def test_multiple_bad(self):
"""MinimalFastaParser should complain or skip bad records"""
self.assertRaises(RecordError, list, MinimalFastaParser(self.twogood))
f = list(MinimalFastaParser(self.twogood, strict=False))
self.assertEqual(len(f), 2)
a, b = f
self.assertEqual(a, ("abc", "caggac"))
self.assertEqual(b, ("456", "cg"))
def test_no_labels(self):
"""MinimalFastaParser should return empty list from file w/o seqs"""
# should fail if strict (the default)
self.assertRaises(RecordError, list,
MinimalFastaParser(self.labels, strict=True))
# if not strict, should skip the records
self.assertEqual(list(MinimalFastaParser(self.labels, strict=False)),
[])
def test_read(self):
"""correctly read content"""
with open("data" + os.sep + "brca1.fasta") as infile:
expect = {l: s for l, s in MinimalFastaParser(infile)}
dstore = self.Class(self.basedir, suffix=".fasta")
data = dstore.read(self.basedir)
data = data.splitlines()
got = {l: s for l, s in MinimalFastaParser(data)}
self.assertEqual(got, expect)
def test_single(self):
"""MinimalFastaParser should read single record as (label, seq) tuple"""
f = list(MinimalFastaParser(self.oneseq))
self.assertEqual(len(f), 1)
a = f[0]
self.assertEqual(a, ("abc", "UCAG"))
f = list(MinimalFastaParser(self.multiline))
self.assertEqual(len(f), 1)
a = f[0]
self.assertEqual(a, ("xyz", "UUUUCCAAAAAG"))
def test_multiple(self):
"""MinimalFastaParser should read multiline records correctly"""
f = list(MinimalFastaParser(self.threeseq))
self.assertEqual(len(f), 3)
a, b, c = f
self.assertEqual(a, ("123", "a"))
self.assertEqual(b, ("abc", "caggac"))
self.assertEqual(c, ("456", "cg"))
def test_gt_bracket_in_seq(self):
"""MinimalFastaParser handles alternate finder function
this test also illustrates how to use the MinimalFastaParser
to handle "sequences" that start with a > symbol, which can
happen when we abuse the MinimalFastaParser to parse
fasta-like sequence quality files.
"""
oneseq_w_gt = ">abc\n>CAG\n".split("\n")
def get_two_line_records(infile):
line1 = None
for line in infile:
if line1 == None:
line1 = line
else:
yield (line1, line)
line1 = None
f = list(MinimalFastaParser(oneseq_w_gt, finder=get_two_line_records))
self.assertEqual(len(f), 1)
a = f[0]
self.assertEqual(a, ("abc", ">CAG"))
def test_empty(self):
"""MinimalFastaParser should return empty list from 'file' w/o labels"""
self.assertEqual(list(MinimalFastaParser(self.empty)), [])
self.assertEqual(list(MinimalFastaParser(self.nolabels, strict=False)),
[])
self.assertRaises(RecordError, list, MinimalFastaParser(self.nolabels))
def test_parser_from_file(self):
"""passing path should work"""
path = os.path.join(data_path, "brca1.fasta")
seqs = dict(p for p in MinimalFastaParser(path))
self.assertTrue("Human" in seqs)
def load_from_fasta(filename):
infile = open_(filename, mode='rt')
parser = MinimalFastaParser(infile)
seqs = [(n, s) for n, s in parser]
infile.close()
return ArrayAlignment(data=seqs, moltype=DNA)
