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_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_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=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)