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#!/usr/bin/env python
# File created on 18 Oct 2010
from __future__ import division
__author__ = "Justin Kuczynski"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Justin Kuczynski", "Catherine Lozupone"]
__license__ = "GPL"
__version__ = "1.4.0"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"
__status__ = "Release"
from qiime.util import parse_command_line_parameters, get_options_lookup
from qiime.util import make_option
from string import strip
from qiime.filter_by_metadata import parse_metadata_state_descriptions,\
get_sample_ids
from qiime.pool_by_metadata import pool_map, pool_otu_table, pool_iterative
from qiime.parse import parse_mapping_file, parse_otu_table
options_lookup = get_options_lookup()
script_info={}
script_info['brief_description']="""pool samples in OTU table and mapping file based on sample metadata from mapping file"""
script_info['script_description']="""this script outputs a new otu table and mapping file with some samples removed and replaced with one pooled sample. the new pooled sample will have fields in the mapping file the same as its constituent samples, if all are idential. Else it will just say 'multipleValues'."""
script_info['script_usage']=[]
script_info['script_usage'].append(("""Examples:""","""The following command pools all the Control samples into one sample named 'pooledControl'. The resulting data is written to seqs_otus.txt.filtered.xls and Fasting_Map.txt.filtered.xls:""","""%prog -i seqs_otus.txt -m Fasting_Map.txt -s 'Treatment:Control' -l pooledControl"""))
script_info['script_usage'].append(("""""","""Some variations are:
Pooling all samples in both Control and Fast in the Treatment field (i.e. pooling everything):""","""%prog -i seqs_otus.txt -m Fasting_Map.txt -s 'Treatment:Control,Fast' -l pooledSamples"""))
script_info['script_usage'].append(("""""","""Excluding Fast in the Treatment field - the syntax here is "*" to keep everything, then !Fast to eliminate the Fast group:""","""%prog -i seqs_otus.txt -m Fasting_Map.txt -s 'Treatment:*,!Fast' -l pooledNonFast"""))
script_info['output_description']="""The result is a pooled OTU table and mapping file."""
script_info['required_options']=[\
options_lookup['otu_table_as_primary_input'],\
make_option('-m', '--map', dest='map_fname',\
help='path to the map file [REQUIRED]'),\
make_option('-s', '--states', dest='valid_states',\
help="string containing valid states, e.g. 'STUDY_NAME:DOG'. Setting just 'STUDY_NAME' will bin samples by all unique category values. e.g. it will pool all samples marked DOG into a sample called STUDY_NAME.DOG all CAT into STUDY_NAME.CAT etc.")\
]
script_info['optional_options']=[\
make_option('-o', '--otu_outfile', dest='otu_out_fname', default=None,\
help='name of otu output file, default is otu_filename.pooled.txt'),\
make_option('-p', '--map_outfile', dest='map_out_fname', default=None,\
help='name of map output file, default is map_filename.pooled.txt'),\
make_option('-l', '--pooled_sample_name', dest='pooled_sample_name', default='pooledSample',\
help='new sample name used in new mapping file and new otu table'),\
]
script_info['version'] = __version__
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
map_file_name, otu_file_name, valid_states_str = \
opts.map_fname, opts.otu_table_fp, opts.valid_states
map_infile = open(map_file_name, 'U')
otu_infile = open(otu_file_name, 'U')
map_out_fname = opts.map_out_fname
otu_out_fname = opts.otu_out_fname
if map_out_fname is None:
map_out_fname = map_file_name + '.pooled.txt'
if otu_out_fname is None:
otu_out_fname = otu_file_name + '.pooled.txt'
# write out the filtered mapping file
map_outfile = open(map_out_fname, 'w')
otu_outfile = open(otu_out_fname, 'w')
map_data, map_header, map_comments = parse_mapping_file(map_infile)
map_infile.close()
map_infile = open(map_file_name, 'U') # reopen for later
valid_states_str_split = valid_states_str.split(':')
if len(valid_states_str_split) > 1:
valid_states = parse_metadata_state_descriptions(valid_states_str)
sample_ids_to_pool = get_sample_ids(map_data, map_header, valid_states)
pool_map(map_infile, map_outfile,
opts.pooled_sample_name, sample_ids_to_pool)
pool_otu_table(otu_infile, otu_outfile,
opts.pooled_sample_name, sample_ids_to_pool)
else:
pool_iterative(map_infile, map_outfile, otu_infile, otu_outfile, \
valid_states_str)
if __name__ == "__main__":
main()
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