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#!/usr/bin/env python
# File created on 12 Aug 2010
from __future__ import division
__author__ = "Jens Reeder"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Jens Reeder"]
__license__ = "GPL"
__version__ = "1.8.0"
__maintainer__ = "Jose Clemente"
__email__ = "jose.clemente@gmail.com"
from glob import glob
from os.path import exists, split, splitext, isdir
from qiime.util import make_option
from qiime.util import parse_command_line_parameters,\
get_options_lookup, create_dir
from qiime.shared_phylotypes import calc_shared_phylotypes
options_lookup = get_options_lookup()
script_info = {}
script_info['brief_description'] = "Compute shared OTUs between all pairs of samples"
script_info['script_description'] = "This script computes from an OTU table a matrix with the number of shared phylotypes between all pairs of samples."
script_info['script_usage'] = [
("Single example","Compute shared OTUs on one OTU table for all samples","%prog -i otu_table.biom -o shared_otus.txt"),
("Reference sample example","Compute shared OTUs with respect to a reference sample. Computes shared OTUs between all pairs of samples and the reference sample. E.g. in a transplant study this can be used to establish a base line count of shared OTUs with the Donor sample before and after the transplant.","%prog -i otu_table.biom -o shared_otus_PC.636.txt -r PC.636"),
("Batch mode example","Compute shared OTUs for a set of OTU tables, e.g. from running multiple_rarefactions.py, with an even number of sequences per sample. The resulting directory can be fed to dissimilarity_mtx_stats.py, which computes mean, median and the standard deviation on the provided tables.", "%prog -i rarefied_otu_tables/ -o shared_otus/")
]
script_info['output_description']= ""
script_info['required_options'] = [\
make_option('-i','--otu_table_fp',type='existing_path',\
help='path to the input OTU table in biom format or a directory containing OTU tables'),
options_lookup['output_fp']
]
script_info['optional_options'] = [\
# Example optional option
make_option('-r','--reference_sample',type='string',
help='Name of reference sample to which all pairs of samples should be compared '
+ '[default: %default]', default=None),
]
script_info['version'] = __version__
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
if isdir(opts.otu_table_fp):
ret_code = create_dir(opts.output_fp, fail_on_exist=False)
#run on each file in dir
for fp in glob(opts.otu_table_fp +'/*biom'):
parent_dir_name, file_name = split(fp)
basename, extension = splitext(file_name)
out_fp = opts.output_fp +"/"+basename+"_shared_OTUs.txt"
out_fh = open(out_fp, "w")
out_fh.write(calc_shared_phylotypes(open(fp, "U"),
opts.reference_sample))
out_fh.close()
else:
#run in single file mode
try:
out_fh = open(opts.output_fp,"w")
except IOError, message:
exit(("Can't open output file %s for writing. Check the permissions "\
+"or existing directory with identical name.\n%s")
% (opts.output_fp,message))
out_fh.write(calc_shared_phylotypes(open(opts.otu_table_fp, "U"),
opts.reference_sample))
if __name__ == "__main__":
main()
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