def test_get_label_dict(): lb = LabelHash(20, 1e7, 4) filename = utils.get_test_data('test-labels.fa') lb.consume_fasta_and_tag_with_labels(filename) labels = lb.get_label_dict() expected = [0, 1, 2, 3] for e_label in expected: assert e_label in labels for a_label in labels: assert a_label in expected
def test_get_label_dict(): lb = LabelHash(20, 1e7, 4) filename = utils.get_test_data('test-labels.fa') lb.consume_fasta_and_tag_with_labels(filename) labels = lb.get_label_dict() expected = [0L, 1L, 2L, 3L] for e_label in expected: assert e_label in labels for a_label in labels: assert a_label in expected
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_get_label_dict_save_load(): lb_pre = LabelHash(20, 1e7, 4) filename = utils.get_test_data('test-labels.fa') lb_pre.consume_fasta_and_tag_with_labels(filename) # save labels to a file savepath = utils.get_temp_filename('saved.labels') lb_pre.save_labels_and_tags(savepath) # trash the old LabelHash del lb_pre # create new, load labels & tags lb = LabelHash(20, 1e7, 4) lb.load_labels_and_tags(savepath) labels = lb.get_label_dict() expected = [0, 1, 2, 3] for e_label in expected: assert e_label in labels for a_label in labels: assert a_label in expected