def sample_variants_csv(self, sample, type):
if not sampleinfo_mongo.is_sample(sample) or not variants_mongo.is_sample_loaded(sample, type):
self.__log_sample_doesnt_exist()
return
out_path = "%s/%s.csv" % ( self.output_files_dir, sample)
print out_path
csv_writer = csv.writer(open(out_path, "w"), delimiter=',', quotechar='"', quoting=csv.QUOTE_NONNUMERIC)
header = ['CHROM', 'POS', 'REF', 'ALT', 'GT', 'RSID', 'Gene',
'ExonicFunc', 'AAChange', 'FREQ', 'QC_Final', 'QC_Cov', 'QC_AF', 'In_Hotspot']
csv_writer.writerow(header)
client, db = mongo.get_connection()
total_loaded_samples = variants_mongo.count_samples()
for var in variants_mongo.get_sample_vars(sample, type, db):
new_variant = {}
chrom, pos, ref, alt = var['CHROM'], var['POS'], var['REF'], var['ALT']
al1, al2 = genotypetools.get_genotype_alleles(ref, alt, var['GT_calc'])
new_variant.update({'CHROM': chrom, 'POS': pos, 'REF': ref, 'ALT': ",".join(alt),
'GT': "/".join([al1, al2])})
hotspot = hotspot_mongo.get_variant(chrom, pos, ref, alt, db)
annot = hotspot['ANNOTATION'][0]
new_variant.update({'RSID': annot['snp137NonFlagged'],
'Gene': annot['Gene_refGene'], 'ExonicFunc': annot['ExonicFunc_refGene'],
'AAChange': annot['AAChange_refGene']})
if 'p.' in new_variant['AAChange']:
new_variant['AAChange'] = new_variant['AAChange'].split('p.')[1].split(",")[0]
zygosity = hotspot['orig_stats']['zygosity']
freq = sum([zygosity['het_count'], zygosity['het_alt_count'], zygosity['hom_count']]) / float(total_loaded_samples)
final_qc, qc_cov, qc_af = var['FINAL_QC'], var['COV_QC'], var['AF_QC']
if hotspot['orig_stats']['qc']['final_qc_count'] > 0:
in_hotspot = "TRUE"
else:
in_hotspot = "FALSE"
new_variant.update({"FREQ": freq, "QC_Final": final_qc, "QC_Cov": qc_cov, "QC_AF": qc_af,
"In_Hotspot": in_hotspot})
out_row = [str(new_variant[field]) for field in header]
csv_writer.writerow(out_row)
#print "\t".join(out_row)
return out_path
def __reconcile(self, chrom, pos, ref, alt, db):
query = {'CHROM': chrom, 'POS': pos, 'REF': ref, 'ALT': {'$all': alt}}
hotspot_coll = hotspot_mongo.get_collection(db)
variants_coll = variants_mongo.get_collection(db)
matched_documents = [doc for doc in hotspot_coll.find(query)]
if len(matched_documents) == 1:
self.__log_reconciling_variant(chrom, pos, ref, alt)
# UPDATING THE ALTERNATE ALLELE FOR THE HOTSPOT VARIANT
modified_count = hotspot_coll.update_one(query, {'$set': {'ALT': alt}}).modified_count
if modified_count != 1:
self.__log_serious_hotspot_discrepancy('THERE WAS A PROBLEM MODIFYING THE OLD HOTSPOT DOCUMENT')
# UPDATING ALL THE PREVIOUSLY LOADED VARIANTS FOR THE HOTSPOT VARIANT
variant_query = {'TYPE': 'orig', 'CHROM': chrom, 'POS': pos, 'REF': ref, 'ALT': {'$all': alt}}
loaded_variants = [doc for doc in variants_coll.find(variant_query)]
for var in loaded_variants:
var_ref, var_alt, var_gt, var_gt_orig = var['REF'], var['ALT'], var['GT_calc'], var['GT_orig']
var_fao, var_af = var['FAO'], var['AF_calc']
new_alleles = [ref] + alt
if var_gt != './.':
al1, al2 = genotypetools.get_genotype_alleles(var_ref, var_alt, var_gt)
al_num1 = new_alleles.index(al1)
al_num2 = new_alleles.index(al2)
corrected_gt_calc = "/".join([str(val) for val in sorted([al_num1, al_num2])])
else:
corrected_gt_calc = './.'
if var_gt_orig != './.':
al1, al2 = genotypetools.get_genotype_alleles(var_ref, var_alt, var_gt_orig)
al_num1 = new_alleles.index(al1)
al_num2 = new_alleles.index(al2)
corrected_gt_orig = "/".join([str(val) for val in sorted([al_num1, al_num2])])
else:
corrected_gt_orig = './.'
if len(var_fao) == 2:
var_fao = list(reversed(var_fao))
var_af = list(reversed(var_af))
########################################################################################
# I'm going to put off correcting the AF_calc and FAO when number of alternate alleles is > 2
# for now, because it just is not needed for downstream analysis
# DO THIS LATER
########################################################################################
query = {'TYPE': 'orig', 'SAMPLE': var['SAMPLE'],'CHROM': chrom, 'POS': pos, 'REF': ref,
'ALT': {'$all': alt}}
update = {'$set': {'ALT': alt, 'GT_calc': corrected_gt_calc, 'FAO': var_fao, 'AF_calc': var_af,
'GT_orig': corrected_gt_orig}}
modified_count = variants_coll.update_one(query, update).modified_count
if modified_count != 1:
self.__log_serious_hotspot_discrepancy('THERE WAS A PROBLEM MODIFYING THE ORIGINAL VARIANTS '
'DOCUMENT')
else:
self.__log_serious_hotspot_discrepancy('THE NUMBER OF DOCUMENTS WITH MATCHING THE '
'ALLELE GROUP IS NOT 1')
def __reconcile(self, chrom, pos, ref, alt, db):
query = {"CHROM": chrom, "POS": pos, "REF": ref, "ALT": {"$all": alt}}
hotspot_coll = hotspot_mongo.get_collection(db)
variants_coll = variants_mongo.get_collection(db)
matched_documents = [doc for doc in hotspot_coll.find(query)]
if len(matched_documents) == 1:
self.__log_reconciling_variant(chrom, pos, ref, alt)
# UPDATING THE ALTERNATE ALLELE FOR THE HOTSPOT VARIANT
modified_count = hotspot_coll.update_one(query, {"$set": {"ALT": alt}}).modified_count
if modified_count != 1:
self.__log_serious_hotspot_discrepancy("THERE WAS A PROBLEM MODIFYING THE OLD HOTSPOT DOCUMENT")
# UPDATING ALL THE PREVIOUSLY LOADED VARIANTS FOR THE HOTSPOT VARIANT
variant_query = {"TYPE": "orig", "CHROM": chrom, "POS": pos, "REF": ref, "ALT": {"$all": alt}}
loaded_variants = [doc for doc in variants_coll.find(variant_query)]
for var in loaded_variants:
var_ref, var_alt, var_gt, var_gt_orig = var["REF"], var["ALT"], var["GT_calc"], var["GT_orig"]
var_fao, var_af = var["FAO"], var["AF_calc"]
new_alleles = [ref] + alt
if var_gt != "./.":
al1, al2 = genotypetools.get_genotype_alleles(var_ref, var_alt, var_gt)
al_num1 = new_alleles.index(al1)
al_num2 = new_alleles.index(al2)
corrected_gt_calc = "/".join([str(val) for val in sorted([al_num1, al_num2])])
else:
corrected_gt_calc = "./."
if var_gt_orig != "./.":
al1, al2 = genotypetools.get_genotype_alleles(var_ref, var_alt, var_gt_orig)
al_num1 = new_alleles.index(al1)
al_num2 = new_alleles.index(al2)
corrected_gt_orig = "/".join([str(val) for val in sorted([al_num1, al_num2])])
else:
corrected_gt_orig = "./."
if len(var_fao) == 2:
var_fao = list(reversed(var_fao))
var_af = list(reversed(var_af))
########################################################################################
# I'm going to put off correcting the AF_calc and FAO when number of alternate alleles is > 2
# for now, because it just is not needed for downstream analysis
# DO THIS LATER
########################################################################################
query = {
"TYPE": "orig",
"SAMPLE": var["SAMPLE"],
"CHROM": chrom,
"POS": pos,
"REF": ref,
"ALT": {"$all": alt},
}
update = {
"$set": {
"ALT": alt,
"GT_calc": corrected_gt_calc,
"FAO": var_fao,
"AF_calc": var_af,
"GT_orig": corrected_gt_orig,
}
}
modified_count = variants_coll.update_one(query, update).modified_count
if modified_count != 1:
self.__log_serious_hotspot_discrepancy(
"THERE WAS A PROBLEM MODIFYING THE ORIGINAL VARIANTS " "DOCUMENT"
)
else:
self.__log_serious_hotspot_discrepancy("THE NUMBER OF DOCUMENTSG THE " "ALLELE GROUP IS NOT 1")