def test_n_labels(): lh = LabelHash(20, 1e7, 4) filename = utils.get_test_data('test-labels.fa') lh.consume_fasta_and_tag_with_labels(filename) print lh.n_labels() assert lh.n_labels() == 4
def test_consume_fasta_and_tag_with_labels(): lb = LabelHash(20, 1e7, 4) read_1 = 'ACGTAACCGGTTAAACCCGGGTTTAAAACCCCGGGGTTTT' filename = utils.get_test_data('test-transcript.fa') total_reads, n_consumed = lb.consume_fasta_and_tag_with_labels(filename) print "doing get" assert lb.get(read_1[:20]) assert total_reads == 3 print "doing n_labels" print lb.n_labels() print "doing label dict" print lb.get_label_dict() print "get tagset" for tag in lb.get_tagset(): print "forward hash" print tag, khmer.forward_hash(tag, 20) for record in screed.open(filename): print "Sweeping tags" print lb.sweep_tag_neighborhood(record.sequence, 40) print "Sweeping labels..." print lb.sweep_label_neighborhood(record.sequence, 40) assert lb.n_labels() == 3
def test_consume_partitioned_fasta_and_tag_with_labels(): lb = LabelHash(20, 1e7, 4) filename = utils.get_test_data('real-partition-small.fa') total_reads, n_consumed = lb.consume_partitioned_fasta_and_tag_with_labels( filename) labels = set() for record in screed.open(filename): seq = record.sequence labels.update(lb.sweep_label_neighborhood(seq, 0, False, False)) # print lb.n_labels() # print labels assert len(labels) == 1 assert labels.pop() == 2 assert lb.n_labels() == 1
def test_consume_partitioned_fasta_and_tag_with_labels(): lb = LabelHash(20, 1e7, 4) filename = utils.get_test_data('real-partition-small.fa') total_reads, n_consumed = lb.consume_partitioned_fasta_and_tag_with_labels( filename) labels = set() for record in screed.open(filename): seq = record.sequence labels.update(lb.sweep_label_neighborhood(seq, 0, False, False)) # print lb.n_labels() # print labels assert len(labels) == 1 assert labels.pop() == 2L assert lb.n_labels() == 1