def testParsing(self): cl = parse_fasta_file('resources/dummy_fasta.txt'); self.assertTrue('1' in cl) self.assertTrue('2' in cl) self.assertTrue('non_numerical_id' in cl) self.assertTrue('10' in cl) self.assertEquals(cl['1'], 5) self.assertEquals(cl['2'], 20) self.assertEquals(cl['non_numerical_id'], 0) self.assertEquals(cl['10'], 10)
def lengthsOfMaps(self): cl = parse_fasta_file('../../../../../data/influenza-A/influenza-A.assembly.fasta') samfile = SamFile.read('../../../../../tutorial/read_coverage/influenza-A.sam') bp_cov = ContigBPCoverage(samfile, cl) w_cov = ContigWindowCoverage(bp_cov, 100, 100) self.assertEquals(len(w_cov.contig_coverage), len(w_cov.contig_window_starting_points))