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_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_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)