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#!/usr/bin/env python
#file cogent.parse.infernal.py
"""Parses various Infernal output formats."""
from cogent.parse.table import ConvertFields, SeparatorFormatParser,is_empty
__author__ = "Jeremy Widmann"
__copyright__ = "Copyright 2007-2009, The Cogent Project"
__credits__ = ["Jeremy Widmann"]
__license__ = "GPL"
__version__ = "1.4.1"
__maintainer__ = "Jeremy Widmann"
__email__ = "jeremy.widmann@colorado.edu"
__status__ = "Development"
def CmsearchParser(lines):
"""Parser for tabfile format cmsearch result.
- IMPORTANT: Will not parse standard output from cmsearch. You must
use --tabfile with cmsearch to get correct format to use this
parser.
- NOTE: Will only work with search result files with a single CM
as a query. Will not work with multiple search result files
that have been concatenated.
- Result will be list of hits with following order:
[target name, target start, target stop, query start, query stop,
bit score, E-value, GC%]
"""
# Converting indices and %GC to integers and bit score to float.
# Since E-value is only present if CM is calibrated, leaving as string.
conversion_fields = [(1,int),(2,int),(3,int),(4,int),(5,float),(7,int)]
cmsearch_converter = ConvertFields(conversion_fields)
#Ignore hash characters and empty lines
ignore_funct = lambda x: x.startswith('#') or is_empty(x)
#make parser
cmsearch_parser = SeparatorFormatParser(with_header=False,\
converter=cmsearch_converter,\
ignore=ignore_funct,\
sep=None)
return cmsearch_parser(lines)
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