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_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))
class FastaParserTests(GenericFastaTest):
"""Tests of FastaParser: returns sequence objects."""
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))
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_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_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_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_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, 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()))