def test_issue_80():
# This issue turned out to not be an actual issue with the alignment
# algorithm. The following alignment is found because it has more matches
# than the 'obvious' one:
#
# TCGTATGCCGTCTTC
# =========X==XX=
# TCGTATGCCCTC--C
#
# This is correct, albeit a little surprising, since an alignment without
# indels would have only two errors.
adapter = Adapter(
sequence="TCGTATGCCGTCTTC",
where=Where.BACK,
remove='suffix',
max_error_rate=0.2,
min_overlap=3,
read_wildcards=False,
adapter_wildcards=False)
read = Sequence(name="seq2", sequence="TCGTATGCCCTCC")
result = adapter.match_to(read)
assert result.errors == 3, result
assert result.astart == 0, result
assert result.astop == 15, result
def test_issue_80(): # This issue turned out to not be an actual issue with the alignment # algorithm. The following alignment is found because it has more matches # than the 'obvious' one: # # TCGTATGCCGTCTTC # =========X==XX= # TCGTATGCCCTC--C # # This is correct, albeit a little surprising, since an alignment without # indels would have only two errors. adapter = Adapter( sequence="TCGTATGCCGTCTTC", where=BACK, remove='suffix', max_error_rate=0.2, min_overlap=3, read_wildcards=False, adapter_wildcards=False) read = Sequence(name="seq2", sequence="TCGTATGCCCTCC") result = adapter.match_to(read) assert result.errors == 3, result assert result.astart == 0, result assert result.astop == 15, result
def test_parse_braces_fail():
for expression in ['{', '}', '{}', '{5', '{1}', 'A{-7}', 'A{', 'A{1', 'N{7', 'AN{7', 'A{4{}',
'A{4}{3}', 'A{b}', 'A{6X}', 'A{X6}']:
print(expression)
try:
Adapter.parse_braces(expression)
except ValueError as e:
print(e)
assert_raises(ValueError, lambda: Adapter.parse_braces(expression))
def test_parse_braces():
assert Adapter.parse_braces('') == ''
assert Adapter.parse_braces('A') == 'A'
assert Adapter.parse_braces('A{0}') == ''
assert Adapter.parse_braces('A{1}') == 'A'
assert Adapter.parse_braces('A{2}') == 'AA'
assert Adapter.parse_braces('A{2}C') == 'AAC'
assert Adapter.parse_braces('ACGTN{3}TGACCC') == 'ACGTNNNTGACCC'
assert Adapter.parse_braces('ACGTN{10}TGACCC') == 'ACGTNNNNNNNNNNTGACCC'
assert Adapter.parse_braces('ACGTN{3}TGA{4}CCC') == 'ACGTNNNTGAAAACCC'
assert Adapter.parse_braces('ACGTN{0}TGA{4}CCC') == 'ACGTTGAAAACCC'
def test_parse_braces():
assert Adapter.parse_braces('') == ''
assert Adapter.parse_braces('A') == 'A'
assert Adapter.parse_braces('A{0}') == ''
assert Adapter.parse_braces('A{1}') == 'A'
assert Adapter.parse_braces('A{2}') == 'AA'
assert Adapter.parse_braces('A{2}C') == 'AAC'
assert Adapter.parse_braces('ACGTN{3}TGACCC') == 'ACGTNNNTGACCC'
assert Adapter.parse_braces('ACGTN{10}TGACCC') == 'ACGTNNNNNNNNNNTGACCC'
assert Adapter.parse_braces('ACGTN{3}TGA{4}CCC') == 'ACGTNNNTGAAAACCC'
assert Adapter.parse_braces('ACGTN{0}TGA{4}CCC') == 'ACGTTGAAAACCC'
def test_issue_265():
"""Crash when accessing the matches property of non-anchored linked adapters"""
s = Sequence('name', 'AAAATTTT')
front_adapter = Adapter('GGG', where=Where.FRONT)
back_adapter = Adapter('TTT', where=Where.BACK)
la = LinkedAdapter(front_adapter,
back_adapter,
front_required=False,
back_required=False,
name='name')
assert la.match_to(s).matches == 3
def test_parse_braces_fail():
for expression in [
'{', '}', '{}', '{5', '{1}', 'A{-7}', 'A{', 'A{1', 'N{7', 'AN{7',
'A{4{}', 'A{4}{3}', 'A{b}', 'A{6X}', 'A{X6}'
]:
print(expression)
try:
Adapter.parse_braces(expression)
except ValueError as e:
print(e)
assert_raises(ValueError, lambda: Adapter.parse_braces(expression))
def test_add_adapter_statistics():
stats = Adapter('A', name='name', where=Where.BACK,
max_error_rate=0.1).create_statistics()
end_stats = stats.back
end_stats.adjacent_bases['A'] = 7
end_stats.adjacent_bases['C'] = 19
end_stats.adjacent_bases['G'] = 23
end_stats.adjacent_bases['T'] = 42
end_stats.adjacent_bases[''] = 45
end_stats.errors[10][0] = 100
end_stats.errors[10][1] = 11
end_stats.errors[10][2] = 3
end_stats.errors[20][0] = 600
end_stats.errors[20][1] = 66
end_stats.errors[20][2] = 6
stats2 = Adapter('A', name='name', where=Where.BACK,
max_error_rate=0.1).create_statistics()
end_stats2 = stats2.back
end_stats2.adjacent_bases['A'] = 43
end_stats2.adjacent_bases['C'] = 31
end_stats2.adjacent_bases['G'] = 27
end_stats2.adjacent_bases['T'] = 8
end_stats2.adjacent_bases[''] = 5
end_stats2.errors[10][0] = 234
end_stats2.errors[10][1] = 14
end_stats2.errors[10][3] = 5
end_stats2.errors[15][0] = 90
end_stats2.errors[15][1] = 17
end_stats2.errors[15][2] = 2
stats += stats2
r = stats.back
assert r.adjacent_bases == {'A': 50, 'C': 50, 'G': 50, 'T': 50, '': 50}
assert r.errors == {
10: {
0: 334,
1: 25,
2: 3,
3: 5
},
15: {
0: 90,
1: 17,
2: 2
},
20: {
0: 600,
1: 66,
2: 6
},
}
def test_random_match_probabilities():
a = Adapter('A', where=BACK, max_error_rate=0.1).create_statistics()
assert a.back.random_match_probabilities(0.5) == [1, 0.25]
assert a.back.random_match_probabilities(0.2) == [1, 0.4]
for s in ('ACTG', 'XMWH'):
a = Adapter(s, where=BACK, max_error_rate=0.1).create_statistics()
assert a.back.random_match_probabilities(0.5) == [1, 0.25, 0.25**2, 0.25**3, 0.25**4]
assert a.back.random_match_probabilities(0.2) == [1, 0.4, 0.4*0.1, 0.4*0.1*0.4, 0.4*0.1*0.4*0.1]
a = Adapter('GTCA', where=FRONT, max_error_rate=0.1).create_statistics()
assert a.front.random_match_probabilities(0.5) == [1, 0.25, 0.25**2, 0.25**3, 0.25**4]
assert a.front.random_match_probabilities(0.2) == [1, 0.4, 0.4*0.1, 0.4*0.1*0.4, 0.4*0.1*0.4*0.1]
def test_info_record():
adapter = Adapter(
sequence='GAACTCCAGTCACNNNNN',
where=BACK,
max_error_rate=0.12,
min_overlap=5,
read_wildcards=False,
adapter_wildcards=True,
name="Foo")
read = Sequence(name="abc", sequence='CCCCAGAACTACAGTCCCGGC')
am = Match(astart=0, astop=17, rstart=5, rstop=21, matches=15, errors=2, remove_before=False,
adapter=adapter, read=read)
assert am.get_info_record() == (
"abc",
2,
5,
21,
'CCCCA',
'GAACTACAGTCCCGGC',
'',
'Foo',
'',
'',
''
)
def test_linked_adapter():
front_adapter = Adapter('AAAA', where=Where.PREFIX, min_overlap=4)
back_adapter = Adapter('TTTT', where=Where.BACK, min_overlap=3)
linked_adapter = LinkedAdapter(front_adapter,
back_adapter,
front_required=True,
back_required=False,
name='name')
assert linked_adapter.front_adapter.min_overlap == 4
assert linked_adapter.back_adapter.min_overlap == 3
sequence = Sequence(name='seq', sequence='AAAACCCCCTTTT')
trimmed = linked_adapter.match_to(sequence).trimmed()
assert trimmed.name == 'seq'
assert trimmed.sequence == 'CCCCC'
def test_end_trim_with_mismatch():
"""
Test the not-so-obvious case where an adapter of length 13 is trimmed from
the end of a sequence with overlap 9 and there is one deletion.
In this case the algorithm starts with 10 bases of the adapter to get
the hit and so the match is considered good. An insertion or substitution
at the same spot is not a match.
"""
adapter = Adapter('TCGATCGATCGAT', BACK, max_error_rate=0.1)
read = Sequence('foo1', 'AAAAAAAAAAATCGTCGATC')
cutter = AdapterCutter([adapter], times=1)
trimmed_read = cutter(read, [])
assert trimmed_read.sequence == 'AAAAAAAAAAA'
assert cutter.adapter_statistics[adapter].back.lengths == {9: 1}
# We see 1 error at length 9 even though the number of allowed mismatches at
# length 9 is 0.
assert cutter.adapter_statistics[adapter].back.errors[9][1] == 1
read = Sequence('foo2', 'AAAAAAAAAAATCGAACGA')
cutter = AdapterCutter([adapter], times=1)
trimmed_read = cutter(read, [])
assert trimmed_read.sequence == read.sequence
assert cutter.adapter_statistics[adapter].back.lengths == {}
def trim(sampleFileName, ADAPT_FRONT="GTGGAAAGGACGAAACACC", max_err=0.1, max_length=24):
adapter_front = [Adapter(ADAPT_FRONT, FRONT, max_err)]
cutter_front = AdapterCutter(adapter_front, times=1)
if not sampleFileName.lower().endswith('gz'):
with open(sampleFileName, "r") as inp:
return [ cutter_front(read).sequence[:20] for lineno, read in enumerate(readFastq(inp)) ]
else:
with gzip.open(sampleFileName, "r") as inp:
return [ (cutter_front(read)).sequence[:20] for lineno, read in enumerate(readFastq(inp)) ]
def test_statistics():
read = Sequence('name', 'AAAACCCCAAAA')
adapters = [Adapter('CCCC', BACK, 0.1)]
cutter = AdapterCutter(adapters, times=3)
trimmed_read = cutter(read)
# TODO make this a lot simpler
trimmed_bp = 0
for adapter in adapters:
for d in (adapter.lengths_front, adapter.lengths_back):
trimmed_bp += sum(seqlen * count for (seqlen, count) in d.items())
assert trimmed_bp <= len(read), trimmed_bp
def test_issue_52(): adapter = Adapter( sequence='GAACTCCAGTCACNNNNN', where=BACK, max_error_rate=0.12, min_overlap=5, read_wildcards=False, adapter_wildcards=True) read = Sequence(name="abc", sequence='CCCCAGAACTACAGTCCCGGC') am = Match(astart=0, astop=17, rstart=5, rstop=21, matches=15, errors=2, front=None, adapter=adapter, read=read) assert am.wildcards() == 'GGC' """
def test_statistics():
read = Sequence('name', 'AAAACCCCAAAA')
adapters = [Adapter('CCCC', BACK, max_error_rate=0.1)]
cutter = AdapterCutter(adapters, times=3)
trimmed_read = cutter(read, [])
# TODO make this a lot simpler
trimmed_bp = 0
for adapter in adapters:
for d in (cutter.adapter_statistics[adapter].front.lengths,
cutter.adapter_statistics[adapter].back.lengths):
trimmed_bp += sum(seqlen * count for (seqlen, count) in d.items())
assert trimmed_bp <= len(read), trimmed_bp
def test_anywhere_with_errors():
adapter = Adapter('CCGCATTTAG', ANYWHERE, max_error_rate=0.1)
for seq, expected_trimmed in (
('AACCGGTTccgcatttagGATC', 'AACCGGTT'),
('AACCGGTTccgcgtttagGATC', 'AACCGGTT'), # one mismatch
('AACCGGTTccgcatttag', 'AACCGGTT'),
('ccgcatttagAACCGGTT', 'AACCGGTT'),
('ccgtatttagAACCGGTT', 'AACCGGTT'), # one mismatch
('ccgatttagAACCGGTT', 'AACCGGTT'), # one deletion
):
read = Sequence('foo', seq)
cutter = AdapterCutter([adapter], times=1)
trimmed_read = cutter(read, [])
assert trimmed_read.sequence == expected_trimmed
def test_no_indels_empty_read(where):
# Issue #376
adapter = Adapter('ACGT', where=where, indels=False)
empty = Sequence('name', '')
adapter.match_to(empty)
def parse_adapters(adapter, error_rate=None):
adapters = []
for name, seq, where in gather_adapters(adapter.split(','), [], []):
adapters.append(Adapter(seq, where, error_rate, name=name))
return adapters
def test_str():
a = Adapter('ACGT', where=BACK, max_error_rate=0.1)
str(a)
str(a.match_to(Sequence(name='seq', sequence='TTACGT')))
ca = ColorspaceAdapter('0123', where=BACK, max_error_rate=0.1)
str(ca)
def test_str():
a = Adapter('ACGT', where=BACK, max_error_rate=0.1)
str(a)
str(a.match_to(Sequence(name='seq', sequence='TTACGT')))
ca = ColorspaceAdapter('0123', where=BACK, max_error_rate=0.1)
str(ca)
def test_str():
a = Adapter('ACGT', where=Where.BACK, remove='suffix', max_error_rate=0.1)
str(a)
str(a.match_to(Sequence(name='seq', sequence='TTACGT')))
def test_no_indels_empty_read(where):
# Issue #376
adapter = Adapter('ACGT', where=where, indels=False)
empty = Sequence('name', '')
adapter.match_to(empty)
def test_str():
a = Adapter('ACGT', where=Where.BACK, remove='suffix', max_error_rate=0.1)
str(a)
str(a.match_to(Sequence(name='seq', sequence='TTACGT')))