def run(self, variants_path):
"""
Run the VEP service and save results in a temporary file.
:param variants_path: File with variants. In BED format. http://www.ensembl.org/info/docs/variation/vep/vep_script.html#custom_formats
:return: True if successfull or False otherwise
"""
if self.results_path is None:
self.results_path = tempfile.mkstemp()[1]
with open(self.results_path, "w") as rf:
with open(variants_path, "r") as vf:
column_types = (str, int, int, str, str, int)
for fields in tsv.lines(vf, column_types):
chr, start, end, allele, strand, var_id = fields
alt = allele[allele.find("/") + 1:]
results = self.get(chr, start, end, strand, alt, var_id)
if results is None:
continue
for r in results:
rf.write(tsv.line_text(
var_id, chr, start, allele,
r.gene, r.transcript, ",".join(sorted(r.consequences)),
r.protein_pos, r.aa_change, r.protein,
r.sift, r.polyphen, null_value="-"))
def liftover(project):
log = task.logger
conf = task.conf
config = GlobalConfig(conf)
lifted_project_port = task.ports("lifted_projects")
log.info("--- [{0}] --------------------------------------------".format(project["id"]))
log.info("Preparing liftOver files ...")
in_path = make_temp_file(task, suffix=".bed")
in_file = open(in_path, "w")
out_path = make_temp_file(task, suffix=".bed")
unmapped_path = os.path.join(project["temp_path"], "liftover_unmapped.bed")
projdb = ProjectDb(project["db"])
for var in projdb.variants(order_by="position"):
in_file.write(tsv.line_text("chr" + var.chr, var.start, var.start + len(var.ref), var.id))
in_file.close()
log.info("Running liftOver ...")
project["from_assembly"] = project["assembly"]
project["assembly"] = "hg19"
cmd = " ".join(
[
conf["liftover_bin"],
in_path,
os.path.join(conf["liftover_chain_path"], "hg18ToHg19.over.chain"),
out_path,
unmapped_path,
]
)
log.debug(cmd)
subprocess.call(cmd, shell=True)
log.info("Annotating unmapped variants ...")
count = 0
with open(unmapped_path, "r") as f:
for line in f:
if line.lstrip().startswith("#"):
continue
fields = line.rstrip().split("\t")
var_id = int(fields[3])
projdb.update_variant_start(var_id, start=None)
count += 1
log.info(" {0} unmapped variants annotated".format(count))
log.info("Updating variants ...")
count = 0
with open(out_path, "r") as f:
for line in f:
fields = line.rstrip().split("\t")
chr, start, end, var_id = fields
projdb.update_variant_start(var_id, start=start)
count += 1
log.info(" {0} variants".format(count))
remove_temp(task, in_path, out_path)
projdb.commit()
projdb.close()
lifted_project_port.send(project)