def test_save_load_corrupted(): 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 lb = GraphLabels(20, 1e7, 4) # produce all possible truncated versions of this file data = open(savepath, 'rb').read() for i in range(len(data)): truncated = utils.get_temp_filename('trunc.labels') fp = open(truncated, 'wb') fp.write(data[:i]) fp.close() try: lb.load_labels_and_tags(truncated) assert 0, "this should not succeed -- truncated file len %d" % ( i, ) except OSError as err: print('expected failure for', i, ': ', str(err))
def test_label_tag_correctness_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) # read A labels = lb.sweep_label_neighborhood( 'ATCGTGTAAGCTATCGTAATCGTAAGCTCTGCCTAGAGCTAGGCTAGGCTCTGCCTAGAG' 'CTAGGCTAGGTGTGCTCTGCCTAGAGCTAGGCTAGGTGT') print( lb.sweep_tag_neighborhood( 'TTCGTGTAAGCTATCGTAATCGTAAGCTCTGCCTAGAGCTAGGCTAGGCTCTGCCTAGAG' 'CTAGGCTAGGTGTGCTCTGCTAGAGCTAGGCTAGGTGT')) print(labels) print(len('ATCGTGTAAGCTATCGTAATCGTAAGCTCTGCCTAGAGCTAGGCTAG') - 19) assert len(labels) == 2 assert 0 in labels assert 1 in labels # read B labels = lb.sweep_label_neighborhood( 'GCGTAATCGTAAGCTCTGCCTAGAGCTAGGCTAGCTCTGCCTAGAGCTAGGCTAGGTGTTGGGGATAG' 'ATAGATAGATGACCTAGAGCTAGGCTAGGTGTTGGGGATAGATAGATAGATGA') print(labels) assert len(labels) == 3 assert 0 in labels assert 1 in labels assert 2 in labels # read C labels = lb.sweep_label_neighborhood( 'TGGGATAGATAGATAGATGACCTAGAGCTAGGCTAGGTGTTGGGGATAGATAGATAGATGACCTAGAG' 'CTAGGCTAGGTGTTGGGGATAGATAGATAGATGAGTTGGGGATAGATAGATAGATGAGTGTAGATCCA' 'ACAACACATACA') print(labels) assert len(labels) == 2 assert 1 in labels assert 2 in labels # read D labels = lb.sweep_label_neighborhood( 'TATATATATAGCTAGCTAGCTAACTAGCTAGCATCGATCGATCGATC') print(labels) assert len(labels) == 1 assert 3 in labels
def test_n_labels(): lh = GraphLabels(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_sweep_label_neighborhood(): lb = GraphLabels(20, 1e7, 4) filename = utils.get_test_data('single-read.fq') lb.consume_fasta_and_tag_with_labels(filename) labels = lb.sweep_label_neighborhood('CAGGCGCCCACCACCGTGCCCTCCAACCTGATGGT') assert len(labels) == 1 assert labels.pop() == 0
def test_sweep_tag_neighborhood(): lb = GraphLabels(20, 1e7, 4) filename = utils.get_test_data('single-read.fq') lb.graph.consume_fasta_and_tag(filename) tags = lb.sweep_tag_neighborhood('CAGGCGCCCACCACCGTGCCCTCCAACCTGATGGT') assert len(tags) == 1 assert list(tags) == [173473779682]
def test_get_tag_labels(): lb = GraphLabels(20, 1e7, 4) filename = utils.get_test_data('single-read.fq') lb.consume_fasta_and_tag_with_labels(filename) tag = 173473779682 labels = lb.get_tag_labels(tag) assert len(labels) == 1 assert labels.pop() == 0
def test_consume_partitioned_seqfile_and_label(Graphtype): infile = utils.get_test_data('valid-read-testing.fq') # read this in consume_and_tag graph = Graphtype(15, *params_1m) x = GraphLabels(graph) x.consume_partitioned_fasta_and_tag_with_labels(infile) assert x.n_labels == 9
def test_link_tag_and_label(): lb = GraphLabels(20, 1, 1) tag = 173473779682 lb.add_tag(tag) lb.link_tag_and_label(tag, 1) labels = lb.get_tag_labels(tag) assert len(labels) == 1 assert labels.pop() == 1
def test_link_tag_and_label_using_string(): lb = GraphLabels(20, 1, 1) kmer = lb.reverse_hash(173473779682) lb.add_tag(kmer) lb.link_tag_and_label(kmer, 1) labels = lb.get_tag_labels(kmer) assert len(labels) == 1 assert labels.pop() == 1
def test_get_labels_save_load_wrong_ksize(): lb_pre = GraphLabels(19, 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) try: lb.load_labels_and_tags(savepath) assert 0, "this should not succeed - different ksize" except OSError as err: print(str(err)) assert "Incorrect k-mer size 19" in str(err)
def test_link_tag_and_label_using_string_2(): lb = GraphLabels(20, 1, 1) tag = 173473779682 kmer = lb.reverse_hash(tag) lb.add_tag(kmer) lb.link_tag_and_label(kmer, 1) labels = lb.get_tag_labels(tag) # <-- use 'tag' instead of 'kmer' assert len(labels) == 1 assert labels.pop() == 1
def test_consume_sequence_and_tag_with_labels(): lb = GraphLabels(20, 1e6, 4) label = 0 sequence = 'ATGCATCGATCGATCGATCGATCGATCGATCGATCGATCG' lb.consume_sequence_and_tag_with_labels(sequence, label) labels = set() labels.update(lb.sweep_label_neighborhood(sequence)) assert label in labels assert len(labels) == 1
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_load_wrong_fileversion(): lb = GraphLabels(20, 1e7, 4) # try to load a tagset from an old version filename = utils.get_test_data('badversion-k32.tagset') try: lb.load_labels_and_tags(filename) assert 0, "this should not succeed - bad file type" except OSError as err: print(str(err)) assert "Incorrect file format version" in str(err)
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_partitioned_fasta_and_tag_with_labels(): lb = GraphLabels(20, 1e7, 4) filename = utils.get_test_data('real-partition-small.fa') 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_save_fail_readonly(): 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') fp = open(savepath, 'w') fp.close() os.chmod(savepath, 0x444) try: lb_pre.save_labels_and_tags(savepath) assert 0, "this should fail: read-only file" except OSError as err: print(str(err))
def test_label_tag_correctness(): lb = GraphLabels(20, 1e7, 4) filename = utils.get_test_data('test-labels.fa') lb.consume_fasta_and_tag_with_labels(filename) # read A labels = lb.sweep_label_neighborhood( 'ATCGTGTAAGCTATCGTAATCGTAAGCTCTGCCTAGAGCTAGGCTAGGCTCTGCCTAGAG' 'CTAGGCTAGGTGTGCTCTGCCTAGAGCTAGGCTAGGTGT') print( lb.sweep_tag_neighborhood( 'TTCGTGTAAGCTATCGTAATCGTAAGCTCTGCCTAGAGCTAGGCTAGGCTCTGCCTAGAG' 'CTAGGCTAGGTGTGCTCTGCTAGAGCTAGGCTAGGTGT')) print(labels) print(len('ATCGTGTAAGCTATCGTAATCGTAAGCTCTGCCTAGAGCTAGGCTAG') - 19) assert len(labels) == 2 assert 0 in labels assert 1 in labels # read B labels = lb.sweep_label_neighborhood( 'GCGTAATCGTAAGCTCTGCCTAGAGCTAGGCTAGCTCTGCCTAGAGCTAGGCTAGGTGTTGGGGATAG' 'ATAGATAGATGACCTAGAGCTAGGCTAGGTGTTGGGGATAGATAGATAGATGA') print(labels) assert len(labels) == 3 assert 0 in labels assert 1 in labels assert 2 in labels # read C labels = lb.sweep_label_neighborhood( 'TGGGATAGATAGATAGATGACCTAGAGCTAGGCTAGGTGTTGGGGATAGATAGATAGATGACCTAGAG' 'CTAGGCTAGGTGTTGGGGATAGATAGATAGATGAGTTGGGGATAGATAGATAGATGAGTGTAGATCCA' 'ACAACACATACA') print(labels) assert len(labels) == 2 assert 1 in labels assert 2 in labels # read D labels = lb.sweep_label_neighborhood( 'TATATATATAGCTAGCTAGCTAACTAGCTAGCATCGATCGATCGATC') print(labels) assert len(labels) == 1 assert 3 in labels
def test_load_wrong_filetype(): lb = GraphLabels(20, 1e7, 4) # try to load a tagset filename = utils.get_test_data('goodversion-k32.tagset') try: lb.load_labels_and_tags(filename) assert 0, "this should not succeed - bad file type" except OSError as err: print(str(err)) assert "Incorrect file format type" in str(err) # try to load a nonsense file filename = utils.get_test_data('all-A.fa') try: lb.load_labels_and_tags(filename) assert 0, "this should not succeed - bad file signature" except OSError as err: print(str(err)) assert "Incorrect file signature" in str(err)
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
def test_toobig(): try: GraphLabels(20, 1e13, 1) assert 0, "This should fail." except MemoryError as err: print(str(err))