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)