def test_correct_calls_are_made(self):
"""
Tests that the correct arguments are passed to the method which calls the DESeq script.
Mostly tests the path renaming, etc.
"""
self.module.call_script = mock.Mock()
project = Project()
project.raw_count_matrices = [
'/path/to/raw_counts/raw_count_matrix.primary.counts',
'/path/to/raw_counts/raw_count_matrix.primary.dedup.counts'
]
project_params = Params()
component_params = Params()
project_params.add(raw_count_matrix_file_prefix='raw_count_matrix')
project_params.add(feature_counts_file_extension='counts')
component_params.add(deseq_output_dir='/path/to/final/deseq_dir')
component_params.add(deseq_script='deseq_original.R')
project_params.add(sample_annotation_file='/path/to/samples.txt')
component_params.add(deseq_output_tag='deseq')
component_params.add(deseq_contrast_flag='_vs_')
component_params.add(number_of_genes_for_heatmap='30')
component_params.add(heatmap_file_tag='heatmap.png')
project.add_parameters(project_params)
project.contrasts = [('X', 'Y'), ('X', 'Z')]
# construct the expected call strings:
call_1 = '/path/to/raw_counts/raw_count_matrix.primary.counts /path/to/samples.txt X Y /path/to/final/deseq_dir/Y_vs_X.primary.deseq /path/to/final/deseq_dir/Y_vs_X.primary.heatmap.png 30'
call_2 = '/path/to/raw_counts/raw_count_matrix.primary.counts /path/to/samples.txt X Z /path/to/final/deseq_dir/Z_vs_X.primary.deseq /path/to/final/deseq_dir/Z_vs_X.primary.heatmap.png 30'
call_3 = '/path/to/raw_counts/raw_count_matrix.primary.dedup.counts /path/to/samples.txt X Y /path/to/final/deseq_dir/Y_vs_X.primary.dedup.deseq /path/to/final/deseq_dir/Y_vs_X.primary.dedup.heatmap.png 30'
call_4 = '/path/to/raw_counts/raw_count_matrix.primary.dedup.counts /path/to/samples.txt X Z /path/to/final/deseq_dir/Z_vs_X.primary.dedup.deseq /path/to/final/deseq_dir/Z_vs_X.primary.dedup.heatmap.png 30'
m = mock.MagicMock(side_effect=[True, True])
path = self.module.os.path
with mock.patch.object(path, 'isfile', m):
self.module.call_deseq(project, component_params)
calls = [
mock.call('deseq_original.R', call_1),
mock.call('deseq_original.R', call_2),
mock.call('deseq_original.R', call_3),
mock.call('deseq_original.R', call_4)
]
self.module.call_script.assert_has_calls(calls)
def test_missing_countfile_raises_exception(self):
"""
Test one of the files is ok (the first), but the second is not found (for whatever reason). Test that we throw an exception,
and that the one successful call was indeed made correctly.
"""
self.module.call_script = mock.Mock()
project = Project()
project.raw_count_matrices = [
'/path/to/raw_counts/raw_count_matrix.primary.counts',
'/path/to/raw_counts/raw_count_matrix.primary.dedup.counts'
]
project_params = Params()
component_params = Params()
project_params.add(raw_count_matrix_file_prefix='raw_count_matrix')
project_params.add(feature_counts_file_extension='counts')
component_params.add(deseq_output_dir='/path/to/final/deseq_dir')
component_params.add(deseq_script='deseq_original.R')
project_params.add(sample_annotation_file='/path/to/samples.txt')
component_params.add(deseq_output_tag='deseq')
component_params.add(deseq_contrast_flag='_vs_')
component_params.add(number_of_genes_for_heatmap='30')
component_params.add(heatmap_file_tag='heatmap.png')
project.add_parameters(project_params)
project.contrasts = [('X', 'Y'), ('X', 'Z')]
# construct the expected call strings:
call_1 = '/path/to/raw_counts/raw_count_matrix.primary.counts /path/to/samples.txt X Y /path/to/final/deseq_dir/Y_vs_X.primary.deseq /path/to/final/deseq_dir/Y_vs_X.primary.heatmap.png 30'
call_2 = '/path/to/raw_counts/raw_count_matrix.primary.counts /path/to/samples.txt X Z /path/to/final/deseq_dir/Z_vs_X.primary.deseq /path/to/final/deseq_dir/Z_vs_X.primary.heatmap.png 30'
m = mock.MagicMock(side_effect=[True, False])
path = self.module.os.path
with mock.patch.object(path, 'isfile', m):
with self.assertRaises(
self.module.MissingCountMatrixFileException):
self.module.call_deseq(project, component_params)
calls = [
mock.call('deseq_original.R', call_1),
mock.call('deseq_original.R', call_2)
]
self.module.call_script.assert_has_calls(calls)
def test_fill_template(self):
project = Project()
parameters = {
'bam_filter_level': 'sort.primary',
'project_directory': 'abc/foo/AB_12345',
'genome': 'hg19',
'genome_source_link':
'ftp://ftp.ensembl.org/pub/release-75/fasta/homo_sapiens/dna/',
'skip_align': False,
'skip_analysis': False
}
project.parameters = parameters
component_params = cp.read_config(
os.path.join(root, 'components', 'pdf_report', 'report.cfg'),
'COMPONENT_SPECIFIC')
extra_params = cp.read_config(
os.path.join(root, 'components', 'pdf_report', 'report.cfg'),
'STAR')
mock_sample_ids = [
os.path.basename(x).split('.')[0] for x in glob.glob(
os.path.join(
'test_data', '*' +
component_params.get('coverage_file_suffix')))
]
project.samples = [Sample(x, 'X') for x in mock_sample_ids]
project.contrasts = [('X', 'Y'), ('X', 'Z'), ('Y', 'Z')]
component_params['report_output_dir'] = os.path.join(
os.path.abspath(os.path.dirname(__file__)), test_output_dir,
component_params.get('report_output_dir'))
if not os.path.isdir(component_params['report_output_dir']):
os.mkdir(component_params['report_output_dir'])
# link figures so they appear where they should be.
figure_list = glob.glob(
os.path.join(os.path.dirname(__file__), 'test_data',
'*' + component_params.get('coverage_plot_suffix')))
figure_list += [
os.path.join(os.path.dirname(__file__), 'test_data',
'bamfile_reads.pdf'),
os.path.join(os.path.dirname(__file__), 'test_data',
'mapping_composition.pdf'),
os.path.join(os.path.dirname(__file__), 'test_data',
'total_reads.pdf'),
os.path.join('components', 'pdf_report', 'igv_typical.png'),
os.path.join('components', 'pdf_report', 'igv_duplicates.png')
]
[
os.symlink(
os.path.join(root, f),
os.path.join(component_params['report_output_dir'],
os.path.basename(f))) for f in figure_list
]
self.module.get_diff_exp_gene_summary = mock.Mock()
self.module.get_diff_exp_gene_summary.return_value = [[
'X', 'Y', 100, 200
], ['Y_1', 'Z_2', 400, 300], ['X_2', 'Z_3', 150, 300]]
env = jinja2.Environment(loader=jinja2.FileSystemLoader(
os.path.join(root, 'components', 'pdf_report')))
template = env.get_template(component_params.get('report_template'))
self.module.fill_template(template, project, component_params)
self.module.compile_report(project, component_params)
