Ejemplo n.º 1
0
 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)
Ejemplo n.º 2
0
 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)
Ejemplo n.º 3
0
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)