parse_fasta 1.0.1 → 1.1.0
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- checksums.yaml +4 -4
- data/README.md +41 -20
- data/lib/parse_fasta/fastq_file.rb +65 -0
- data/lib/parse_fasta/quality.rb +33 -0
- data/lib/parse_fasta/sequence.rb +2 -5
- data/lib/parse_fasta/version.rb +1 -1
- data/lib/parse_fasta.rb +2 -0
- data/parse_fasta.gemspec +4 -4
- data/spec/lib/fastq_file_spec.rb +50 -0
- data/spec/lib/quality.rb +35 -0
- data/test_files/benchmark.rb +32 -10
- data/test_files/test.fq +8 -0
- metadata +25 -18
checksums.yaml
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SHA1:
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metadata.gz:
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metadata.gz: 964e83c4a500490c9c5b9cb6f709fe7405b9f856
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data.tar.gz: eca56db94b3e639849699da0baf25e06ceedbbd6
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metadata.gz:
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metadata.gz: b0ae81b8ccf5bf0867b4457a7ceb65fecfe7b23bfb489132e4547bf62207707ee94ae0085444036c4683d9b5cc05cbeb1e177fc53c67dc249aedc4432cde41bb
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data.tar.gz: 39a9dea187dae22817b8fdcfc5f1c67ed2e8357abc3d89631544f8d94256df1f6c2aec8d07d957c792adbd039e18968f91c8c133c1e53608a38623896d73d40d
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data/README.md
CHANGED
@@ -18,17 +18,20 @@ Or install it yourself as:
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## Overview ##
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I wanted a simple, fast way to parse fasta files so I
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keep writing annoying boilerplate
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do something with
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that I find myself doing over
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I wanted a simple, fast way to parse fasta and fastq files so I
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wouldn't have to keep writing annoying boilerplate parsing code
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everytime I go to do something with a fasta or fastq file. I will
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probably add more, but likely only tasks that I find myself doing over
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and over.
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##
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## Documentation ##
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Checkout [parse_fasta docs](http://rubydoc.info/gems/parse_fasta/1.1.0/frames) to see
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the full documentation.
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-
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## Usage ##
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length example:
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A little script to print header and length of each record.
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require 'parse_fasta'
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@@ -38,28 +41,37 @@ length example:
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And here, a script to calculate GC content:
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require 'parse_fasta'
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-
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FastaFile.open(ARGV.first, 'r').each_record do |header, sequence|
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puts [header, sequence.gc].join("\t")
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end
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-
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Now we can parse fastq files as well!
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-
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-
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FastqFile.open(ARGV.first, 'r').each_record do |head, seq, desc, qual|
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puts [header, seq, desc, qual.qual_scores.join(',')].join("\t")
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end
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-
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## Versions ##
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### 1.1.0 ###
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Added: Fastq and Quality classes
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### 1.0.0 ###
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Added: Fasta and Sequence classes
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Removed: File monkey patch
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### 0.0.5 ###
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Last version with File monkey patch.
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## Benchmark ##
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Take these with a grain of salt since `BioRuby` is a
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Take these with a grain of salt since `BioRuby` is a big module
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module with lots of features and error checking, whereas `parse_fasta`
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is meant to be lightweight and easy to use for my own
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is meant to be lightweight and easy to use for my own research.
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### FastaFile#each_record ###
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@@ -78,12 +90,21 @@ was 1.1 gigabytes. Here are the results from Ruby's `Benchmark` class:
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I just wanted a nice, clean way to parse fasta files, but being nearly
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twice as fasta as BioRuby doesn't hurt either!
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### FastqFile#each_record ###
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The same sequence length test as above, but this time with a fastq
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file containing 4,000,000 illumina reads.
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user system total real
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this_fastq 62.610000 1.660000 64.270000 ( 64.389408)
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bioruby_fastq 165.500000 2.100000 167.600000 (167.969636)
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### Sequence#gc ###
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I played around with a few different implementations for the `#gc`
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method and found this one to be the fastest.
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The test is done
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The test is done on random strings mating `/[AaCcTtGgUu]/`. `this_gc`
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is `Sequence.new(str).gc`, and `bioruby_gc` is
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`Bio::Sequence::NA.new(str).gc_content`.
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# Copyright 2014 Ryan Moore
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# Contact: moorer@udel.edu
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#
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# This file is part of parse_fasta.
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#
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# parse_fasta is free software: you can redistribute it and/or modify
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# it under the terms of the GNU General Public License as published by
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# the Free Software Foundation, either version 3 of the License, or
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# (at your option) any later version.
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#
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# parse_fasta is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU General Public License for more details.
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#
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# You should have received a copy of the GNU General Public License
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# along with parse_fasta. If not, see <http://www.gnu.org/licenses/>.
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# Provides simple interface for parsing four-line-per-record fastq
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# format files.
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class FastqFile < File
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# Analagous to File#each_line, #each_record is used to go through a
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# fastq file record by record.
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#
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# @example Parsing a fastq file
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# FastqFile.open('reads.fq', 'r').each_record do |head, seq, desc, qual|
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# # do some fun stuff here!
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# end
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#
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# @yield The header, sequence, description and quality string for
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# each record in the fastq file to the block
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# @yieldparam header [String] The header of the fastq record without
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# the leading '@'
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# @yieldparam sequence [Sequence] The sequence of the fastq record
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# @yieldparam sequence [String] The description line of the fastq
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# record without the leading '+'
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# @yieldparam sequence [Quality] The quality string of the fastq
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# record
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def each_record
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count = 0
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header = ''
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sequence = ''
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description = ''
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quality = ''
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self.each_line do |line|
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line.chomp!
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case count % 4
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when 0
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header = line.sub(/^@/, '')
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when 1
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sequence = Sequence.new(line)
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when 2
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description = line.sub(/^\+/, '')
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when 3
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quality = Quality.new(line)
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yield(header, sequence, description, quality)
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end
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count += 1
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end
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end
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end
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# Copyright 2014 Ryan Moore
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# Contact: moorer@udel.edu
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#
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# This file is part of parse_fasta.
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#
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# parse_fasta is free software: you can redistribute it and/or modify
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# it under the terms of the GNU General Public License as published by
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# the Free Software Foundation, either version 3 of the License, or
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# (at your option) any later version.
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#
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# parse_fasta is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU General Public License for more details.
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#
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# You should have received a copy of the GNU General Public License
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# along with parse_fasta. If not, see <http://www.gnu.org/licenses/>.
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# Provide some methods for dealing with common tasks regarding
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# quality strings.
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class Quality < String
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# Returns an array of illumina style quality scores. The quality
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# scores generated will be Phred+33.
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#
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# @example Get quality score array of a Quality
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# Quality.new("!+5?I").qual_scores #=> [0, 10, 20, 30, 40]
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#
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# @return [Array<Fixnum>] the quality scores
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def qual_scores
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self.each_byte.map { |b| b - 33 }
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end
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end
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data/lib/parse_fasta/sequence.rb
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# Provide some methods for dealing with common tasks regarding
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# nucleotide sequences.
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class Sequence < String
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def initialize(str)
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super(str)
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end
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#
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# Calculates GC content
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#
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# Calculates GC content by dividing count of G + C divided by count
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# of G + C + T + A +U. If there are both T's and U's in the
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# of G + C + T + A + U. If there are both T's and U's in the
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# Sequence, things will get weird, but then again, that wouldn't
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# happen, now would it!
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#
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data/lib/parse_fasta/version.rb
CHANGED
data/lib/parse_fasta.rb
CHANGED
data/parse_fasta.gemspec
CHANGED
@@ -19,8 +19,8 @@ Gem::Specification.new do |spec|
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spec.require_paths = ["lib"]
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spec.add_development_dependency "bundler", "~> 1.6"
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spec.add_development_dependency "rake"
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spec.add_development_dependency "rspec"
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spec.add_development_dependency "bio"
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spec.add_development_dependency "yard"
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spec.add_development_dependency "rake", "~> 10.3"
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spec.add_development_dependency "rspec", "~> 2.14"
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spec.add_development_dependency "bio", "~> 1.4"
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spec.add_development_dependency "yard", "~> 0.8"
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end
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# Copyright 2014 Ryan Moore
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# Contact: moorer@udel.edu
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#
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# This file is part of parse_fasta.
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#
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# parse_fasta is free software: you can redistribute it and/or modify
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# it under the terms of the GNU General Public License as published by
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# the Free Software Foundation, either version 3 of the License, or
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# (at your option) any later version.
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#
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# parse_fasta is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU General Public License for more details.
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#
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# You should have received a copy of the GNU General Public License
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# along with parse_fasta. If not, see <http://www.gnu.org/licenses/>.
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require 'spec_helper'
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describe FastqFile do
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describe "#each_record" do
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let(:fname) { "#{File.dirname(__FILE__)}/../../test_files/test.fq" }
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context "with a 4 line per record fastq file" do
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before do
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@records = []
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FastqFile.open(fname, 'r').each_record do |head, seq, desc, qual|
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@records << [head, seq, desc, qual]
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end
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end
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it "yields the header, sequence, desc, and qual" do
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expect(@records).to eq([["seq1", "AACCTTGG", "", ")#3gTqN8"],
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["seq2 apples", "ACTG", "seq2 apples",
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"*ujM"]])
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end
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it "yields the sequence as a Sequence class" do
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the_sequence = @records[0][1]
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expect(the_sequence).to be_a(Sequence)
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end
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it "yields the quality string as a Quality class" do
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the_quality = @records[0][3]
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expect(the_quality).to be_a(Quality)
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end
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end
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end
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end
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data/spec/lib/quality.rb
ADDED
@@ -0,0 +1,35 @@
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# Copyright 2014 Ryan Moore
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# Contact: moorer@udel.edu
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#
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# This file is part of parse_fasta.
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#
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# parse_fasta is free software: you can redistribute it and/or modify
|
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# it under the terms of the GNU General Public License as published by
|
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# the Free Software Foundation, either version 3 of the License, or
|
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# (at your option) any later version.
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#
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# parse_fasta is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
|
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
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# GNU General Public License for more details.
|
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#
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# You should have received a copy of the GNU General Public License
|
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# along with parse_fasta. If not, see <http://www.gnu.org/licenses/>.
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+
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require 'spec_helper'
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require 'bio'
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+
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describe Quality do
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let(:qual_string) { qual_string = Quality.new('ab%63:K') }
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let(:bioruby_qual_scores) do
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Bio::Fastq.new("@seq1\nACTGACT\n+\n#{qual_string}").quality_scores
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end
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describe "#qual_scores" do
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context "with illumina style quality scores" do
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it "returns an array of quality scores" do
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expect(qual_string.qual_scores).to eq bioruby_qual_scores
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end
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end
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end
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end
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data/test_files/benchmark.rb
CHANGED
@@ -54,17 +54,39 @@ def make_seq(num)
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num.times.reduce('') { |str, n| str << %w[A a C c T t G g N n].sample }
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end
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-
s1 = make_seq(2000000)
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-
s2 = make_seq(4000000)
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-
s3 = make_seq(8000000)
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# s1 = make_seq(2000000)
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# s2 = make_seq(4000000)
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# s3 = make_seq(8000000)
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Benchmark.bmbm do |x|
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-
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-
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# Benchmark.bmbm do |x|
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# x.report('this_gc 1') { this_gc(s1) }
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# x.report('bioruby_gc 1') { bioruby_gc(s1) }
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+
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# x.report('this_gc 2') { this_gc(s2) }
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# x.report('bioruby_gc 2') { bioruby_gc(s2) }
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+
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# x.report('this_gc 3') { this_gc(s3) }
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# x.report('bioruby_gc 3') { bioruby_gc(s3) }
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# end
|
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-
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|
-
x.report('bioruby_gc 2') { bioruby_gc(s2) }
|
72
|
+
# fastq = ARGV.first
|
67
73
|
|
68
|
-
|
69
|
-
|
74
|
+
def bioruby_fastq(fastq)
|
75
|
+
Bio::FlatFile.open(Bio::Fastq, fastq) do |fq|
|
76
|
+
fq.each do |entry|
|
77
|
+
[entry.definition, entry.seq.length].join("\t")
|
78
|
+
end
|
79
|
+
end
|
70
80
|
end
|
81
|
+
|
82
|
+
def this_fastq(fastq)
|
83
|
+
FastqFile.open(fastq).each_record do |head, seq, desc, qual|
|
84
|
+
[head, seq.length].join("\t")
|
85
|
+
end
|
86
|
+
end
|
87
|
+
|
88
|
+
# file is 4 million illumina reads (16,000,000 lines) 1.4gb
|
89
|
+
# Benchmark.bmbm do |x|
|
90
|
+
# x.report('this_fastq') { this_fastq(ARGV.first) }
|
91
|
+
# x.report('bioruby_fastq') { bioruby_fastq(ARGV.first) }
|
92
|
+
# end
|
data/test_files/test.fq
ADDED
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: parse_fasta
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 1.0
|
4
|
+
version: 1.1.0
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Ryan Moore
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2014-06-
|
11
|
+
date: 2014-06-13 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: bundler
|
@@ -28,58 +28,58 @@ dependencies:
|
|
28
28
|
name: rake
|
29
29
|
requirement: !ruby/object:Gem::Requirement
|
30
30
|
requirements:
|
31
|
-
- - "
|
31
|
+
- - "~>"
|
32
32
|
- !ruby/object:Gem::Version
|
33
|
-
version: '
|
33
|
+
version: '10.3'
|
34
34
|
type: :development
|
35
35
|
prerelease: false
|
36
36
|
version_requirements: !ruby/object:Gem::Requirement
|
37
37
|
requirements:
|
38
|
-
- - "
|
38
|
+
- - "~>"
|
39
39
|
- !ruby/object:Gem::Version
|
40
|
-
version: '
|
40
|
+
version: '10.3'
|
41
41
|
- !ruby/object:Gem::Dependency
|
42
42
|
name: rspec
|
43
43
|
requirement: !ruby/object:Gem::Requirement
|
44
44
|
requirements:
|
45
|
-
- - "
|
45
|
+
- - "~>"
|
46
46
|
- !ruby/object:Gem::Version
|
47
|
-
version: '
|
47
|
+
version: '2.14'
|
48
48
|
type: :development
|
49
49
|
prerelease: false
|
50
50
|
version_requirements: !ruby/object:Gem::Requirement
|
51
51
|
requirements:
|
52
|
-
- - "
|
52
|
+
- - "~>"
|
53
53
|
- !ruby/object:Gem::Version
|
54
|
-
version: '
|
54
|
+
version: '2.14'
|
55
55
|
- !ruby/object:Gem::Dependency
|
56
56
|
name: bio
|
57
57
|
requirement: !ruby/object:Gem::Requirement
|
58
58
|
requirements:
|
59
|
-
- - "
|
59
|
+
- - "~>"
|
60
60
|
- !ruby/object:Gem::Version
|
61
|
-
version: '
|
61
|
+
version: '1.4'
|
62
62
|
type: :development
|
63
63
|
prerelease: false
|
64
64
|
version_requirements: !ruby/object:Gem::Requirement
|
65
65
|
requirements:
|
66
|
-
- - "
|
66
|
+
- - "~>"
|
67
67
|
- !ruby/object:Gem::Version
|
68
|
-
version: '
|
68
|
+
version: '1.4'
|
69
69
|
- !ruby/object:Gem::Dependency
|
70
70
|
name: yard
|
71
71
|
requirement: !ruby/object:Gem::Requirement
|
72
72
|
requirements:
|
73
|
-
- - "
|
73
|
+
- - "~>"
|
74
74
|
- !ruby/object:Gem::Version
|
75
|
-
version: '0'
|
75
|
+
version: '0.8'
|
76
76
|
type: :development
|
77
77
|
prerelease: false
|
78
78
|
version_requirements: !ruby/object:Gem::Requirement
|
79
79
|
requirements:
|
80
|
-
- - "
|
80
|
+
- - "~>"
|
81
81
|
- !ruby/object:Gem::Version
|
82
|
-
version: '0'
|
82
|
+
version: '0.8'
|
83
83
|
description: So you want to parse a fasta file...
|
84
84
|
email:
|
85
85
|
- moorer@udel.edu
|
@@ -94,14 +94,19 @@ files:
|
|
94
94
|
- Rakefile
|
95
95
|
- lib/parse_fasta.rb
|
96
96
|
- lib/parse_fasta/fasta_file.rb
|
97
|
+
- lib/parse_fasta/fastq_file.rb
|
98
|
+
- lib/parse_fasta/quality.rb
|
97
99
|
- lib/parse_fasta/sequence.rb
|
98
100
|
- lib/parse_fasta/version.rb
|
99
101
|
- parse_fasta.gemspec
|
100
102
|
- spec/lib/fasta_file_spec.rb
|
103
|
+
- spec/lib/fastq_file_spec.rb
|
104
|
+
- spec/lib/quality.rb
|
101
105
|
- spec/lib/sequence_spec.rb
|
102
106
|
- spec/spec_helper.rb
|
103
107
|
- test_files/benchmark.rb
|
104
108
|
- test_files/test.fa
|
109
|
+
- test_files/test.fq
|
105
110
|
homepage: https://github.com/mooreryan/parse_fasta
|
106
111
|
licenses:
|
107
112
|
- 'GPLv3: http://www.gnu.org/licenses/gpl.txt'
|
@@ -128,6 +133,8 @@ specification_version: 4
|
|
128
133
|
summary: Easy-peasy parsing of fasta files
|
129
134
|
test_files:
|
130
135
|
- spec/lib/fasta_file_spec.rb
|
136
|
+
- spec/lib/fastq_file_spec.rb
|
137
|
+
- spec/lib/quality.rb
|
131
138
|
- spec/lib/sequence_spec.rb
|
132
139
|
- spec/spec_helper.rb
|
133
140
|
has_rdoc:
|