def test_no_labels(self):
"""FastaParser should return empty list from file w/o seqs"""
# should fail if strict (the default)
self.assertRaises(RecordError, list,
FastaParser(self.labels, strict=True))
# if not strict, should skip the records
self.assertEqual(list(FastaParser(self.labels, strict=False)), [])
def test_multiple_bad(self):
"""Parser should complain or skip bad records"""
self.assertRaises(RecordError, list, FastaParser(self.twogood))
f = list(FastaParser(self.twogood, strict=False))
self.assertEqual(len(f), 2)
a, b = f
a, b = a[1], b[1] # field 0 is name
self.assertEqual((a.name, a), ("abc", "caggac"))
self.assertEqual((b.name, b), ("456", "cg"))
def test_single(self):
"""FastaParser should read single record as seq object"""
f = list(FastaParser(self.oneseq))
self.assertEqual(len(f), 1)
a = f[0]
self.assertEqual(a, ("abc", "UCAG"))
self.assertEqual(a[1].name, "abc")
f = list(FastaParser(self.multiline))
self.assertEqual(len(f), 1)
a = f[0]
self.assertEqual(a, ("xyz", "UUUUCCAAAAAG"))
self.assertEqual(a[1].name, "xyz")
def test_multiple_constructor_bad(self):
"""Parser should complain or skip bad records w/ constructor"""
def dnastrict(x, **kwargs):
try:
return Dna(x, check=True, **kwargs)
except Exception as e:
raise RecordError("Could not convert sequence")
self.assertRaises(RecordError, list, FastaParser(self.oneX, dnastrict))
f = list(FastaParser(self.oneX, dnastrict, strict=False))
self.assertEqual(len(f), 2)
a, b = f
a, b = a[1], b[1]
self.assertEqual((a.name, a), ("abc", "caggac".upper()))
self.assertEqual((b.name, b), ("456", "cg".upper()))
def test_single_constructor(self):
"""FastaParser should use constructors if supplied"""
f = list(FastaParser(self.oneseq, Dna))
self.assertEqual(len(f), 1)
a = f[0]
self.assertEqual(a, ("abc", "TCAG"))
self.assertEqual(a[1].name, "abc")
def upper_abc(x):
return None, {"ABC": x.upper()}
f = list(FastaParser(self.multiline, Dna, upper_abc))
self.assertEqual(len(f), 1)
a = f[0]
self.assertEqual(a, (None, "TTTTCCAAAAAG"))
self.assertEqual(a[1].name, None)
self.assertEqual(a[1].info.ABC, "XYZ")
def test_multiple(self):
"""FastaParser should read multiline records correctly"""
f = list(FastaParser(self.threeseq))
self.assertEqual(len(f), 3)
for i in f:
assert isinstance(i[1], Sequence)
a, b, c = f
self.assertEqual((a[1].name, a[1]), ("123", "a"))
self.assertEqual((b[1].name, b[1]), ("abc", "caggac"))
self.assertEqual((c[1].name, c[1]), ("456", "cg"))
def test_annotate_from_gff(self):
"""correctly annotates a Sequence from a gff file"""
from cogent3.parse.fasta import FastaParser
fasta_path = os.path.join("data/c_elegans_WS199_dna_shortened.fasta")
gff3_path = os.path.join("data/c_elegans_WS199_shortened_gff.gff3")
name, seq = next(FastaParser(fasta_path))
sequence = Sequence(seq)
sequence.annotate_from_gff(gff3_path)
matches = [m for m in sequence.get_annotations_matching("*", extend_query=True)]
# 13 features with one having 2 parents, so 14 instances should be found
self.assertEqual(len(matches), 14)
def test_empty(self):
"""FastaParser should return empty list from 'file' w/o labels"""
self.assertEqual(list(FastaParser(self.empty)), [])
self.assertEqual(list(FastaParser(self.nolabels, strict=False)), [])
self.assertRaises(RecordError, list, FastaParser(self.nolabels))
