def test_consensus(self):
self.indel_algn.rewind()
with pytest.raises(sam.UnmappedReadError):
sam.consensus([self.single_read])
assert sam.consensus(list(self.indel_algn)) ==\
"AGATGACGGAAGCTTGATCTCACGAANNNNNNNNTTNNCATCCNNNTNNT"
assert sam.consensus(self.reverse_complement_align) == \
"AAAGGGAAAA"
self.mate_pair_align.rewind()
mate_pair_loci = sam.expressed_loci(self.mate_pair_align)
con = sam.consensus(next(mate_pair_loci))
assert con == self.mate_pair_consensus
def test_speed_test():
align = sam.SamAlignment(TEST_FOLDER + "/test_data/speed_test.sam")
annotation = gff.GenomeAnnotation(TEST_FOLDER + "/test_data/speed_test.gff")
for locus in sam.expressed_loci(align):
gff.in_features(locus, annotation.features)
sam.consensus(locus)
