Bio::Kseq 
Ruby bindings for a very fast FASTA/Q parser kseq.h by Heng Li.
A default FASTA/Q parser from BioRuby is extremly slow. One alternative is to use bio-faster but that lacks support for FASTA files. However, bio-faster does parse qualities, unlike bio-kseq.
Timings
user system total real
BioRuby 2.130000 0.270000 2.400000 ( 2.403145)
Bio::Faster 0.420000 0.070000 0.490000 ( 0.486809)
Bio::Kseq 0.030000 0.010000 0.040000 ( 0.037176)
Installation
Add this line to your application's Gemfile:
gem 'bio-kseq'
And then execute:
$ bundle
Or install it yourself as:
$ gem install bio-kseq
Usage
require 'bio/kseq'
# Convert FASTQ to FASTA
kseq = Bio::Kseq.new("test.fastq")
while kseq.read! # returns truthy values when there is an entry
puts ">" + kseq.name
puts kseq.seq
end
kseq = Bio::Kseq.new("test.fastq.gz") # You can open GZIPed files flawlessly
kseq.read! or throw("Failed to read test.fastq.gz")
# Suppose entry is like this:
# @SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=36
# GGGTGATGGCCGCTGCCGATGGCGTCAAATCCCACC
# +SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=36
# IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IG9IC
kseq.name # = "SRR001666.1"
kseq.comment # = "071112_SLXA-EAS1_s_7:5:1:817:345 length=36", may be nil
kseq.seq # = "GGGTGATGGCCGCTGCCGATGGCGTCAAATCCCACC"
kseq.qual # = "IIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IG9IC", may be nil
kseq = Bio::Kseq.new(IO.popen("zcat test.fastq.gz")) # You can also process Ruby IO objects
kseq.read! or throw("Failed to read test.fastq.gz")
puts kseq # Outputs a valid FASTQ entryContributing
- Fork it ( http://github.com/gusevfe/bio-kseq/fork )
- Create your feature branch (
git checkout -b my-new-feature) - Commit your changes (
git commit -am 'Add some feature') - Push to the branch (
git push origin my-new-feature) - Create new Pull Request