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#!/usr/bin/env python
# File created on 08 Nov 2009.
from __future__ import division
__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Greg Caporaso", "Dan Knights"]
__license__ = "GPL"
__version__ = "1.4.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
__status__ = "Release"
from qiime.util import make_option
from qiime.pick_otus import map_otu_map_files
from qiime.format import write_otu_map
from qiime.util import parse_command_line_parameters
script_info={}
script_info['brief_description']="""Merge OTU mapping files"""
script_info['script_description']="""This script merges OTU mapping files generated by denoise_wrapper.py and/or pick_otus.py
For example, if otu_map1.txt contains:
= ==== ==== ====
0 seq1 seq2 seq5
1 seq3 seq4
2 seq6 seq7 seq8
= ==== ==== ====
and otu_map2.txt contains:
=== = =
110 0 2
221 1
=== = =
The resulting OTU map will be:
=== ==== ==== ==== ==== ==== ====
110 seq1 seq2 seq5 seq6 seq7 seq8
221 seq3 seq4
=== ==== ==== ==== ==== ==== ====
"""
script_info['script_usage']=[]
script_info['script_usage'].append(("""Expand an OTU map:""","""If the seq_ids in otu_map2.txt are otu_ids in otu_map1.txt, expand the seq_ids in otu_map2.txt to be the full list of associated seq_ids from otu_map1.txt. Write the resulting otu map to otu_map.txt (-o).""","""merge_otu_maps.py -i otu_map1.txt,otu_map2.txt -o otu_map.txt"""))
script_info['script_usage'].append(("""Expand a failures file:""",""" Some OTU pickers (e.g. uclust_ref) will generate a list of failures for sequences which could not be assigned to OTUs. If this occurs in a chained OTU picking process, the failures file will need to be expanded to include the orignal sequence ids. To do this, pass the failures file via -f, and the otu maps up to, but not including, the step that generated the failures file. ""","""merge_otu_maps.py -i otu_map1.txt,otu_map2.txt -f fail.txt -o all_failures.txt"""))
script_info['output_description']="""The result of this script is an OTU mapping file."""
script_info['required_options']=[
make_option('-i','--otu_map_fps',
help=('the otu map filepaths, comma-separated and '
'ordered as the OTU pickers were run [REQUIRED]')),
make_option('-o','--output_fp',
help='path to write output OTU map [REQUIRED]')
]
script_info['optional_options']=[
make_option('-f','--failures_fp',
help='failures filepath, if applicable')
]
script_info['version'] = __version__
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
otu_files = map(open,opts.otu_map_fps.split(','))
failures_fp = opts.failures_fp
output_fp = opts.output_fp
if failures_fp:
failures_f = open(failures_fp,'U')
else:
failures_f = None
try:
result = map_otu_map_files(otu_files,failures_file=failures_f)
except KeyError,e:
print ('Some keys do not map ('+ str(e) +') -- is the order of'
' your OTU maps equivalent to the order in which the OTU pickers'
' were run? If expanding a failures file, did you remember to leave'
' out the otu map from the run which generated the failures file?')
exit(1)
if failures_fp != None:
of = open(output_fp,'w')
of.write('\n'.join(result))
of.close()
else:
write_otu_map(result.items(),output_fp)
if __name__ == "__main__":
main()
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