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#!/usr/bin/env python
# File created on 15 Feb 2011
from __future__ import division
__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.4.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
__status__ = "Release"
from qiime.util import make_option
from qiime.parse import parse_mapping_file, parse_otu_table
from qiime.format import format_otu_table
from qiime.util import parse_command_line_parameters, get_options_lookup
from qiime.sort import sort_otu_table, sort_otu_table_by_mapping_field
options_lookup = get_options_lookup()
script_info = {}
script_info['brief_description'] = "Script for sorting the sample IDs in an OTU table based on a specified value in a mapping file."
script_info['script_description'] = ""
script_info['script_usage'] = [("",
"sort samples by the age field in the mapping file",
"sort_otu_table.py -i otu_table.txt -o age_sorted_otu_table.txt -m map.txt -s Age"),
("",
"sort samples based on order in a file where each line starts with a sample id",
"sort_otu_table.py -i otu_table.txt -o age_sorted_otu_table.txt -l sorted_sample_id_list.txt")]
script_info['output_description']= ""
script_info['required_options'] = [
make_option('-i','--input_otu_table',
help='Input OTU table filepath.',
type='existing_filepath'),
make_option('-o','--output_fp',
help='Output OTU table filepath.',
type='new_filepath'),
]
script_info['optional_options'] = [
make_option('-m','--mapping_fp',
help='Input metadata mapping filepath. [default: %default]',
type='existing_filepath'),
make_option('-s','--sort_field',
help='Category to sort OTU table by. [default: %default]'),
make_option('-l','--sorted_sample_ids_fp',
help='Sorted sample id filepath [default: %default]',
type='existing_filepath')
]
script_info['option_label']={'input_otu_table':'OTU table filepath',
'output_fp': 'Output filepath',
'mapping_fp':'QIIME-formatted mapping filepath',
'sort_field':'Category to sort by',
'sorted_sample_ids_fp': 'Sorted sample id filepath'}
script_info['version'] = __version__
def sample_ids_from_f(lines):
result = []
for line in lines:
line = line.strip()
if line and not line.startswith('#'):
result.append(line.split()[0])
return result
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
otu_table_data = parse_otu_table(open(opts.input_otu_table,'U'))
sort_field = opts.sort_field
mapping_fp = opts.mapping_fp
sorted_sample_ids_fp = opts.sorted_sample_ids_fp
if sort_field and mapping_fp:
mapping_data = parse_mapping_file(open(mapping_fp,'U'))
result = sort_otu_table_by_mapping_field(otu_table_data,
mapping_data,
sort_field)
elif sorted_sample_ids_fp:
sorted_sample_ids = sample_ids_from_f(open(sorted_sample_ids_fp,'U'))
result = sort_otu_table(otu_table_data,
sorted_sample_ids)
else:
parser.error("must provide either --sort_field and --mapping_fp OR --sorted_sample_ids_fp")
# format and write the otu table
result_str = format_otu_table(result[0],result[1],result[2],result[3])
of = open(opts.output_fp,'w')
of.write(result_str)
of.close()
if __name__ == "__main__":
main()
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