def main(argv):
parser = make_parser()
args = parser.parse_args(argv)
log_level = getattr(logging, args.loglevel)
kwargs = {'format' : LOG_FORMAT,
'datefmt' : LOG_DATEFMT,
'level' : log_level}
if args.logfile:
kwargs['filename'] = args.logfile
logging.basicConfig(**kwargs)
logger = logging.getLogger()
kb = KB(driver='omero')(args.host, args.user, args.passwd)
logger.info('Loading GenotypeDataSample objects')
dsamples = kb.get_objects(kb.GenotypeDataSample)
logger.info('Loaded %d objects' % len(dsamples))
logger.info('Loading SNPMarkersSet')
query = 'SELECT snpm FROM SNPMarkersSet snpm WHERE snpm.label = :mset_label'
mset = kb.find_all_by_query(query, {'mset_label' : args.marker_set})[0]
if not mset:
logger.error('Unable to load SNPMarkersSet with label %s' % args.marker_set)
sys.exit(2)
else:
logger.info('Object loaded')
gdo_iterator = kb.get_gdo_iterator(mset, dsamples[:args.fetch_size])
gdos = []
logger.info('Loading GDOs')
for gdo in gdo_iterator:
logger.info(gdo['vid'])
gdos.append(gdo)
logger.debug('%d/%d GDOs loaded' % (len(gdos), args.fetch_size))
logger.info('Loaded %d GDOs' % len(gdos))
def main(argv):
parser = make_parser()
args = parser.parse_args(argv)
log_level = getattr(logging, args.loglevel)
kwargs = {'format': LOG_FORMAT, 'datefmt': LOG_DATEFMT, 'level': log_level}
if args.logfile:
kwargs['filename'] = args.logfile
logging.basicConfig(**kwargs)
logger = logging.getLogger()
kb = KB(driver='omero')(args.host, args.user, args.passwd)
logger.info('Loading GenotypeDataSample objects')
dsamples = kb.get_objects(kb.GenotypeDataSample)
logger.info('Loaded %d objects' % len(dsamples))
logger.info('Loading SNPMarkersSet')
query = 'SELECT snpm FROM SNPMarkersSet snpm WHERE snpm.label = :mset_label'
mset = kb.find_all_by_query(query, {'mset_label': args.marker_set})[0]
if not mset:
logger.error('Unable to load SNPMarkersSet with label %s' %
args.marker_set)
sys.exit(2)
else:
logger.info('Object loaded')
gdo_iterator = kb.get_gdo_iterator(mset, dsamples[:args.fetch_size])
gdos = []
logger.info('Loading GDOs')
for gdo in gdo_iterator:
logger.info(gdo['vid'])
gdos.append(gdo)
logger.debug('%d/%d GDOs loaded' % (len(gdos), args.fetch_size))
logger.info('Loaded %d GDOs' % len(gdos))
user = args.user or vlu.ome_user()
passwd = args.passwd or vlu.ome_passwd()
except ValueError, ve:
logger.critical(ve)
sys.exit(ve)
kb = KB(driver="omero")(host, user, passwd)
logger.info("getting data samples")
ms = kb.get_snp_markers_set(label=args.marker_set)
if ms is None:
msg = "marker set %s not present in kb, bailing out" % args.marker_set
logger.critical(msg)
sys.exit(msg)
query = "from GenotypeDataSample g where g.snpMarkersSet.id = :id"
params = {"id": ms.omero_id}
gds = kb.find_all_by_query(query, params)
logger.info("found %d data samples for marker set %s" %
(len(gds), args.marker_set))
logger.info("updating dep tree")
kb.update_dependency_tree()
individuals = [get_individual(kb, ds) for ds in gds]
ds_by_ind_id = dict((i.id, ds) for i, ds in zip(individuals, gds))
logger.info("getting families")
families = get_all_families(kb)
ped_writer = PedWriter(ms, base_path=args.prefix)
logger.info("writing map file")
ped_writer.write_map()
logger.info("writing ped file")
for i, fam in enumerate(families):
if set(ds_by_ind_id.get(i.id) for i in fam) != set([None]):
fam_label = "FAM_%d" % (i+1)
