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# coding: utf-8
from __future__ import print_function, division, absolute_import
from cutadapt.align import (locate, compare_prefixes, compare_suffixes,
Aligner)
from cutadapt.adapters import BACK
class TestAligner():
def test(self):
reference = 'CTCCAGCTTAGACATATC'
aligner = Aligner(reference, 0.1, flags=BACK)
aligner.locate('CC')
def test_100_percent_error_rate(self):
reference = 'GCTTAGACATATC'
aligner = Aligner(reference, 1.0, flags=BACK)
aligner.locate('CAA')
def test_polya():
s = 'AAAAAAAAAAAAAAAAA'
t = 'ACAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA'
result = locate(s, t, 0.0, BACK)
#start_s, stop_s, start_t, stop_t, matches, cost = result
assert result == (0, len(s), 4, 4 + len(s), len(s), 0)
# Sequences with IUPAC wildcards
# R=A|G, Y=C|T, S=G|C, W=A|T, K=G|T, M=A|C, B=C|G|T, D=A|G|T, H=A|C|T, V=A|C|G,
# N=A|C|G|T, X={}
WILDCARD_SEQUENCES = [
'CCCATTGATC', # original sequence without wildcards
'CCCRTTRATC', # R=A|G
'YCCATYGATC', # Y=C|T
'CSSATTSATC', # S=G|C
'CCCWWWGATC', # W=A|T
'CCCATKKATC', # K=G|T
'CCMATTGMTC', # M=A|C
'BCCATTBABC', # B=C|G|T
'BCCATTBABC', # B
'CCCDTTDADC', # D=A|G|T
'CHCATHGATC', # H=A|C|T
'CVCVTTVATC', # V=A|C|G
'CCNATNGATC', # N=A|C|G|T
'CCCNTTNATC', # N
# 'CCCXTTXATC', # X
]
def test_compare_prefixes():
assert compare_prefixes('AAXAA', 'AAAAATTTTTTTTT') == (0, 5, 0, 5, 4, 1)
assert compare_prefixes('AANAA', 'AACAATTTTTTTTT', wildcard_ref=True) == (0, 5, 0, 5, 5, 0)
assert compare_prefixes('AANAA', 'AACAATTTTTTTTT', wildcard_ref=True) == (0, 5, 0, 5, 5, 0)
assert compare_prefixes('XAAAAA', 'AAAAATTTTTTTTT') == (0, 6, 0, 6, 4, 2)
a = WILDCARD_SEQUENCES[0]
for s in WILDCARD_SEQUENCES:
r = s + 'GCCAGGGTTGATTCGGCTGATCTGGCCG'
result = compare_prefixes(a, r, wildcard_query=True)
assert result == (0, 10, 0, 10, 10, 0), result
result = compare_prefixes(r, a, wildcard_ref=True)
assert result == (0, 10, 0, 10, 10, 0)
for s in WILDCARD_SEQUENCES:
for t in WILDCARD_SEQUENCES:
r = s + 'GCCAGGG'
result = compare_prefixes(s, r, )
assert result == (0, 10, 0, 10, 10, 0)
result = compare_prefixes(r, s, wildcard_ref=True, wildcard_query=True)
assert result == (0, 10, 0, 10, 10, 0)
r = WILDCARD_SEQUENCES[0] + 'GCCAGG'
for wildc_ref in (False, True):
for wildc_query in (False, True):
result = compare_prefixes('CCCXTTXATC', r, wildcard_ref=wildc_ref, wildcard_query=wildc_query)
assert result == (0, 10, 0, 10, 8, 2)
def test_compare_suffixes():
assert compare_suffixes('AAXAA', 'TTTTTTTAAAAA') == (0, 5, 7, 12, 4, 1)
assert compare_suffixes('AANAA', 'TTTTTTTAACAA', wildcard_ref=True) == (0, 5, 7, 12, 5, 0)
assert compare_suffixes('AANAA', 'TTTTTTTAACAA', wildcard_ref=True) == (0, 5, 7, 12, 5, 0)
assert compare_suffixes('AAAAAX', 'TTTTTTTAAAAA') == (0, 6, 6, 12, 4, 2)
def test_wildcards_in_adapter():
r = 'CATCTGTCC' + WILDCARD_SEQUENCES[0] + 'GCCAGGGTTGATTCGGCTGATCTGGCCG'
for a in WILDCARD_SEQUENCES:
result = locate(a, r, 0.0, BACK, wildcard_ref=True)
assert result == (0, 10, 9, 19, 10, 0), result
a = 'CCCXTTXATC'
result = locate(a, r, 0.0, BACK, wildcard_ref=True)
assert result is None
def test_wildcards_in_read():
a = WILDCARD_SEQUENCES[0]
for s in WILDCARD_SEQUENCES:
r = 'CATCTGTCC' + s + 'GCCAGGGTTGATTCGGCTGATCTGGCCG'
result = locate(a, r, 0.0, BACK, wildcard_query=True)
if 'X' in s:
assert result is None
else:
assert result == (0, 10, 9, 19, 10, 0), result
def test_wildcards_in_both():
for a in WILDCARD_SEQUENCES:
for s in WILDCARD_SEQUENCES:
if 'X' in s or 'X' in a:
continue
r = 'CATCTGTCC' + s + 'GCCAGGGTTGATTCGGCTGATCTGGCCG'
result = locate(a, r, 0.0, BACK, wildcard_ref=True, wildcard_query=True)
assert result == (0, 10, 9, 19, 10, 0), result
def test_no_match():
a = locate('CTGATCTGGCCG', 'AAAAGGG', 0.1, BACK)
assert a is None, a
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