def test_in_features(self):
self.expressed_locus_alignment.rewind()
alignment = self.expressed_locus_alignment
genes = self.test_annotation.filter_features(lambda x: x.f_type == "gene")
locus_gen = sam.expressed_loci(alignment)
group1 = next(locus_gen)
group2 = next(locus_gen)
assert not gff.in_features(group1, genes)
assert gff.in_features(group2, genes)
def test_expressed_loci(self):
self.expressed_locus_alignment.rewind()
alignment = self.expressed_locus_alignment
locus_gen = sam.expressed_loci(alignment)
group1 = next(locus_gen)
group2 = next(locus_gen)
assert group1[0].qname == "SRR360147.1"
assert group1[1].qname == "SRR360147.3"
assert group2[0].qname == "SRR360147.2"
assert group2[1].qname == "SRR360147.4"
def test_in_features(self):
self.expressed_locus_alignment.rewind()
alignment = self.expressed_locus_alignment
genes = self.test_annotation.filter_features(
lambda x: x.f_type == "gene")
locus_gen = sam.expressed_loci(alignment)
group1 = next(locus_gen)
group2 = next(locus_gen)
assert not gff.in_features(group1, genes)
assert gff.in_features(group2, genes)
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)