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))
