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# coding: utf-8
from __future__ import print_function, division, absolute_import
from nose.tools import raises, assert_raises
from cutadapt.seqio import Sequence
from cutadapt.adapters import (Adapter, Match, ColorspaceAdapter, FRONT, BACK,
parse_braces, LinkedAdapter)
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'
"""
The result above should actually be 'CGGC' since the correct
alignment is this one:
adapter GAACTCCAGTCACNNNNN
mismatches X X
read CCCCAGAACTACAGTC-CCGGC
Since we do not keep the alignment, guessing 'GGC' is the best we
can currently do.
"""
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,
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_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)
@raises(ValueError)
def test_color():
ColorspaceAdapter('0123', where=FRONT, max_error_rate=0.1)
def test_parse_braces():
assert parse_braces('') == ''
assert parse_braces('A') == 'A'
assert parse_braces('A{0}') == ''
assert parse_braces('A{1}') == 'A'
assert parse_braces('A{2}') == 'AA'
assert parse_braces('A{2}C') == 'AAC'
assert parse_braces('ACGTN{3}TGACCC') == 'ACGTNNNTGACCC'
assert parse_braces('ACGTN{10}TGACCC') == 'ACGTNNNNNNNNNNTGACCC'
assert parse_braces('ACGTN{3}TGA{4}CCC') == 'ACGTNNNTGAAAACCC'
assert parse_braces('ACGTN{0}TGA{4}CCC') == 'ACGTTGAAAACCC'
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}']:
assert_raises(ValueError, lambda: parse_braces(expression))
def test_linked_adapter():
linked_adapter = LinkedAdapter('AAAA', 'TTTT')
sequence = Sequence(name='seq', sequence='AAAACCCCCTTTT')
match = linked_adapter.match_to(sequence)
trimmed = linked_adapter.trimmed(match)
assert trimmed.name == 'seq'
assert trimmed.sequence == 'CCCCC'
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, front=None,
adapter=adapter, read=read)
print(am.get_info_record())
assert am.get_info_record() == (
"abc",
2,
5,
21,
'CCCCA',
'GAACTACAGTCCCGGC',
'',
'Foo',
'',
'',
''
)
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