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_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_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_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_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_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_get_label_dict_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_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_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_get_label_dict_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_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_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