def test_constructor_is_none(self):
lrf = LabeledRecordFinder(lambda x: x.strip().startswith('>'),
constructor=None)
lines = ' \t >abc \n \t def\n // \t\n\t\t >efg \n//'.split('\n')
obs = list(lrf(lines))
exp = [[' \t >abc ', ' \t def', ' // \t'], ['\t\t >efg ', '//']]
self.assertEqual(obs, exp)
def test_parsers_ignore(self):
def never(line):
return False
def ignore_labels(line):
return (not line) or line.isspace() or line.startswith('#')
def is_start(line):
return line.startswith('>')
lines = ['>abc', '\n', '1', '>def', '#ignore', '2']
self.assertEqual(list(LabeledRecordFinder(is_start)(lines)),
[['>abc', '1'], ['>def', '#ignore', '2']])
self.assertEqual(
list(LabeledRecordFinder(is_start, ignore=never)(lines)),
[['>abc', '', '1'], ['>def', '#ignore', '2']])
self.assertEqual(
list(LabeledRecordFinder(is_start, ignore=ignore_labels)(lines)),
[['>abc', '1'], ['>def', '2']])
def is_fasta_label(x):
"""Checks if x looks like a FASTA label line."""
return x.startswith('>')
def is_blank_or_comment(x):
"""Checks if x is blank or a FASTA comment line."""
return (not x) or x.startswith('#') or x.isspace()
def is_blank(x):
"""Checks if x is blank."""
return (not x) or x.isspace()
FastaFinder = LabeledRecordFinder(is_fasta_label, ignore=is_blank_or_comment)
def parse_fasta(infile,
strict=True,
label_to_name=str,
finder=FastaFinder,
is_label=None,
label_characters='>'):
r"""yields label and seq from a fasta file.
Parameters
----------
data : open file object or str
An open fasta file or a path to it.
def setUp(self):
"""Define a standard LabeledRecordFinder"""
self.FastaLike = LabeledRecordFinder(lambda x: x.startswith('>'))
def setUp(self):
self.FastaLike = LabeledRecordFinder(lambda x: x.startswith('>'))