def test_checkalignment_arg_maxgaps(self):
# check maxgaps argument (proportion of internal gaps)
# check with good alignment
res = atools.checkAlignment(test_alignment, maxgaps=0.5, minoverlap=1,
minlen=1, logger=self.logger)
self.assertTrue(res)
# check with bad alignment
# this sequence has a large internal gap covering
# 50% of the alignment
bad_seq = '-A' * 50
bad_seq = SeqRecord(Seq(bad_seq), id='bad')
bad_alignment = test_alignment[:]
bad_alignment.append(bad_seq)
res = atools.checkAlignment(bad_alignment, maxgaps=0.1, minoverlap=50,
minlen=1, logger=self.logger)
self.assertFalse(res)
def test_checkalignment_arg_minoverlap(self):
# check minoverlap argument (minimum number of
# overlapping nucleotides)
# bad seq has a large external gap -- the first 51
# nucleotides are missing
bad_seq = '-' * 51 + 'A' * 49
bad_seq = SeqRecord(Seq(bad_seq), id='bad')
bad_alignment = test_alignment[:]
bad_alignment.append(bad_seq)
res = atools.checkAlignment(bad_alignment, maxgaps=0.5, minoverlap=50,
minlen=1, logger=self.logger)
self.assertFalse(res)
def test_checkalignment_arg_minlen(self):
# check minlen argument
res = atools.checkAlignment(test_alignment, maxgaps=0.5, minoverlap=1,
minlen=101, logger=self.logger)
self.assertFalse(res)