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#!/usr/bin/env python
# File created on 09 Feb 2010
#file filter_otus_by_sample.py
from __future__ import division
__author__ = "Jesse Stombaugh"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Jesse Stombaugh"]
__license__ = "GPL"
__version__ = "1.4.0"
__maintainer__ = "Jesse Stombaugh"
__email__ = "jesse.stombaugh@colorado.edu"
__status__ = "Release"
from qiime.util import make_option
from qiime.util import parse_command_line_parameters, get_options_lookup
from qiime.filter_otus_by_sample import filter_samples,process_extract_samples
import os
from cogent import LoadSeqs
from qiime.parse import fields_to_dict
options_lookup = get_options_lookup()
#filter_otus_by_sample.py
script_info={}
script_info['brief_description']="""Filter OTU mapping file and sequences by SampleIDs"""
script_info['script_description']="""This filter allows for the removal of sequences and OTUs containing user-specified Sample IDs, for instance, the removal of negative control samples. This script identifies OTUs containing the specified Sample IDs and removes its corresponding sequence from the sequence collection."""
script_info['script_usage']=[]
script_info['script_usage'].append(("""Example:""","""The following command can be used, where all options are passed (using the resulting OTU file from pick_otus.py, FASTA file from split_libraries.py and removal of Sample1) with the resulting data being written to the output directory "filtered_otus/":""","""filter_otus_by_sample.py -i seqs_otus.txt -f seqs.fna -s Sample1 -o filtered_otus/"""))
script_info['output_description']="""As a result a new OTU and sequence file is generated and written to a randomly generated folder where the name of the folder starts with "filter_by_otus" Also included in the folder, is another FASTA file containing the removed sequences, leaving the user with 3 files."""
script_info['required_options']=[\
options_lookup['otu_map_as_primary_input'],
options_lookup['input_fasta'],
make_option('-s', '--samples_to_extract', help='This is a list of sample \
ids, which should be removed from the OTU file')]
script_info['optional_options']=[\
options_lookup['output_dir']
]
script_info['version'] = __version__
def main():
"""opens files as necessary based on prefs"""
option_parser, opts, args = parse_command_line_parameters(**script_info)
data = {}
fasta_file = opts.input_fasta_fp
# load the input alignment
data['aln'] = LoadSeqs(fasta_file,aligned=False)
#Load the otu file
otu_path=opts.otu_map_fp
otu_f = open(otu_path, 'U')
otus = fields_to_dict(otu_f)
otu_f.close()
data['otus']=otus
#Determine which which samples to extract from representative seqs
#and from otus file
if opts.samples_to_extract:
prefs=process_extract_samples(opts.samples_to_extract)
filepath=opts.input_fasta_fp
filename=filepath.strip().split('/')[-1]
filename=filename.split('.')[0]
if opts.output_dir:
if os.path.exists(opts.output_dir):
dir_path=opts.output_dir
else:
try:
os.mkdir(opts.output_dir)
dir_path=opts.output_dir
except OSError:
pass
else:
dir_path='./'
try:
action = filter_samples
except NameError:
action = None
#Place this outside try/except so we don't mask NameError in action
if action:
action(prefs, data, dir_path,filename)
if __name__ == "__main__":
main()
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