def command(self):
from qtools.constants.job import JOB_ID_PROCESS_ASSAY
from qtools.messages.sequence import ProcessSequenceGroupMessage
app = self.load_wsgi_app()
mgr = create_manager(app.config)
if len(self.args) < 3:
raise ValueError, self.usage
infile = open(self.args[-3], 'r')
mode = self.args[-2].lower()
#read in liens
lines = [l for l in infile]
infile.close()
assay_line_dict = defaultdict(lambda: defaultdict(lambda: None))
for line in lines:
toks = self.__split_line(line)
name = self.__assay_name(toks)
if not name:
continue
comp = self.__assay_component(toks)
seq = self.__assay_sequence(toks)
assay_line_dict[name][comp] = seq
Owner = Session.query(Person).filter_by(name_code=u'NielsK').first()
for k, v in sorted(assay_line_dict.items()):
sg = SequenceGroup(name=k,
owner_id=Owner.id,
gene=v['gene'],
kit_type = SequenceGroup.CHEMISTRY_TYPE_TAQMAN,
type = {'red': SequenceGroup.ASSAY_TYPE_RED,
'cnv': SequenceGroup.ASSAY_TYPE_CNV,
'snp': SequenceGroup.ASSAY_TYPE_SNP,
'gex': SequenceGroup.ASSAY_TYPE_GEX,
'abs': SequenceGroup.ASSAY_TYPE_ABS}[mode],
notes = mode + ' Content Project assay design. ' + \
'Imported from %s' % os.path.basename(self.args[-3]),
status = v['status'],
analyzed = False)
fps = Sequence(sequence=v['for'],
strand='+')
rps = Sequence(sequence=v['rev'],
strand='+')
if v['taq']:
ps = Sequence(sequence=v['taq'],
strand='+')
sg.forward_primers.append(SequenceGroupComponent(
sequence=fps,
role=SequenceGroupComponent.FORWARD_PRIMER,
barcode_label='%s_FP1' % k[:12],
primary=True,
order=0))
sg.reverse_primers.append(SequenceGroupComponent(
sequence=rps,
role=SequenceGroupComponent.REVERSE_PRIMER,
barcode_label='%s_RP1' % k[:12],
primary=True,
order=0))
if v['taq']:
sg.probes.append(SequenceGroupComponent(
sequence=ps,
role=SequenceGroupComponent.PROBE,
barcode_label='%s_P1FM' % k[:11],
primary=True,
order=0,
dye=v['dye'],
quencher='IABkFQ'))
print "Committing %s..." % k
Session.add(sg)
Session.commit()
job_queue = mgr.jobqueue()
job = job_queue.add(JOB_ID_PROCESS_ASSAY, ProcessSequenceGroupMessage(sg.id))
sg.pending_job_id = job.id
Session.commit()
