dna 0.0.9 → 0.0.10

data/.rspec

@@ -0,0 +1 @@
+--color

data/.rvmrc

@@ -0,0 +1 @@
+rvm use --create 1.8.7@dna

data/Gemfile

@@ -0,0 +1,2 @@
+source :rubygems
+gem 'rspec'

data/bin/dna

@@ -0,0 +1,16 @@
+#!/usr/bin/env ruby
+
+require File.expand_path(File.join(File.dirname(__FILE__), '..', 'lib', 'dna'))
+
+input, regexp = [File.open(ARGV[0]), ARGV[1]]
+
+fail 'usage: dna input regexp > output' if regexp.nil?
+
+records = Dna.new input
+regexp  = Regexp.new(regexp)
+
+records.each do |record|
+  puts record if record.name =~ regexp
+end
+
+input.close

data/dna.gemspec

@@ -0,0 +1,19 @@
+Gem::Specification.new do |s|
+	s.name    = 'dna'
+	s.version = '0.0.10'
+	s.date    = '2012-05-21'
+
+	s.summary     = 'DNA sequence parser'
+	s.description = 'for parsing various types of DNA sequence files'
+
+	s.authors = ["Austin G. Davis-Richardson"]
+	s.email   = "harekrishna@gmail.com"
+
+	s.rubyforge_project = 'dna'
+
+	s.files         = `git ls-files`.split("\n")
+	s.test_files    = `git ls-files -- {test,spec,features}/*`.split("\n")
+  s.executables   = `git ls-files -- bin/*`.split("\n").map{ |f| File.basename(f) }
+
+	s.homepage = "http://github.com/audy/dna"
+end

data/readme.md

@@ -18,6 +18,32 @@ With Ruby 1.8.7 or better:
 
 `gem install dna`
 
+## CLI
+
+DNA gem has grep-like capabilities. Print records with (Ruby) regexp match in header.
+
+```
+$ dna input.fastq "[1-2]"
+
+@1
+TGAAACTTATTGATCACCCCGCTTGGCGTTGGGGAGAAATTCAGAAAAGAGTGCTTGATGGGGCGCCACATGCCGTGCAACCCACTCTCTTTCACGCAGCGCGCCCCA
++1
+5888.6778888650/-//&,(,./*-11'//0&,-0.(.,,,,/2/&-,,,,,.(.,(,..&---&-,,,((*-----*+.&,,,,,(//&,,,-(,,+(,,,--&(
+@2
+GTCGCGGCTTACCACCCAACGATTTTTTTTAGAGGTGCTGGTTTCA
++2
+2550//*-1./4.--/'+.2.,,,,,,,,&(/00.11426554+13
+
+$ cat input.fasta | dna "\d"
+
+>1
+GAGAGATCTCATGACACAGCCGAAG
+>2
+GAGACAUAUCCNNNAA
+
+```
+
+
 ## Usage
 
 ```ruby

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: dna
 version: !ruby/object:Gem::Version 
-  hash: 13
+  hash: 11
   prerelease: 
   segments: 
   - 0
   - 0
-  - 9
-  version: 0.0.9
+  - 10
+  version: 0.0.10
 platform: ruby
 authors: 
 - Austin G. Davis-Richardson
@@ -15,30 +15,35 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2012-04-05 00:00:00 Z
+date: 2012-05-21 00:00:00 Z
 dependencies: []
 
 description: for parsing various types of DNA sequence files
 email: harekrishna@gmail.com
-executables: []
-
+executables: 
+- dna
 extensions: []
 
 extra_rdoc_files: []
 
 files: 
+- .rspec
+- .rvmrc
+- Gemfile
+- bin/dna
+- dna.gemspec
 - lib/dna.rb
 - lib/parsers/fasta.rb
 - lib/parsers/fastq.rb
 - lib/parsers/qseq.rb
-- spec/dna_spec.rb
-- spec/record_spec.rb
-- spec/spec_helper.rb
+- readme.md
 - spec/data/empty.txt
 - spec/data/test.fasta
 - spec/data/test.fastq
 - spec/data/test.qseq
-- readme.md
+- spec/dna_spec.rb
+- spec/record_spec.rb
+- spec/spec_helper.rb
 homepage: http://github.com/audy/dna
 licenses: []
 
@@ -67,10 +72,16 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: "0"
 requirements: []
 
-rubyforge_project: 
-rubygems_version: 1.8.21
+rubyforge_project: dna
+rubygems_version: 1.8.24
 signing_key: 
 specification_version: 3
 summary: DNA sequence parser
-test_files: []
-
+test_files: 
+- spec/data/empty.txt
+- spec/data/test.fasta
+- spec/data/test.fastq
+- spec/data/test.qseq
+- spec/dna_spec.rb
+- spec/record_spec.rb
+- spec/spec_helper.rb