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)