def validate_chipseq_experiments(self):
for rec_id in self.chipseq_experiment_ids:
exp = models.ChipseqExperiment(rec_id)
str_exp_id = str(exp.id)
target = models.Target(exp.target_id)
target_upstream = target.upstream_identifier.strip()
if not target_upstream:
if target.id not in self.unregistered_targets:
self.unregistered_targets.append(target.id)
msg = "Target {} not registred.".format(target.id)
self.fout.write(str_exp_id + "\t" + msg + "\n")
exp_rep_ids = exp.replicate_ids
if not exp_rep_ids:
msg = "ChipseqExperiment missing replicates."
self.fout.write(str_exp_id + "\t" + msg + "\n")
else:
for rep_id in exp_rep_ids:
self.validate_gm_for_crispr_biosample(chip_exp_id=exp.id,
biosample_id=rep_id)
# Check WT input present
if not exp.wild_type_control_id:
msg = "ChipseqExperiment missing WT control."
self.fout.write(str_exp_id + "\t" + msg + "\n")
# Check Paired input present and has GM
pi_ids = exp.control_replicate_ids
if not pi_ids:
msg = "ChipseqExperiment missing paired input."
self.fout.write(str_exp_id + "\t" + msg + "\n")
else:
for pi_id in pi_ids:
self.validate_gm_for_crispr_biosample(chip_exp_id=exp.id,
biosample_id=pi_id)
self.fout.close()
def main():
parser = get_parser()
args = parser.parse_args()
url = args.url
infile = args.infile
if url:
conn = euc.Connection("prod")
results = conn.search(url=url)
else:
fh = open(infile)
results = json.load(fh)
admin = models.User.find_by({"first_name": "Admin"})
if not admin:
raise Exception("Could not find the Admin user in the database, which is needed for associating with new records.")
created = 0
patched = 0
total = 0
for rec in results:
patch = False
total += 1
organism = rec["organism"]["scientific_name"]
if organism != SPECIES:
continue
payload = {}
label = rec["label"]
payload["name"] = label
# Check if the target already exists in the database.
pulsar_record = models.Target.find_by({"name": label})
upstream = rec["@id"].strip("/").split("/")[-1]
if pulsar_record and upstream != pulsar_record["upstream_identifier"]:
patch = True
elif pulsar_record:
continue # Can add support for patch operation later.
payload["upstream_identifier"] = upstream
payload["user_id"] = admin["id"]
xrefs = rec["dbxref"]
for ref in xrefs:
tokens = ref.split(":")
prefix, ref = ref.rsplit(":", 1)
if prefix == "ENSEMBL":
payload["ensembl"] = ref
elif prefix == "UniProtKB":
payload["uniprotkb"] = ref
elif prefix == "RefSeq":
payload["refseq"] = ref
print("Creating {}".format(payload))
if patch:
target = models.Target(pulsar_record["id"])
target.patch(payload)
patched += 1
print("Patched: {}".format(patched))
else:
models.Target.post(payload)
created += 1
print("Created: {}".format(created))
print("Total processed: {}".format(total))
def validate_gm_for_crispr_biosample(self, chip_exp_id, biosample_id):
biosample = models.Biosample(biosample_id)
gm_id = biosample.crispr_modification_id
if not gm_id:
msg = "Exp. biosample {} missing GM.".format(biosample.id)
self.fout.write((str(chip_exp_id) + "\t" + msg + "\n"))
else:
# Verify that GM target is present.
gm = models.CrisprModification(gm_id)
donor_construct = models.DonorConstruct(gm.donor_construct_id)
dc_target = models.Target(donor_construct.target_id)
if not dc_target.upstream_identifier:
if dc_target.id not in self.unregistered_targets:
self.unregistered_targets.append(dc_target.id)
msg = "Target {} not registred.".format(dc_target.id)
self.fout.write(str(chip_exp_id) + "\t" + msg + "\n")
ccs = [models.CrisprConstruct(x) for x in gm.crispr_construct_ids]
for c in ccs:
cc_target = models.Target(c.target_id)
if not cc_target.upstream_identifier:
if cc_target.id not in self.unregistered_targets:
self.unregistered_targets.append(cc_target.id)
msg = "Target {} not registred.".format(cc_target.id)
self.fout.write((str(chip_exp_id) + "\t" + msg + "\n"))