def test_merge_bam():
with get_input_files('1.bam',
'1.bam') as input_files, get_tmp_path() as outpath:
Bam.merge(input_files, outpath)
alignment_count_output = int(view("-c", outpath).strip())
alignment_count_input = int(view("-c", input_files[0]).strip()) * 2
assert alignment_count_input == alignment_count_output
def test_set_meta_presorted():
b = Bam()
with get_dataset('1.bam') as dataset:
b.set_meta(dataset=dataset)
assert dataset.metadata.sort_order == 'coordinate'
bam_file = pysam.AlignmentFile(dataset.file_name, mode='rb',
index_filename=dataset.metadata.bam_index.file_name)
assert bam_file.has_index() is True
def test_set_meta_presorted():
b = Bam()
with get_dataset('1.bam') as dataset:
b.set_meta(dataset=dataset)
assert dataset.metadata.sort_order == 'coordinate'
bam_file = pysam.AlignmentFile(dataset.file_name, mode='rb',
index_filename=dataset.metadata.bam_index.file_name)
assert bam_file.has_index() is True
def test_set_meta_header_info():
"""
check if information from the bam header is set
as metadata
"""
b = Bam()
with get_dataset('bam_from_sam.bam') as dataset:
b.set_meta(dataset=dataset)
assert dataset.metadata.bam_header == {'HD': {'VN': '1.3', 'SO': 'coordinate'}, 'SQ': [{'SN': 'ref', 'LN': 45}, {'SN': 'ref2', 'LN': 40}]}
assert dataset.metadata.reference_names == ['ref', 'ref2']
def test_groom_dataset_content():
b = Bam()
try:
with get_input_files('2.shuffled.bam') as input_files:
b.groom_dataset_content(input_files[0])
assert b.dataset_content_needs_grooming(input_files[0]) is False
except AssertionError as e:
# Grooming modifies files in-place, so the md5 hash comparison has to fail
assert 'Unexpected change' in e.message
return
# should not reach this part of the test
raise Exception('Bam grooming did not occur in-place')
def test_groom_dataset_content():
b = Bam()
try:
with get_input_files('2.shuffled.bam') as input_files:
b.groom_dataset_content(input_files[0])
assert b.dataset_content_needs_grooming(input_files[0]) is False
except AssertionError as e:
# Grooming modifies files in-place, so the md5 hash comparison has to fail
assert 'Unexpected change' in e.message
return
# should not reach this part of the test
raise Exception('Bam grooming did not occur in-place')
def test_dataset_content_needs_grooming():
b = Bam()
with get_input_files('1.bam', '2.shuffled.bam') as input_files:
sorted_bam, shuffled_bam = input_files
assert b.dataset_content_needs_grooming(sorted_bam) is False
assert b.dataset_content_needs_grooming(shuffled_bam) is True
def test_merge_bam():
with get_input_files('1.bam', '1.bam') as input_files, get_tmp_path() as outpath:
Bam.merge(input_files, outpath)
alignment_count_output = int(pysam.view('-c', outpath).strip())
alignment_count_input = int(pysam.view('-c', input_files[0]).strip()) * 2
assert alignment_count_input == alignment_count_output
def test_dataset_content_needs_grooming():
b = Bam()
with get_input_files('1.bam', '2.shuffled.bam') as input_files:
sorted_bam, shuffled_bam = input_files
assert b.dataset_content_needs_grooming(sorted_bam) is False
assert b.dataset_content_needs_grooming(shuffled_bam) is True