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__author__ = "Gavin Huttley, Anuj Pahwa"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Gavin Huttley", "Anuj Pahwa"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Gavin Huttley"
__email__ = "Gavin.Huttley@anu.edu.au"
__status__ = "Development"
def MinimalFastqParser(data, strict=True):
"""yields name, seq, qual from fastq file
Arguments:
- strict: checks the quality and sequence labels are the same
"""
if type(data) == str:
data = open(data)
# fastq format is very simple, defined by blocks of 4 lines
line_num = -1
record = []
for line in data:
line_num += 1
if line_num == 4:
if strict: # make sure the seq and qual labels match
assert record[0][1:] == record[2][1:], \
'Invalid format: %s -- %s' % (record[0][1:], record[2][1:])
yield record[0][1:], record[1], record[3]
line_num = 0
record = []
record.append(line.strip())
if record:
if strict and record[0]: # make sure the seq and qual labels match
assert record[0][1:] == record[2][1:], 'Invalid format'
if record[0]: # could be just an empty line at eof
yield record[0][1:], record[1], record[3]
if type(data) == file:
data.close()
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