def test_per_sample_ainfo_error(self):
in_dir = mkdtemp()
self._clean_up_files.append(in_dir)
makedirs(join(in_dir, 'sampleA'))
makedirs(join(in_dir, 'sampleB'))
# Paired-end
with self.assertRaises(ValueError):
_per_sample_ainfo(in_dir, (('sampleA', None, None, None),
('sampleB', None, None, None)), [],
'filtering', 'QC_Filter Files', True)
def filter(qclient, job_id, parameters, out_dir):
"""Run filtering using Bowtie2 with the given parameters
Parameters
----------
qclient : tgp.qiita_client.QiitaClient
The Qiita server client
job_id : str
The job id
parameters : dict
The parameter values to run split libraries
out_dir : str
The path to the job's output directory
Returns
-------
bool, list, str
The results of the job
"""
# Step 1 get the rest of the information need to run Bowtie2
qclient.update_job_step(job_id, "Step 1 of 4: Collecting information")
artifact_id = parameters['input']
del parameters['input']
# Get the artifact filepath information
artifact_info = qclient.get("/qiita_db/artifacts/%s/" % artifact_id)
fps = artifact_info['files']
# Get the artifact metadata
prep_info = qclient.get('/qiita_db/prep_template/%s/' %
artifact_info['prep_information'][0])
qiime_map = prep_info['qiime-map']
# Step 2 generating command
qclient.update_job_step(job_id, "Step 2 of 4: Generating"
" QC_Filter commands")
# Creating temporary directory for intermediate files
with TemporaryDirectory(dir=out_dir, prefix='filter_') as temp_dir:
rs = fps['raw_reverse_seqs'] if 'raw_reverse_seqs' in fps else []
commands, samples = generate_filter_commands(fps['raw_forward_seqs'],
rs, qiime_map, out_dir,
temp_dir, parameters)
# Step 3 execute filtering command
len_cmd = len(commands)
msg = "Step 3 of 4: Executing QC_Filter job (%d/{0})".format(len_cmd)
success, msg = _run_commands(qclient, job_id, commands, msg,
'QC_Filter')
if not success:
return False, None, msg
# Step 4 generating artifacts
msg = "Step 4 of 4: Generating new artifacts (%d/{0})".format(len_cmd)
suffixes = ['%s.R1.fastq.gz', '%s.R2.fastq.gz']
prg_name = 'Filtering'
file_type_name = 'Filtered files'
ainfo = _per_sample_ainfo(out_dir, samples, suffixes, prg_name,
file_type_name, bool(rs))
return True, ainfo, ""