def test_init(self):
'''test init'''
expected = {
'samples_per_dir': 42,
'samples': {
'sample1': {
'name': 'sample1',
'reads': ['file1.1', 'file1.2'],
'number': 0,
'dir': '0/0'
},
'sample2': {
'name': 'sample2',
'reads': ['file2.1', 'file2.2'],
'number': 1,
'dir': '0/1'
}
}
}
pipe_dir = os.path.join(data_dir, 'init')
pipe_dir_obj = pipeline_output_dir.PipelineOutputDir(pipe_dir)
self.assertEqual(expected, pipe_dir_obj.data)
expected = {'samples_per_dir': 42, 'samples': {}}
pipe_dir_obj = pipeline_output_dir.PipelineOutputDir(
'does_not_exist', samples_per_dir=42)
self.assertEqual(expected, pipe_dir_obj.data)
def test_add_data_from_file(self):
'''test add_data_from_file'''
tmp_dir = 'tmp.test_add_data_from_file'
data_file = os.path.join(data_dir, 'add_data_from_file.1.tsv')
pipe_dir = pipeline_output_dir.PipelineOutputDir(tmp_dir)
pipe_dir.add_data_from_file(data_file)
expected_data = {
'samples_per_dir': 100,
'samples': {
's1': {
'name': 's1',
'reads': ['s1_1.fq.gz', 's1_2.fq.gz'],
'number': 0,
'dir': os.path.join('0', '0')
}
},
}
self.assertEqual(expected_data, pipe_dir.data)
self.assertTrue(os.path.exists(os.path.join(tmp_dir, '0', '0')))
data_file = os.path.join(data_dir, 'add_data_from_file.2.tsv')
pipe_dir.add_data_from_file(data_file)
expected_data['samples']['s2'] = {
'name': 's2',
'reads': ['s2_1.fq.gz', 's2_2.fq.gz'],
'number': 1,
'dir': os.path.join('0', '1')
}
self.assertEqual(expected_data, pipe_dir.data)
self.assertTrue(os.path.exists(os.path.join(tmp_dir, '0', '1')))
shutil.rmtree(tmp_dir)
def test_write_tsv_file(self):
'''test write_tsv_file'''
tmp_tsv = 'tmp.pipeline_output_dir.write_tsv_file.tsv'
pipe_dir = pipeline_output_dir.PipelineOutputDir(
os.path.join(data_dir, 'test_write_tsv_file'))
pipe_dir.write_tsv_file(tmp_tsv)
expected = os.path.join(data_dir, 'write_tsv_file.expect.tsv')
self.assertTrue(filecmp.cmp(expected, tmp_tsv, shallow=False))
os.unlink(tmp_tsv)
def test_write_json_data_file(self):
'''test write_json_data_file'''
tmp_dir = 'tmp.pipeline_output_dir.write_json_data_file'
pipe_dir = pipeline_output_dir.PipelineOutputDir(tmp_dir)
pipe_dir.data = {'spam': 'eggs', 'rush': ['lifeson', 'lee', 'peart']}
pipe_dir.write_json_data_file()
expected = os.path.join(data_dir, 'write_json_data_file.json')
self.assertTrue(
filecmp.cmp(expected, pipe_dir.json_data_file, shallow=False))
shutil.rmtree(tmp_dir)
def test_make_summary_json_of_all_samples(self):
'''test make_summary_json_of_all_samples'''
tmp_pipe_dir = 'tmp.make_summary_json_of_all_samples'
tmp_data_file = 'tmp.make_summary_json_of_all_samples.in.tsv'
tmp_json = 'tmp.make_summary_json_of_all_samples.json'
with open(tmp_data_file, 'w') as f:
print('sample1', 'reads1.1', 'reads1.2', sep='\t', file=f)
print('sample2', 'reads2.1', 'reads2.2', sep='\t', file=f)
pipe_dir = pipeline_output_dir.PipelineOutputDir(tmp_pipe_dir)
pipe_dir.add_data_from_file(tmp_data_file)
json_data_to_write = {
'sample1': {
'foo': 'bar',
'spam': ['eggs', 'shrubbery']
},
'sample2': {
'x': 'y',
'swallow': ['african', 'european']
},
}
for sample in json_data_to_write:
outfile = os.path.join(tmp_pipe_dir,
pipe_dir.data['samples'][sample]['dir'],
'summary.json')
with open(outfile, 'w') as f:
print(json.dumps(json_data_to_write[sample],
sort_keys=True,
indent=4),
file=f)
pipe_dir.make_summary_json_of_all_samples(tmp_json)
with open(tmp_json) as f:
got_data = data = json.load(f)
self.assertEqual(json_data_to_write, got_data)
os.unlink(tmp_json)
pipe_dir.make_summary_json_of_all_samples(tmp_json, threads=2)
with open(tmp_json) as f:
got_data = data = json.load(f)
self.assertEqual(json_data_to_write, got_data)
shutil.rmtree(tmp_pipe_dir)
os.unlink(tmp_data_file)
os.unlink(tmp_json)
def run(options):
pipe_dir = pipeline_output_dir.PipelineOutputDir(options.outdir)
if not options.no_new_data:
pipe_dir.add_data_from_file(options.data_tsv)
pipe_dir.write_json_data_file()
pipe_dir.write_tsv_file(options.out_tsv)
def run(options):
pipe_dir = pipeline_output_dir.PipelineOutputDir(options.pipeline_dir)
pipe_dir.make_summary_json_of_all_samples(options.outfile, threads=options.threads)