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()