Sha256: 81ceec650c53bea5f95e7514c7cdcc2c470971e50ccd24faa17b199f1abacfbe
Contents?: true
Size: 1.83 KB
Versions: 11
Compression:
Stored size: 1.83 KB
Contents
##
# Split a fasta file into many fasta files with n reads
#
require 'zlib'
module Lederhosen
class CLI
desc 'split_fasta',
'splits input fasta file into separate fasta files containing n reads'
method_option :input, :type => :string, :required => true
method_option :out_dir, :type => :string, :required => true
method_option :n, :type => :numeric, :required => true
method_option :gzip, :type => :boolean, :default => false
def split_fasta
input = options[:input]
out_dir = options[:out_dir]
n = options[:n].to_i
gzip = options[:gzip]
ohai "splitting #{input} into files with #{n} reads stored in #{out_dir}"
ohai "using gzip" if gzip
`mkdir -p #{out_dir}`
File.open input do |handle|
pbar = ProgressBar.new 'splitting', File.size(handle)
Dna.new(handle).each_with_index do |record, i|
pbar.set handle.pos
# I have to use a class variable here because
# if I don't the variable gets set to nil after
# after each iteration.
@out =
if i%n == 0 # start a new file
# GzipWriter must be closed explicitly
# this raises an exception this first time
@out.close rescue nil
# create an IO object depending on whether or
# not the user wants to use gzip
if gzip
Zlib::GzipWriter.open(File.join(out_dir, "split_#{i/n}.fasta.gz"))
else
File.open(File.join(out_dir, "split_#{i/n}.fasta"), 'w')
end
else # keep using current handle
@out
end
@out.puts record
end
pbar.finish
@out.close
end
ohai "created #{Dir[File.join(out_dir, '*')].size} files"
end
end
end
Version data entries
11 entries across 11 versions & 1 rubygems