/usr/share/pyshared/cogent/parse/bowtie.py is in python-cogent 1.5.3-2.
This file is owned by root:root, with mode 0o644.
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"""Parser for the default bowtie output
Compatible with version 0.12.5
"""
from cogent import LoadTable
from cogent.parse.table import ConvertFields
__author__ = "Gavin Huttley, Anuj Pahwa"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Rob Knight","Peter Maxwell", "Gavin Huttley", "Anuj Pahwa"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Gavin Huttley"
__email__ = "gavin.huttley@anu.edu.au"
__status__ = "Development"
# The 4th and the 7th elements of the row of data returned from bowtie are
# integer values and can thus be converted.
row_converter = ConvertFields([(3, int), (6, int)])
def BowtieOutputParser(data, row_converter=row_converter):
"""yields a header and row of data from the default bowtie output
Arguments:
- row_converter: if not provided, uses a default converter which casts
the Offset and Other Matches fields to ints. If set to None, all
returned data will be strings (this is faster).
"""
header = ['Query Name', 'Strand Direction','Reference Name', 'Offset',
'Query Seq', 'Quality', 'Other Matches', 'Mismatches']
yield header
# If given a filename for the data
if type(data) == str:
data = open(data)
for record in data:
row = record.rstrip('\n').split('\t')
if row_converter:
row = row_converter(row)
# convert the last element to a list of strings
if row[-1] is '':
row[-1] = []
else:
row[-1] = row[-1].split(',')
yield row
def BowtieToTable(data, row_converter=row_converter):
"""Converts bowtie output to a table
Arguments:
- row_converter: if not provided, uses a default converter which casts
the Offset and Other Matches fields to ints. If set to None, all
returned data will be strings (this is faster).
"""
parser = BowtieOutputParser(data, row_converter=row_converter)
header = parser.next()
rows = [row for row in parser]
table = LoadTable(header=header, rows=rows)
return table
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