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+ s.description = 'for parsing various types of DNA sequence files'
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+
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+ s.authors = ["Austin G. Davis-Richardson"]
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+ s.email = "harekrishna@gmail.com"
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+
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+ s.rubyforge_project = 'dna'
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+
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+ s.files = `git ls-files`.split("\n")
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+ s.test_files = `git ls-files -- {test,spec,features}/*`.split("\n")
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+ s.executables = `git ls-files -- bin/*`.split("\n").map{ |f| File.basename(f) }
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+
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+ s.homepage = "http://github.com/audy/dna"
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+ end
data/readme.md CHANGED
@@ -18,6 +18,32 @@ With Ruby 1.8.7 or better:
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  `gem install dna`
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+ ## CLI
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+
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+ DNA gem has grep-like capabilities. Print records with (Ruby) regexp match in header.
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+
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+ ```
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+ $ dna input.fastq "[1-2]"
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+
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+ @1
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+ TGAAACTTATTGATCACCCCGCTTGGCGTTGGGGAGAAATTCAGAAAAGAGTGCTTGATGGGGCGCCACATGCCGTGCAACCCACTCTCTTTCACGCAGCGCGCCCCA
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+ +1
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+ 5888.6778888650/-//&,(,./*-11'//0&,-0.(.,,,,/2/&-,,,,,.(.,(,..&---&-,,,((*-----*+.&,,,,,(//&,,,-(,,+(,,,--&(
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+ @2
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+ GTCGCGGCTTACCACCCAACGATTTTTTTTAGAGGTGCTGGTTTCA
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+ +2
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+ 2550//*-1./4.--/'+.2.,,,,,,,,&(/00.11426554+13
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+
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+ $ cat input.fasta | dna "\d"
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+
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+ >1
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+ GAGAGATCTCATGACACAGCCGAAG
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+ >2
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+ GAGACAUAUCCNNNAA
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+
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+ ```
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+
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+
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  ## Usage
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  ```ruby
metadata CHANGED
@@ -1,13 +1,13 @@
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  --- !ruby/object:Gem::Specification
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  name: dna
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  version: !ruby/object:Gem::Version
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- hash: 13
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+ hash: 11
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  prerelease:
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  segments:
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  - 0
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  - 0
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- - 9
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- version: 0.0.9
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+ - 10
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+ version: 0.0.10
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  platform: ruby
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  authors:
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  - Austin G. Davis-Richardson
@@ -15,30 +15,35 @@ autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2012-04-05 00:00:00 Z
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+ date: 2012-05-21 00:00:00 Z
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  dependencies: []
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  description: for parsing various types of DNA sequence files
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  email: harekrishna@gmail.com
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- executables: []
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-
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+ executables:
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+ - dna
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  extensions: []
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  extra_rdoc_files: []
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  files:
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+ - .rspec
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+ - .rvmrc
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+ - Gemfile
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+ - bin/dna
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+ - dna.gemspec
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  - lib/dna.rb
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  - lib/parsers/fasta.rb
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  - lib/parsers/fastq.rb
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  - lib/parsers/qseq.rb
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- - spec/dna_spec.rb
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- - spec/record_spec.rb
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- - spec/spec_helper.rb
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+ - readme.md
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  - spec/data/empty.txt
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  - spec/data/test.fasta
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  - spec/data/test.fastq
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  - spec/data/test.qseq
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- - readme.md
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+ - spec/dna_spec.rb
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+ - spec/record_spec.rb
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+ - spec/spec_helper.rb
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  homepage: http://github.com/audy/dna
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  licenses: []
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@@ -67,10 +72,16 @@ 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: 1.8.21
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+ rubyforge_project: dna
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+ rubygems_version: 1.8.24
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  signing_key:
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  specification_version: 3
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  summary: DNA sequence parser
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- test_files: []
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-
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+ test_files:
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+ - spec/data/empty.txt
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+ - spec/data/test.fasta
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+ - spec/data/test.fastq
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+ - spec/data/test.qseq
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+ - spec/dna_spec.rb
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+ - spec/record_spec.rb
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+ - spec/spec_helper.rb