dna 0.1.0 → 0.1.1

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Files changed (5) hide show
  1. data/dna.gemspec +2 -2
  2. data/lib/dna/dna.rb +1 -1
  3. data/lib/dna/version.rb +1 -1
  4. data/readme.md +39 -36
  5. metadata +4 -4
data/dna.gemspec CHANGED
@@ -5,11 +5,11 @@
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  Gem::Specification.new do |s|
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  s.name = "dna"
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- s.version = "0.1.0"
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+ s.version = "0.1.1"
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  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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  s.authors = ["Austin G. Davis-Richardson"]
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- s.date = "2012-08-09"
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+ s.date = "2012-08-15"
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  s.description = "Simple FASTA/FASTQ/QSEQ parser library for Ruby."
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  s.email = "harekrishna@gmail.com"
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  s.executables = ["dna"]
data/lib/dna/dna.rb CHANGED
@@ -20,7 +20,7 @@ class Dna
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  when :qseq
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  QSEQParser.new @handle
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  else
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- raise "#{@format} not supported."
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+ raise IOError, "format '#{@format}' not supported. (or file is empty)"
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  end
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  end
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data/lib/dna/version.rb CHANGED
@@ -2,7 +2,7 @@ class Dna
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  class Version
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  MAJOR = 0
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  MINOR = 1
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- PATCH = 0
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+ PATCH = 1
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  STRING = [MAJOR, MINOR, PATCH].join('.')
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  end
data/readme.md CHANGED
@@ -1,60 +1,38 @@
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  # DNA
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- A minimalistic sequence file parser.
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+ A biological sequence file parser for Ruby
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  Austin G. Davis-Richardson
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- Supported Formats:
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+ Features
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- - [fasta](http://en.wikipedia.org/wiki/FASTA)
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- - [fastq](http://en.wikipedia.org/wiki/Fastq)
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- - [qseq](http://blog.kokocinski.net/index.php/qseq-files-format?blog=2)
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-
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- [Request a format](https://github.com/audy/dna/issues/new?title=request%20for%20new%20format)
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+ - Supported Formats ([submit a format request](https://github.com/audy/dna/issues/new?title=request%20for%20new%20format))
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+ - [fasta](http://en.wikipedia.org/wiki/FASTA)
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+ - [fastq](http://en.wikipedia.org/wiki/Fastq)
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+ - [qseq](http://blog.kokocinski.net/index.php/qseq-files-format?blog=2)
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+ - Autodetection of file formats so your scripts can be format agnostic
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+ - Automatic Gzip support
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+ - Files are read from disk (not stored in memory)
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  ## Installation
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  With Ruby 1.8.7 or better:
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- `gem install dna`
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-
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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 spec/data/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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- $ dna spec/data/test.fasta "\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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+ $ (sudo) gem install dna
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  ```
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-
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  ## Usage
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  ```ruby
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  require 'dna'
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- # format detected automatically by inspecting the contents of the file.
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+ # Automatic Format Detection
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  File.open('sequences.fasta') do |handle|
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  records = Dna.new handle
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-
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+
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  records.each do |record|
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  puts record.length
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  end
@@ -73,8 +51,7 @@ File.open('sequences.qseq') do |handle|
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  puts records.first.inspect
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  end
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- # even works on gzipped data
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-
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+ # Even supports Gzip
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  File.open('sequences.fasta.gz') do |handle|
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  records = Dna.new handle
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@@ -83,3 +60,29 @@ File.open('sequences.fasta.gz') do |handle|
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  end
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  end
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  ```
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+
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+ ## Bonus Feature
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+
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+ The DNA gem is also a command-line tool with grep-like capabilities. Print records with (Ruby) regexp match in header.
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+
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+ ```
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+ $ dna spec/data/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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+ $ dna spec/data/test.fasta "\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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+
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: 27
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+ hash: 25
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  prerelease:
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  segments:
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  - 0
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  - 1
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- - 0
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- version: 0.1.0
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+ - 1
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+ version: 0.1.1
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  platform: ruby
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  authors:
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  - Austin G. Davis-Richardson
@@ -15,7 +15,7 @@ autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2012-08-09 00:00:00 Z
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+ date: 2012-08-15 00:00:00 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  type: :runtime