def test_get_all_labels(): lb = GraphLabels(20, 1e7, 4) filename = utils.get_test_data('test-labels.fa') lb.consume_seqfile_and_tag_with_labels(filename) labels = lb.get_all_labels() 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_all_labels(): lb = GraphLabels(20, 1e7, 4) filename = utils.get_test_data('test-labels.fa') lb.consume_fasta_and_tag_with_labels(filename) labels = lb.get_all_labels() 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_labels_save_load(): lb_pre = GraphLabels(20, 1e7, 4) filename = utils.get_test_data('test-labels.fa') lb_pre.consume_seqfile_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 GraphLabels del lb_pre # create new, load labels & tags lb = GraphLabels(20, 1e7, 4) lb.load_labels_and_tags(savepath) labels = lb.get_all_labels() 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_labels_save_load(): lb_pre = GraphLabels(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 GraphLabels del lb_pre # create new, load labels & tags lb = GraphLabels(20, 1e7, 4) lb.load_labels_and_tags(savepath) labels = lb.get_all_labels() 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_consume_seqfile_and_tag_with_labels(): lb = GraphLabels(20, 1e7, 4) read_1 = 'ACGTAACCGGTTAAACCCGGGTTTAAAACCCCGGGGTTTT' filename = utils.get_test_data('test-transcript.fa') total_reads, _ = lb.consume_seqfile_and_tag_with_labels(filename) print("doing get") assert lb.graph.get(read_1[:20]) assert total_reads == 3 print("doing n_labels") print(lb.n_labels()) print("doing all labels") print(lb.get_all_labels()) print("get tagset") for tag in lb.graph.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_fasta_and_tag_with_labels(): lb = GraphLabels(20, 1e7, 4) read_1 = 'ACGTAACCGGTTAAACCCGGGTTTAAAACCCCGGGGTTTT' filename = utils.get_test_data('test-transcript.fa') total_reads, _ = lb.consume_fasta_and_tag_with_labels(filename) print("doing get") assert lb.graph.get(read_1[:20]) assert total_reads == 3 print("doing n_labels") print(lb.n_labels()) print("doing all labels") print(lb.get_all_labels()) print("get tagset") for tag in lb.graph.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