def test_general_portion_of_template_injected_correctly(self): template = 'STAR=%STAR%\nSAMTOOLS=%SAMTOOLS%\nPICARD_DIR=%PICARD_DIR%\nGTF=%GTF%\nGENOME_INDEX=%GENOME_INDEX%' expected_result = 'STAR=STARPATH\nSAMTOOLS=SAM\nPICARD_DIR=PIC\nGTF=my.gtf\nGENOME_INDEX=GI' p = Params() p.add(star_align = 'STARPATH') p.add(samtools = 'SAM') p.add(gtf = 'my.gtf') p.add(star_genome_index= 'GI') p.add(picard = 'PIC') myproject = Project() myproject.parameters = p result = self.module.fill_out_general_template_portion(myproject, template) self.assertEqual( result, expected_result)
def test_system_call_to_bedtools(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
mock_dir = '/abc/def/'
mock_sample_names = ['AAA', 'BBB', 'CCC']
levels = ['sort.bam', 'sort.primary.bam', 'sort.primary.dedup.bam']
all_samples = []
for sn in mock_sample_names:
bamfiles = map(lambda x: os.path.join(mock_dir, sn + '.' + x),
levels)
s = Sample(sn, 'X', bamfiles=bamfiles)
all_samples.append(s)
project.samples = all_samples
component_params = cp.read_config(
os.path.join(root, 'components', 'pdf_report', 'report.cfg'),
'COMPONENT_SPECIFIC')
self.module.subprocess.Popen = mock.Mock()
mock_process = mock.Mock()
mock_process.communicate.return_value = (('abc', 'def'))
mock_process.returncode = 0
self.module.subprocess.Popen.return_value = mock_process
self.module.subprocess.STDOUT = 'abc'
self.module.subprocess.STDERR = 'def'
m = mock.mock_open()
with mock.patch.object(__builtin__, 'open', m) as x:
expected_calls = [
mock.call([
component_params.get('bedtools_path'),
component_params.get('bedtools_cmd'), '-ibam',
'/abc/def/AAA.sort.primary.bam', '-bga'
],
stderr='abc',
stdout=m()),
mock.call().communicate(),
mock.call([
component_params.get('bedtools_path'),
component_params.get('bedtools_cmd'), '-ibam',
'/abc/def/BBB.sort.primary.bam', '-bga'
],
stderr='abc',
stdout=m()),
mock.call().communicate(),
mock.call([
component_params.get('bedtools_path'),
component_params.get('bedtools_cmd'), '-ibam',
'/abc/def/CCC.sort.primary.bam', '-bga'
],
stderr='abc',
stdout=m()),
mock.call().communicate()
]
self.module.calculate_coverage_data(project, component_params)
self.module.subprocess.Popen.assert_has_calls(expected_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)
