def process_folder(result_folder, qai_server, qai_user, qai_password,
pipeline_version):
logger.info('Uploading data to Oracle from {}'.format(result_folder))
collated_conseqs = os.path.join(result_folder, 'conseq.csv')
collated_counts = os.path.join(result_folder, 'remap_counts.csv')
cascade = os.path.join(result_folder, 'cascade.csv')
coverage_scores = os.path.join(result_folder, 'coverage_scores.csv')
all_results_path, _ = os.path.split(os.path.normpath(result_folder))
run_path, _ = os.path.split(all_results_path)
sample_sheet_file = os.path.join(run_path, "SampleSheet.csv")
with open(sample_sheet_file, "rU") as f:
sample_sheet = sample_sheet_parser.sample_sheet_parser(f)
ok_sample_regions = load_ok_sample_regions(result_folder)
with qai_helper.Session() as session:
session.login(qai_server, qai_user, qai_password)
run = find_run(session, sample_sheet["Experiment Name"])
with open(collated_conseqs, "rU") as f:
conseqs = build_conseqs(f, run, sample_sheet, ok_sample_regions)
with open(coverage_scores, "rU") as f, \
open(collated_counts, "rU") as f2, \
open(cascade, "rU") as f3:
upload_review_to_qai(f, f2, f3, run, sample_sheet, conseqs,
session, pipeline_version)
def download_quality(self, folder):
""" Download quality control data for the run.
@return path for the quality CSV file
"""
trimmed_folder = self.trim_folder(folder)
destination_folder = os.path.join(settings.home,
os.path.basename(folder))
destination = os.path.join(destination_folder,
'{}_quality.csv'.format(trimmed_folder))
if not os.path.exists(destination_folder):
os.makedirs(destination_folder)
run_info_path = os.path.join(folder, 'RunInfo.xml')
run_info = self.parse_run_info(run_info_path)
with qai_helper.Session() as session:
session.login(settings.qai_path, settings.qai_user,
settings.qai_password)
metrics = session.get_json('/miseqqc_errormetrics?runid=' +
run_info.miseq_run_id)
if not metrics:
raise RuntimeError(
'No quality control metrics found for run ' +
run_info.miseq_run_id)
with open(destination, 'w') as f:
self.write_quality(f, metrics, run_info)
return destination
def main():
args = parse_args()
dump = {}
used_regions = set()
with qai_helper.Session() as session:
session.login(args.qai_server, args.qai_user, args.qai_password)
dump['regions'] = session.get_json("/lab_miseq_regions?mode=dump",
retries=0)
dump['projects'] = session.get_json(
"/lab_miseq_projects?mode=dump&pipeline=" + args.pipeline_version,
retries=0)
empty_projects = []
for name, project in dump['projects'].items():
project['regions'].sort(key=itemgetter('coordinate_region'))
for region in project['regions']:
used_regions.add(region['coordinate_region'])
used_regions.update(region['seed_region_names'])
if not project['regions']:
empty_projects.append(name)
for name in empty_projects:
del dump['projects'][name]
errors = dump['projects'].get('errors')
if errors:
raise RuntimeError('\n'.join(errors))
check_key_positions(dump['projects'], sys.stdout)
dump['regions'] = {
key: value
for key, value in dump['regions'].items() if key in used_regions
}
dump_scoring = deepcopy(dump)
for project in dump['projects'].values():
for region in project['regions']:
del region['key_positions']
del region['min_coverage1']
del region['min_coverage2']
del region['min_coverage3']
dump_json(dump, "../projects.json")
for project in dump_scoring['projects'].values():
for region in project['regions']:
name = region['coordinate_region']
seq = ''.join(dump_scoring['regions'][name]['reference'])
region['coordinate_region_length'] = len(seq)
del dump_scoring['regions']
dump_json(dump_scoring, "../project_scoring.json")
print("Done.")
def upload_loop(qai_server, qai_user, qai_password, pipeline_version,
upload_queue):
# noinspection PyBroadException
try:
with qai_helper.Session() as session:
# Try logging in to QAI, just so we learn about problems at launch.
session.login(qai_server, qai_user, qai_password)
except Exception:
logger.error('Unable to log in to QAI.', exc_info=True)
while True:
item = upload_queue.get()
if item is None:
break
process_folder(item, qai_server, qai_user, qai_password,
pipeline_version)
def main():
dump = {}
with qai_helper.Session() as session:
session.login(settings.qai_project_path, settings.qai_project_user,
settings.qai_project_password)
dump['regions'] = session.get_json("/lab_miseq_regions?mode=dump",
retries=0)
dump['projects'] = session.get_json(
"/lab_miseq_projects?mode=dump&pipeline=" +
settings.pipeline_version,
retries=0)
for project in dump['projects'].itervalues():
project['regions'].sort()
errors = dump['projects'].get('errors')
if errors:
raise StandardError('\n'.join(errors))
check_key_positions(dump['projects'], sys.stdout)
dump_scoring = deepcopy(dump)
for project in dump['projects'].itervalues():
for region in project['regions']:
del region['key_positions']
del region['min_coverage1']
del region['min_coverage2']
del region['min_coverage3']
dump_json(dump, "../projects.json")
for project in dump_scoring['projects'].itervalues():
for region in project['regions']:
name = region['coordinate_region']
seq = ''.join(dump_scoring['regions'][name]['reference'])
region['coordinate_region_length'] = len(seq)
del dump_scoring['regions']
dump_json(dump_scoring, "../project_scoring.json")
print "Done."
def main():
project_config = ProjectConfig.loadDefault()
with open('../project_scoring.json', 'rU') as scoring_file:
scoring_config = json.load(scoring_file)
with qai_helper.Session() as session:
session.login(settings.qai_path, settings.qai_user,
settings.qai_password)
pipelines = session.get_json("/lab_miseq_pipelines?version=" +
settings.pipeline_version,
retries=0)
if pipelines:
raise RuntimeError('Pipeline {} already exists.'.format(
settings.pipeline_version))
seed_groups = session.get_json("/lab_miseq_seed_groups")
seed_group_ids = dict(map(itemgetter('name', 'id'), seed_groups))
old_regions = session.get_json("/lab_miseq_regions", retries=0)
regions = dict(((region['name'], region) for region in old_regions))
for region_name, region_data in project_config.config[
'regions'].iteritems():
region = regions.get(region_name)
if region is None:
seed_group_name = region_data['seed_group']
seed_group_id = seed_group_ids.get(seed_group_name)
if seed_group_id is None and seed_group_name:
seed_group = session.post_json("/lab_miseq_seed_groups",
{'name': seed_group_name})
seed_group_id = seed_group['id']
seed_group_ids[seed_group_name] = seed_group_id
region = session.post_json(
"/lab_miseq_regions", {
'name': region_name,
'is_nucleotide': region_data['is_nucleotide'],
'reference': ''.join(region_data['reference']),
'seed_group_id': seed_group_id
})
regions[region_name] = region
pipeline = session.post_json("/lab_miseq_pipelines",
{'version': settings.pipeline_version})
pipeline_id = pipeline['id']
old_projects = session.get_json("/lab_miseq_projects", retries=0)
projects = dict(
((project['name'], project) for project in old_projects))
for project_name, project_data in project_config.config[
'projects'].iteritems():
project = projects.get(project_name)
if project is None:
project = session.post_json(
"/lab_miseq_projects", {
'name': project_name,
'max_variants': project_data['max_variants']
})
project_version = session.post_json("/lab_miseq_project_versions",
{
'pipeline_id': pipeline_id,
'project_id': project['id']
})
for i, region_data in enumerate(project_data['regions']):
scoring_data = scoring_config['projects'][project_name][
'regions'][i]
coordinate_region = regions[region_data['coordinate_region']]
seed_region = regions[region_data['seed_region_names'][0]]
seed_group_id = seed_region['seed_group_id']
project_region = session.post_json(
"/lab_miseq_project_regions", {
'project_version_id': project_version['id'],
'coordinate_region_id': coordinate_region['id'],
'min_coverage1': scoring_data['min_coverage1'],
'min_coverage2': scoring_data['min_coverage2'],
'min_coverage3': scoring_data['min_coverage3'],
'seed_group_id': seed_group_id
})
for key_position in scoring_data['key_positions']:
session.post_json(
"/lab_miseq_key_positions", {
'project_region_id': project_region['id'],
'start_pos': key_position['start_pos'],
'end_pos': key_position['end_pos']
})
print "Done."
def main():
args = parse_args()
project_config = ProjectConfig.loadDefault()
scoring_path = Path(__file__).parent.parent / 'project_scoring.json'
with scoring_path.open() as scoring_file:
scoring_config = json.load(scoring_file)
with qai_helper.Session() as session:
session.login(args.qai_server, args.qai_user, args.qai_password)
pipelines = session.get_json("/lab_miseq_pipelines?version=" +
args.pipeline_version,
retries=0)
if pipelines:
raise RuntimeError('Pipeline {} already exists.'.format(
args.pipeline_version))
seed_groups = session.get_json("/lab_miseq_seed_groups")
# noinspection PyTypeChecker
seed_group_ids = dict(map(itemgetter('name', 'id'), seed_groups))
old_regions = session.get_json("/lab_miseq_regions", retries=0)
regions = dict(((region['name'], region) for region in old_regions))
for region_name, region_data in project_config.config['regions'].items(
):
ref_seq = ''.join(region_data['reference'])
region = regions.get(region_name)
if region is None:
seed_group_name = region_data['seed_group']
seed_group_id = seed_group_ids.get(seed_group_name)
if seed_group_id is None and seed_group_name:
seed_group = session.post_json("/lab_miseq_seed_groups",
{'name': seed_group_name})
seed_group_id = seed_group['id']
seed_group_ids[seed_group_name] = seed_group_id
region = session.post_json(
"/lab_miseq_regions", {
'name': region_name,
'is_nucleotide': region_data['is_nucleotide'],
'reference': ref_seq,
'seed_group_id': seed_group_id
})
regions[region_name] = region
elif region['reference'] != ref_seq:
print("Reference doesn't match:", region_name)
if args.update_sequences:
region['reference'] = ref_seq
session.post_json(f"/lab_miseq_regions/{region['id']}",
region)
pipeline = session.post_json("/lab_miseq_pipelines",
{'version': args.pipeline_version})
pipeline_id = pipeline['id']
old_projects = session.get_json("/lab_miseq_projects", retries=0)
projects = dict(
((project['name'], project) for project in old_projects))
for project_name, project_data in project_config.config[
'projects'].items():
project = projects.get(project_name)
if project is None:
project = session.post_json(
"/lab_miseq_projects", {
'name': project_name,
'max_variants': project_data['max_variants']
})
project_version = session.post_json("/lab_miseq_project_versions",
{
'pipeline_id': pipeline_id,
'project_id': project['id']
})
for i, region_data in enumerate(project_data['regions']):
scoring_data = scoring_config['projects'][project_name][
'regions'][i]
coordinate_region = regions[region_data['coordinate_region']]
seed_region = regions[region_data['seed_region_names'][0]]
seed_group_id = seed_region['seed_group_id']
project_region = session.post_json(
"/lab_miseq_project_regions", {
'project_version_id': project_version['id'],
'coordinate_region_id': coordinate_region['id'],
'min_coverage1': scoring_data['min_coverage1'],
'min_coverage2': scoring_data['min_coverage2'],
'min_coverage3': scoring_data['min_coverage3'],
'seed_group_id': seed_group_id
})
for key_position in scoring_data['key_positions']:
session.post_json(
"/lab_miseq_key_positions", {
'project_region_id': project_region['id'],
'start_pos': key_position['start_pos'],
'end_pos': key_position['end_pos']
})
print("Done.")
def main():
filename = 'HIV1_COM_2015_genome_DNA.csv'
args = parse_args()
if not os.path.exists(filename):
form = {
'ORGANISM': 'HIV',
'ALIGN_TYPE': 'COM',
'SUBORGANISM': 'HIV1',
'PRE_USER': '******',
'REGION': 'GENOME',
'START': '',
'END': '',
'GENO_SUB': 'All',
'BASETYPE': 'DNA',
'YEAR': '2015',
'FORMAT': 'csv',
'submit': 'Get Alignment'
}
response = requests.post(
"https://www.hiv.lanl.gov/cgi-bin/NEWALIGN/align.cgi", data=form)
response.raise_for_status()
# print(response.text)
match = re.search(r'<pre>(.*)</pre>', response.text, re.DOTALL)
with open(filename, 'w') as f:
f.write(match.group(1))
with qai_helper.Session() as session:
session.login(args.qai_server, args.qai_user, args.qai_password)
seed_groups = session.get_json("/lab_miseq_seed_groups")
seed_group_name = 'HIV1-seed'
for seed_group in seed_groups:
if seed_group['name'] == seed_group_name:
break
else:
raise RuntimeError(
'Seed group {} not found.'.format(seed_group_name))
old_regions = session.get_json("/lab_miseq_regions", retries=0)
hiv_seeds = {
region['name']: region
for region in old_regions
if region['seed_group_id'] == seed_group['id']
}
del old_regions
clean_count = 0
dirty_count = 0
recombinant_names = []
with open(filename, 'rU') as f:
reader = csv.reader(f)
for description, seed_seq in reader:
seed_seq = seed_seq.replace('-', '')
name_fields = description.split('.')
subtype, country = name_fields[:2]
accession = name_fields[-1]
if subtype[0].isdigit():
recombinant_names.append(description)
continue
seed_name = '-'.join(
('HIV1', subtype, country, accession, 'seed'))
groups = re.findall(r'([^ACGT]+)', seed_seq)
if groups:
dirty_count += 1
print('Unexpected bases found in {}: {}'.format(
seed_name, ', '.join(groups)))
else:
clean_count += 1
old_region = hiv_seeds.pop(seed_name, None)
if old_region:
old_seq = ''.join(old_region['reference'])
if old_seq != seed_seq:
print('expected: ' + seed_seq)
print('found: ' + old_seq)
raise RuntimeError(
'Seed sequence {} does not match.'.format(
seed_name))
elif len(seed_name) > 30:
print('Name too long: {!r}.'.format(seed_name))
else:
session.post_json(
"/lab_miseq_regions", {
'name': seed_name,
'description': description,
'is_nucleotide': True,
'reference': seed_seq,
'seed_group_id': seed_group['id']
})
if recombinant_names:
print('Skipped recombinants: ' +
', '.join(sorted(recombinant_names)))
if hiv_seeds:
seed_names = sorted(hiv_seeds.keys())
should_delete = True
print('Left over seeds:')
if not should_delete:
print(', '.join(seed_names))
else:
for seed_name in seed_names:
print(seed_name)
seed_id = hiv_seeds[seed_name]['id']
session.delete('{}/lab_miseq_regions/{}'.format(
args.qai_server, seed_id))
print('Done with {} clean and {} dirty.'.format(
clean_count, dirty_count))