def add_vcf_file_to_annotator(self, vcf_file_path, force_all=False):
"""
Add the variants in vcf_file_path to annotator
Convenience wrapper around add_variants_to_annotator
"""
if not force_all and self.get_annotator_datastore().vcf_files.find_one(
{'vcf_file_path': vcf_file_path}):
print "VCF already annotated"
return
print "Scanning VCF file first..."
variant_t_list = []
for variant_t in vcf_stuff.iterate_tuples(
compressed_file(vcf_file_path)):
variant_t_list.append(variant_t)
if len(variant_t_list) == 100000:
print "Adding another 100000 variants, through {}".format(
variant_t_list[-1][0])
self.add_variants_to_annotator(variant_t_list, force_all)
variant_t_list = []
self.add_variants_to_annotator(variant_t_list, force_all)
self.get_annotator_datastore().vcf_files.insert({
'vcf_file_path':
vcf_file_path,
'date_added':
datetime.datetime.utcnow()
})
def add_vcf_file_to_annotator(self, vcf_file_path, force_all=False):
"""
Add the variants in vcf_file_path to annotator
Convenience wrapper around add_variants_to_annotator
"""
print "Scanning VCF file first..."
variant_t_list = []
for variant_t in vcf_stuff.iterate_tuples(compressed_file(vcf_file_path)):
variant_t_list.append(variant_t)
if len(variant_t_list) == 100000:
print "Adding another 100000 variants, through {}".format(variant_t_list[-1][0])
self.add_variants_to_annotator(variant_t_list, force_all)
variant_t_list = []
self.add_variants_to_annotator(variant_t_list, force_all)
def add_vcf_file_to_annotator(self, vcf_file_path, force_all=False):
"""
Add the variants in vcf_file_path to annotator
Convenience wrapper around add_variants_to_annotator
"""
if not force_all and self._db.vcf_files.find_one({'vcf_file_path': vcf_file_path}):
print "VCF already annotated"
return
print "Scanning VCF file first..."
variant_t_list = []
for variant_t in vcf_stuff.iterate_tuples(compressed_file(vcf_file_path)):
variant_t_list.append(variant_t)
if len(variant_t_list) == 100000:
print "Adding another 100000 variants, through {}".format(variant_t_list[-1][0])
self.add_variants_to_annotator(variant_t_list, force_all)
variant_t_list = []
self.add_variants_to_annotator(variant_t_list, force_all)
self._db.vcf_files.insert({'vcf_file_path': vcf_file_path, 'date_added': datetime.datetime.utcnow()})
