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#!/usr/bin/env python
# File created on 09 Feb 2010
from __future__ import division
__author__ = "Doug Wendel"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Rob Knight", "Doug Wendel"]
__license__ = "GPL"
__version__ = "1.4.0"
__maintainer__ = "Kyle Bittinger"
__email__ = "kylebittinger@gmail.com"
__status__ = "Release"
from qiime.make_library_id_lists import get_first_id, get_ids
from qiime.util import parse_command_line_parameters
from qiime.util import make_option
from os.path import exists, join
from os import makedirs
script_info={}
script_info['brief_description']="""Make library id lists"""
script_info['script_description']="""Makes a list of the ids corresponding to each library represented in the input fasta file. Assumes that the libraries are the output of split_libraries.py and that they contain the 454 read id for each sequence as is standard in the split_libraries.py output. Produces a separate file for each library."""
script_info['script_usage']=[]
script_info['script_usage'].append(("""Example:""","""Create a list containing library ids for a fasta file (seqs.fna):""","""make_library_id_lists.py -i seqs.fna -o results/"""))
script_info['output_description']="""This script produces a separate file for each library."""
script_info['required_options']=[\
make_option("-i","--input_fasta",dest='in_fasta',default = None,\
help="The path to a FASTA file containing input sequences")
]
script_info['optional_options']=[\
make_option("-s", "--screened_rep_seqs",dest="screened_rep_seqs",
default=None,
help="The path to a FASTA file containing screened representative seqs" +
"[DEFAULT: %default]"),\
make_option("-u", "--otus",dest="otus",
default=None,
help="The path to an OTU file mapping OTUs onto rep seqs" +
"[DEFAULT: %default]"),\
make_option("-o","--outdir",dest='outdir',\
default = '.',\
help=""" The base directory to save results (one file per library)."""),\
make_option("-f", "--field",dest="field", type=int,\
default = 1,\
help="Index of space-delimited field to read id from [DEFAULT: %default]"),\
make_option("--debug", dest="debug", action="store_true",
default=False, help="Show debug output.")
]
script_info['version'] = __version__
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
options, args = option_parser.parse_args()
if options.debug:
print "PRODUCING DEBUG OUTPUT"
bad_seq_ids = set()
bad_otu_ids = None
#if we got a file to screen against, find the relevant ids and delete them
if options.screened_rep_seqs:
bad_otu_ids = get_first_id(open(options.screened_rep_seqs, 'U'))
if not options.otus:
raise RuntimeError, "Must specify an OTU file if performing a screen."
for line in open(options.otus, 'U'):
fields = line.split()
if fields[0] in bad_otu_ids:
bad_seq_ids.update(fields[1:])
if options.debug:
if bad_otu_ids is not None:
print "Found %s bad otu ids: %s" % (len(bad_otu_ids), bad_otu_ids)
print "Found %s bad seq ids: %s" % (len(bad_seq_ids), bad_seq_ids)
ids = get_ids(open(options.in_fasta, 'U'), options.field, bad_seq_ids,
options.debug)
#add empty unassigned ids for file creation
if 'Unassigned' not in ids:
ids['Unassigned'] = []
if not exists(options.outdir):
makedirs(options.outdir)
for k, idlist in ids.items():
outfile = open(join(options.outdir, k + '.txt'), 'w')
outfile.write('\n'.join(sorted(idlist)))
outfile.close()
if __name__ == "__main__":
main()
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