def test_ok_multi_ref_genome(self):
args = [
'mavis',
'validate',
'--library',
'translib',
'--protocol',
'genome',
'--bam_file',
get_data('mock_trans_reads_for_events.sorted.bam'),
'--stdev_fragment_size',
'50',
'--median_fragment_size',
'200',
'--input',
get_data('mock_sv_events.tsv'),
'--output',
'outdir',
'--reference_genome',
get_data('mock_reference_genome.fa'),
get_data('example_genes.fa'),
'--aligner_reference',
get_data('mock_reference_genome.fa'),
'--read_length',
'125',
]
with patch.object(validate_main, 'main', util.DEVNULL):
with patch.object(sys, 'argv', args):
mavis_main()
def test_trans_multiple_annotations_no_masking(self, configpath,
output_dir):
configpath.write_text(
json.dumps({
'reference.annotations': [
get_data('example_genes.json'),
get_data('mock_annotations.json'),
],
'libraries': {
'translib': {
'disease_status': 'diseased',
'protocol': 'transcriptome',
'assign': [get_data('mock_sv_events.tsv')],
}
},
'output_dir':
output_dir,
}))
args = [
'mavis',
'cluster',
'--library',
'translib',
'--inputs',
get_data('mock_sv_events.tsv'),
'--output',
output_dir,
'--config',
str(configpath),
]
with patch.object(cluster_main, 'main', Mock()):
with patch.object(sys, 'argv', args):
mavis_main()
def test_ok_missing_annotations_translib_nofilter(self):
args = [
'mavis', 'cluster', '--library', 'translib', '--protocol',
'transcriptome', '--disease_status', 'diseased', '--input',
get_data('mock_sv_events.tsv'), '--output', 'outdir'
]
with patch.object(cluster_main, 'main', util.DEVNULL):
with patch.object(sys, 'argv', args):
mavis_main()
def test_trans_multiple_annotations_no_masking(self):
args = [
'mavis', 'cluster', '--annotations',
get_data('example_genes.json'),
get_data('mock_annotations.json'), '--library', 'translib',
'--protocol', 'transcriptome', '--disease_status', 'diseased',
'--input',
get_data('mock_sv_events.tsv'), '--output', 'outdir'
]
with patch.object(cluster_main, 'main', util.DEVNULL):
with patch.object(sys, 'argv', args):
mavis_main()
def test_ok_multi_ref_genome(self, configpath, output_dir):
configpath.write_text(
json.dumps({
'libraries': {
'translib': {
'disease_status':
'diseased',
'protocol':
'genome',
'assign': [get_data('mock_sv_events.tsv')],
'bam_file':
get_data('mock_trans_reads_for_events.sorted.bam'),
'read_length':
125,
'median_fragment_size':
200,
'stdev_fragment_size':
50,
}
},
'reference.annotations': [
get_data('example_genes.json'),
get_data('mock_annotations.json'),
],
'cluster.uninformative_filter':
True,
'reference.reference_genome': [
get_data('mock_reference_genome.fa'),
get_data('example_genes.fa'),
],
'reference.aligner_reference':
[get_data('mock_reference_genome.fa')],
'output_dir':
output_dir,
}))
args = [
'mavis',
'validate',
'--library',
'translib',
'--input',
get_data('mock_sv_events.tsv'),
'--output',
output_dir,
'--config',
str(configpath),
]
with patch.object(validate_main, 'main', Mock()):
with patch.object(sys, 'argv', args):
mavis_main()