Allan Espinosa

FASTA splitting with BioRuby

2009 December 9

In reference to my previous post, here’s the splitter using BioRuby.  Note that I also changed the outer loop to one file per iteration instead of some crazy rules of when to create the file.

`[sourcecode lang=“ruby”] #!/usr/bin/env ruby # # Script: dumpseq.rb [file] [N] [prefix] # Description: Splits a fasta file evenl across N files. dumps files in the # [prefix] directory require ‘bio’ require ‘fileutils’

include Bio

seqs =[0]) ncpus = ARGV[1].to_i prefix = ARGV[2]

Remove and hardwire n_seqs if you know beforehand the number of sequences in

a file. Saves readtime

n_seqs = 0 seqs.each do |seq| n_seqs += 1 end seqs.rewind

overflow = n_seqs % ncpus split_size = n_seqs / ncpus

ncpus.times do |i| filename = sprintf “%s/D%07d/seq%07d.fasta”, prefix, i, i FileUtils.mkdir_p File.dirname(filename) dump =, “w”) split_size.times do |j| dump << seqs.next_entry.to_s end if i < overflow dump << seqs.next_entry.to_s end dump.close end