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
