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https://github.com/audy/dna
A biological sequence file (fasta, fastq, qseq) parser for Ruby
https://github.com/audy/dna
bioinformatics dna parser ruby
Last synced: about 18 hours ago
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A biological sequence file (fasta, fastq, qseq) parser for Ruby
- Host: GitHub
- URL: https://github.com/audy/dna
- Owner: audy
- Created: 2012-01-27T19:00:28.000Z (over 12 years ago)
- Default Branch: master
- Last Pushed: 2015-10-30T19:56:20.000Z (almost 9 years ago)
- Last Synced: 2024-09-17T16:43:38.924Z (16 days ago)
- Topics: bioinformatics, dna, parser, ruby
- Language: Ruby
- Homepage: audy.github.com/dna
- Size: 252 KB
- Stars: 4
- Watchers: 3
- Forks: 3
- Open Issues: 2
-
Metadata Files:
- Readme: readme.md
Awesome Lists containing this project
README
# DNA [](http://badge.fury.io/rb/dna) [](http://travis-ci.org/audy/dna) [](https://coveralls.io/r/audy/dna)
A biological sequence file parser for Ruby
Austin G. Davis-Richardson
Features
- Supported Formats ([submit a format request](https://github.com/audy/dna/issues/new?title=request%20for%20new%20format))
- [fasta](http://en.wikipedia.org/wiki/FASTA)
- [fastq](http://en.wikipedia.org/wiki/Fastq)
- [qseq](http://blog.kokocinski.net/index.php/qseq-files-format?blog=2)
- Automatic format detection
- Lazy iteration
## Installation
Tested on Ruby 1.9.3 and 2.0.0
```
$ (sudo) gem install dna
```
## Usage
```ruby
require 'dna'
# Automatic Format Detection
File.open('sequences.fasta') do |handle|
records = Dna.new handle
records.each do |record|
puts record.length
end
end
File.open('sequences.fastq') do |handle|
records = Dna.new handle
records.each do |record|
puts record.quality
end
end
File.open('sequences.qseq') do |handle|
records = Dna.new handle
puts records.first.inspect
end
# **caveat:** If you are reading from a compressed file
# or `stdin` you MUST specify the sequence format:
require 'zlib'
Zlib::GzipReader('sequences.fasta.gz') do |handle|
records = Dna.new handle, :format => :fasta
records.each do |record|
puts record.length
end
end
```
## Support for PHRED score parsing
```ruby
# Illumina > 1.3)
record.illumina_qualities # => [31, ..., 37]
# Error probabilities
record.illumina_probabilities
# => [1.0, 0.7943282347242815, ..., 0.3981071705534972]
# Solexa + Illumina =< 1.3
record.solexa_qualities
record.solexa_probabilities
# Sanger
record.sanger_qualities
record.sanger_probabilities
```
## Bonus Feature
The DNA gem is also a command-line tool with grep-like capabilities. Print records with (Ruby) regexp match in header.
```
$ dna spec/data/input.fastq "[1-2]"
@1
TGAAACTTATTGATCACCCCGCTTGGCGTTGGGGAGAAATTCAGAAAAGAGTGCTTGATGGGGCGCCACATGCCGTGCAACCCACTCTCTTTCACGCAGCGCGCCCCA
+1
5888.6778888650/-//&,(,./*-11'//0&,-0.(.,,,,/2/&-,,,,,.(.,(,..&---&-,,,((*-----*+.&,,,,,(//&,,,-(,,+(,,,--&(
@2
GTCGCGGCTTACCACCCAACGATTTTTTTTAGAGGTGCTGGTTTCA
+2
2550//*-1./4.--/'+.2.,,,,,,,,&(/00.11426554+13
$ dna spec/data/test.fasta "\d"
>1
GAGAGATCTCATGACACAGCCGAAG
>2
GAGACAUAUCCNNNAA
```