Quick-and-dirty script to take combined bl6 file and split it into per-metagenome bl6 files.

qiime_to_humann.py

#!/usr/bin/env python
# File created on 19 Jul 2012
from __future__ import division

__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.5.0-dev"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
__status__ = "Development"

from os.path import join
from cogent.util.misc import create_dir
from qiime.util import parse_command_line_parameters, make_option, gzip_open

script_info = {}
script_info['brief_description'] = "Quick-and-dirty script to take combined bl6 file and split it into per-metagenome bl6 files."
script_info['script_description'] = ""
script_info['script_usage'] = [("","","")]
script_info['output_description']= ""
script_info['required_options'] = [
 make_option('-i','--input_fp',type="existing_filepath",help='the input filepath'),\
 make_option('-o','--output_dir',type="new_dirpath",help='the output directory'),\
]
script_info['optional_options'] = []
script_info['version'] = __version__

def qiime_to_humann(bl6_lines,output_dir):
    output_fs = {}
    for line in bl6_lines:
        id_ = line.split('_')[0]
        try:
            f = output_fs[id_]
        except KeyError:
            output_fs[id_] = open(join(output_dir,'%s.bl6' % id_),'w')
            f = output_fs[id_]
        f.write(line)
    for e in output_fs.values():
        e.close()
    


def main():
    option_parser, opts, args =\
       parse_command_line_parameters(**script_info)
    print "WARNING: This script is untested! Use at your own risk!"
    
    create_dir(opts.output_dir)
    if opts.input_fp.endswith('.gz'):
        qiime_to_humann(gzip_open(opts.input_fp),opts.output_dir)
    else:
        qiime_to_humann(open(opts.input_fp,'U'),opts.output_dir)


if __name__ == "__main__":
    main()