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Contents
require_relative '../../bioinform'
require 'docopt'
module Bioinform
module CLI
module SplitMotifs
extend Bioinform::CLI::Helpers
def self.main(argv)
doc = <<-DOCOPT
Motif splitter.
It get a file with a set of motifs and splits it into motifs according to their names.
Usage:
split_motifs [options] <collection-file>
Options:
-h --help Show this screen.
-e --extension EXT Extension of output files
-f --folder FOLDER Where to save output files [default: .]
DOCOPT
doc.gsub!(/^#{doc[/\A +/]}/,'')
options = Docopt::docopt(doc, argv: argv)
folder = options['--folder']
extension = options['--extension']
collection_filename = options['<collection-file>']
Dir.mkdir(folder) unless Dir.exist?(folder)
raise "File #{collection_filename} not exist" unless File.exist? collection_filename
input = File.read(collection_filename)
Parser.choose(input).split.each do |motif|
if motif.is_a? PM
File.open(set_folder(folder, set_extension(motif.name, extension || motif.class.name.gsub(/^.*::/,'').downcase)), 'w'){|f| f.puts motif}
else
motif = PM.new(motif)
File.open(set_folder(folder, set_extension(motif.name, extension || 'mat')), 'w'){|f| f.puts motif}
end
end
rescue Docopt::Exit => e
puts e.message
end
end
end
end
Version data entries
5 entries across 5 versions & 1 rubygems