Sha256: c95c300bd5e9e1fc9f3e560533eb882bc4254a8f8b12de3652e4bc745c4a5eb2
Contents?: true
Size: 864 Bytes
Versions: 5
Compression:
Stored size: 864 Bytes
Contents
##
# Split a fasta file into many fasta files with n reads
#
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
def split_fasta
input = options[:input]
out_dir = options[:out_dir]
n = options[:n].to_i
ohai "splitting #{input} into files with #{n} reads stored in #{out_dir}"
`mkdir -p #{out_dir}`
File.open input do |handle|
Dna.new(handle).each_with_index do |record, i|
@out = File.open(File.join(out_dir, "split_#{i/n}.fasta"), 'w') if i%n == 0
@out.puts record
end
end
end
end
end
Version data entries
5 entries across 5 versions & 1 rubygems