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genomicVariations_vcf.py
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from cyvcf2 import VCF
import json
from tqdm import tqdm
import glob
import re
import conf.conf as conf
import uuid
import json
import gc
import gzip
from pymongo.mongo_client import MongoClient
from validators.genomicVariations import GenomicVariations
client = MongoClient(
#"mongodb://127.0.0.1:27017/"
"mongodb://{}:{}@{}:{}/{}?authSource={}".format(
conf.database_user,
conf.database_password,
conf.database_host,
conf.database_port,
conf.database_name,
conf.database_auth_source,
)
)
with open('files/deref_schemas/genomicVariations.json') as json_file:
dict_properties = json.load(json_file)
try:
with open('pipelines/default/templates/populations.json') as pipeline_file:
pipeline = json.load(pipeline_file)
except Exception:
pipeline = None
try:
with open('pipelines/default/templates/template.json') as template_file:
template = json.load(template_file)
if template["template"]==False:
template=None
except Exception:
template = None
def commas(prova):
length_iter=0
array_of_newdicts=[]
for key, value in prova.items():
if isinstance(value, str):
valuesplitted = value.split('|')
length_iter=len(valuesplitted)
elif isinstance(value, dict):
for kval, vval in value.items():
if isinstance(vval, str):
valsplitted = vval.split('|')
length_iter=len(valsplitted)
if length_iter > 0:
i=0
while i < length_iter:
newdict={}
for key, value in prova.items():
if isinstance(value, str):
valuesplitted = value.split('|')
try:
newdict[key]=valuesplitted[i]
except Exception:
newdict[key]=valuesplitted[0]
elif isinstance(value, int):
valuesplitted = value.split('|')
newdict[key]=valuesplitted[i]
elif isinstance(value, dict):
newdict[key]={}
for k, v in value.items():
if isinstance(v, str):
vsplitted = v.split('|')
try:
newdict[key][k]=float(vsplitted[i])
newdict[key][k]="unknown"
except Exception:
newdict[key][k]=vsplitted[i]
elif isinstance(v, int):
newdict[key][k]=v
elif isinstance(v, dict):
newdict[key][k]={}
for k1, v1 in v.items():
if isinstance(v1, str):
v1splitted = v1.split('|')
newdict[key][k][k1]=v1splitted[i]
array_of_newdicts.append(newdict)
i+=1
else:
array_of_newdicts.append(prova)
return(array_of_newdicts)
def num_rows_in_vcf_files():
total_lines = 0
for vcf_filename in glob.glob("files/vcf/files_to_read/*.vcf.gz"):
with gzip.open(vcf_filename, 'rt') as f:
total_lines += sum(1 for line in f if not line.startswith('#'))
return total_lines
num_rows = conf.num_rows
def generate(dict_properties):
total_dict =[]
total_dict2 =[]
dict_true={}
i=1
l=0
if conf.case_level_data == True:
try:
client.beacon.create_collection(name="caseLevelData")
except Exception:
pass
for vcf_filename in glob.glob("files/vcf/files_to_read/*.vcf.gz"):
print(vcf_filename)
vcf = VCF(vcf_filename, strict_gt=True)
formatted=False
for rec in vcf.header_iter():
d = rec.info()
try:
if d['ID'] == 'CSQ' and template == None:
format_annotation = d['Description']
format_list=format_annotation.split('|')
formatted=True
w=0
for entry in format_list:
if 'uploaded_allele' in entry.lower():
varianttype_num=w
elif 'symbol' in entry.lower():
gene_num=w
elif 'hgvsp' in entry.lower():
protein_num=w
elif 'consequence' in entry.lower():
moleculareffect_num=w
w+=1
except Exception:
continue
if conf.case_level_data == False:
vcf.set_samples([])
else:
my_target_list = vcf.samples
try:
client.beacon.create_collection(name="targets")
found_item=client.beacon.targets.find_one({"datasetId": conf.datasetId})
if found_item == None:
dict_target={}
dict_target["datasetId"]=conf.datasetId
dict_target["biosampleIds"]=my_target_list
target_list=[dict_target]
client.beacon.targets.insert_many(target_list)
except Exception:
dict_target={}
dict_target["datasetId"]=conf.datasetId
dict_target["biosampleIds"]=my_target_list
target_list=[dict_target]
client.beacon.targets.insert_many(target_list)
pbar = tqdm(total = num_rows)
for v in vcf:
dict_to_xls={}
if template != None:
varianttype=v.INFO.get(template["variantType"])
gene=v.INFO.get(template["geneId"])
aminoacidchange=v.INFO.get(template["aminoacidChange"])
moleculareffectt=v.INGO.get(template["molecularEffects"])
if "&" in moleculareffectt:
moleculareffects=moleculareffectt.split("&")
dict_to_xls['molecularAttributes|molecularEffects|id']=""
else:
moleculareffects=[moleculareffectt]
dict_to_xls['molecularAttributes|molecularEffects|id']=""
for moleculareffect in moleculareffects:
if dict_to_xls['molecularAttributes|molecularEffects|id']=="":
if moleculareffect == 'missense_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] = "ENSGLOSSARY:0000150"
dict_to_xls['molecularAttributes|molecularEffects|label'] = moleculareffect
elif moleculareffect == 'intron_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] = "ENSGLOSSARY:0000161"
dict_to_xls['molecularAttributes|molecularEffects|label'] = moleculareffect
elif moleculareffect == 'upstream_gene_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] = "SO:0001631"
dict_to_xls['molecularAttributes|molecularEffects|label'] = moleculareffect
elif moleculareffect == '5_prime_UTR_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] = "SO:0001623"
dict_to_xls['molecularAttributes|molecularEffects|label'] = moleculareffect
elif moleculareffect == 'synonymous_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] = "SO:0001819"
dict_to_xls['molecularAttributes|molecularEffects|label'] = moleculareffect
elif moleculareffect == 'downstream_gene_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] = "SO:0001632"
dict_to_xls['molecularAttributes|molecularEffects|label'] = moleculareffect
elif moleculareffect == 'non_coding_transcript_exon_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] = "SO:0001792"
dict_to_xls['molecularAttributes|molecularEffects|label'] = moleculareffect
elif moleculareffect == '5_prime_UTR_premature_start_codon_gain_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] = "SO:0001988"
dict_to_xls['molecularAttributes|molecularEffects|label'] = moleculareffect
elif moleculareffect == 'splice_region_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] = "SO:0001630"
dict_to_xls['molecularAttributes|molecularEffects|label'] = moleculareffect
elif moleculareffect == 'intergenic_region':
dict_to_xls['molecularAttributes|molecularEffects|id'] = "SO:0000605"
dict_to_xls['molecularAttributes|molecularEffects|label'] = moleculareffect
elif moleculareffect == 'splice_donor_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] = "SO:0001575"
dict_to_xls['molecularAttributes|molecularEffects|label'] = moleculareffect
elif moleculareffect == '3_prime_UTR_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] = "SO:0001624"
dict_to_xls['molecularAttributes|molecularEffects|label'] = moleculareffect
elif moleculareffect == 'splice_acceptor_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] = "SO:0001574"
dict_to_xls['molecularAttributes|molecularEffects|label'] = moleculareffect
elif moleculareffect == 'stop_retained_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] = "SO:0001567"
dict_to_xls['molecularAttributes|molecularEffects|label'] = moleculareffect
elif moleculareffect == 'coding_sequence_variant':
dict_to_xls['molecularAttributes|molecularEffects|id']="SO:0001580"
dict_to_xls['molecularAttributes|molecularEffects|label'] = moleculareffect
else:
if moleculareffect == 'missense_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] += "|"+ "ENSGLOSSARY:0000150"
dict_to_xls['molecularAttributes|molecularEffects|label'] += "|"+ moleculareffect
elif moleculareffect == 'intron_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] += "|"+ "ENSGLOSSARY:0000161"
dict_to_xls['molecularAttributes|molecularEffects|label'] += "|"+ moleculareffect
elif moleculareffect == 'upstream_gene_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] += "|"+ "SO:0001631"
dict_to_xls['molecularAttributes|molecularEffects|label'] += "|"+ moleculareffect
elif moleculareffect == '5_prime_UTR_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] += "|"+ "SO:0001623"
dict_to_xls['molecularAttributes|molecularEffects|label'] += "|"+ moleculareffect
elif moleculareffect == 'synonymous_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] += "|"+ "SO:0001819"
dict_to_xls['molecularAttributes|molecularEffects|label'] += "|"+ moleculareffect
elif moleculareffect == 'downstream_gene_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] += "|"+ "SO:0001632"
dict_to_xls['molecularAttributes|molecularEffects|label'] += "|"+ moleculareffect
elif moleculareffect == 'non_coding_transcript_exon_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] += "|"+ "SO:0001792"
dict_to_xls['molecularAttributes|molecularEffects|label'] += "|"+ moleculareffect
elif moleculareffect == '5_prime_UTR_premature_start_codon_gain_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] += "|"+ "SO:0001988"
dict_to_xls['molecularAttributes|molecularEffects|label'] += "|"+ moleculareffect
elif moleculareffect == 'splice_region_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] += "|"+ "SO:0001630"
dict_to_xls['molecularAttributes|molecularEffects|label'] += "|"+ moleculareffect
elif moleculareffect == 'intergenic_region':
dict_to_xls['molecularAttributes|molecularEffects|id'] += "|"+ "SO:0000605"
dict_to_xls['molecularAttributes|molecularEffects|label'] += "|"+ moleculareffect
elif moleculareffect == 'splice_donor_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] += "|"+ "SO:0001575"
dict_to_xls['molecularAttributes|molecularEffects|label'] += "|"+ moleculareffect
elif moleculareffect == '3_prime_UTR_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] += "|"+ "SO:0001624"
dict_to_xls['molecularAttributes|molecularEffects|label'] += "|"+ moleculareffect
elif moleculareffect == 'splice_acceptor_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] += "|"+ "SO:0001574"
dict_to_xls['molecularAttributes|molecularEffects|label'] += "|"+ moleculareffect
elif moleculareffect == 'stop_retained_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] += "|"+ "SO:0001567"
dict_to_xls['molecularAttributes|molecularEffects|label'] += "|"+ moleculareffect
elif moleculareffect == 'coding_sequence_variant':
dict_to_xls['molecularAttributes|molecularEffects|id']+= "|"+ "SO:0001580"
dict_to_xls['molecularAttributes|molecularEffects|label'] += "|"+ moleculareffect
if gene != '':
dict_to_xls['molecularAttributes|geneIds']=gene
if aminoacidchange!='':
dict_to_xls['molecularAttributes|aminoacidChanges']=aminoacidchange
elif formatted == True:
annotation_list=v.INFO.get('CSQ')
if annotation_list != None:
annotation_list=annotation_list.split('|')
#print(annotation_list)
#print(varianttype_num)
try:
varianttype=annotation_list[varianttype_num]
if '/' in varianttype:
if len(varianttype)> 3:
varianttype='INDEL'
else:
varianttype='SNP'
else:
varianttype='Structural Variant'
except Exception:
varianttype='UNKNOWN'
#print(varianttype)
gene=annotation_list[gene_num]
if gene != '':
dict_to_xls['molecularAttributes|geneIds']=gene
protein=annotation_list[protein_num]
#print(protein)
if protein != '':
protein=protein.split('p.')
aminoacidchange=protein[1]
dict_to_xls['molecularAttributes|aminoacidChanges']=aminoacidchange
moleculareffectt=annotation_list[moleculareffect_num]
if "&" in moleculareffectt:
moleculareffects=moleculareffectt.split("&")
dict_to_xls['molecularAttributes|molecularEffects|id']=""
else:
moleculareffects=[moleculareffectt]
dict_to_xls['molecularAttributes|molecularEffects|id']=""
for moleculareffect in moleculareffects:
if dict_to_xls['molecularAttributes|molecularEffects|id']=="":
if moleculareffect == 'missense_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] = "ENSGLOSSARY:0000150"
dict_to_xls['molecularAttributes|molecularEffects|label'] = moleculareffect
elif moleculareffect == 'intron_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] = "ENSGLOSSARY:0000161"
dict_to_xls['molecularAttributes|molecularEffects|label'] = moleculareffect
elif moleculareffect == 'upstream_gene_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] = "SO:0001631"
dict_to_xls['molecularAttributes|molecularEffects|label'] = moleculareffect
elif moleculareffect == '5_prime_UTR_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] = "SO:0001623"
dict_to_xls['molecularAttributes|molecularEffects|label'] = moleculareffect
elif moleculareffect == 'synonymous_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] = "SO:0001819"
dict_to_xls['molecularAttributes|molecularEffects|label'] = moleculareffect
elif moleculareffect == 'downstream_gene_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] = "SO:0001632"
dict_to_xls['molecularAttributes|molecularEffects|label'] = moleculareffect
elif moleculareffect == 'non_coding_transcript_exon_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] = "SO:0001792"
dict_to_xls['molecularAttributes|molecularEffects|label'] = moleculareffect
elif moleculareffect == '5_prime_UTR_premature_start_codon_gain_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] = "SO:0001988"
dict_to_xls['molecularAttributes|molecularEffects|label'] = moleculareffect
elif moleculareffect == 'splice_region_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] = "SO:0001630"
dict_to_xls['molecularAttributes|molecularEffects|label'] = moleculareffect
elif moleculareffect == 'intergenic_region':
dict_to_xls['molecularAttributes|molecularEffects|id'] = "SO:0000605"
dict_to_xls['molecularAttributes|molecularEffects|label'] = moleculareffect
elif moleculareffect == 'splice_donor_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] = "SO:0001575"
dict_to_xls['molecularAttributes|molecularEffects|label'] = moleculareffect
elif moleculareffect == '3_prime_UTR_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] = "SO:0001624"
dict_to_xls['molecularAttributes|molecularEffects|label'] = moleculareffect
elif moleculareffect == 'splice_acceptor_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] = "SO:0001574"
dict_to_xls['molecularAttributes|molecularEffects|label'] = moleculareffect
elif moleculareffect == 'stop_retained_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] = "SO:0001567"
dict_to_xls['molecularAttributes|molecularEffects|label'] = moleculareffect
elif moleculareffect == 'coding_sequence_variant':
dict_to_xls['molecularAttributes|molecularEffects|id']="SO:0001580"
dict_to_xls['molecularAttributes|molecularEffects|label'] = moleculareffect
else:
if moleculareffect == 'missense_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] += "|"+ "ENSGLOSSARY:0000150"
dict_to_xls['molecularAttributes|molecularEffects|label'] += "|"+ moleculareffect
elif moleculareffect == 'intron_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] += "|"+ "ENSGLOSSARY:0000161"
dict_to_xls['molecularAttributes|molecularEffects|label'] += "|"+ moleculareffect
elif moleculareffect == 'upstream_gene_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] += "|"+ "SO:0001631"
dict_to_xls['molecularAttributes|molecularEffects|label'] += "|"+ moleculareffect
elif moleculareffect == '5_prime_UTR_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] += "|"+ "SO:0001623"
dict_to_xls['molecularAttributes|molecularEffects|label'] += "|"+ moleculareffect
elif moleculareffect == 'synonymous_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] += "|"+ "SO:0001819"
dict_to_xls['molecularAttributes|molecularEffects|label'] += "|"+ moleculareffect
elif moleculareffect == 'downstream_gene_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] += "|"+ "SO:0001632"
dict_to_xls['molecularAttributes|molecularEffects|label'] += "|"+ moleculareffect
elif moleculareffect == 'non_coding_transcript_exon_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] += "|"+ "SO:0001792"
dict_to_xls['molecularAttributes|molecularEffects|label'] += "|"+ moleculareffect
elif moleculareffect == '5_prime_UTR_premature_start_codon_gain_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] += "|"+ "SO:0001988"
dict_to_xls['molecularAttributes|molecularEffects|label'] += "|"+ moleculareffect
elif moleculareffect == 'splice_region_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] += "|"+ "SO:0001630"
dict_to_xls['molecularAttributes|molecularEffects|label'] += "|"+ moleculareffect
elif moleculareffect == 'intergenic_region':
dict_to_xls['molecularAttributes|molecularEffects|id'] += "|"+ "SO:0000605"
dict_to_xls['molecularAttributes|molecularEffects|label'] += "|"+ moleculareffect
elif moleculareffect == 'splice_donor_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] += "|"+ "SO:0001575"
dict_to_xls['molecularAttributes|molecularEffects|label'] += "|"+ moleculareffect
elif moleculareffect == '3_prime_UTR_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] += "|"+ "SO:0001624"
dict_to_xls['molecularAttributes|molecularEffects|label'] += "|"+ moleculareffect
elif moleculareffect == 'splice_acceptor_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] += "|"+ "SO:0001574"
dict_to_xls['molecularAttributes|molecularEffects|label'] += "|"+ moleculareffect
elif moleculareffect == 'stop_retained_variant':
dict_to_xls['molecularAttributes|molecularEffects|id'] += "|"+ "SO:0001567"
dict_to_xls['molecularAttributes|molecularEffects|label'] += "|"+ moleculareffect
elif moleculareffect == 'coding_sequence_variant':
dict_to_xls['molecularAttributes|molecularEffects|id']+= "|"+ "SO:0001580"
dict_to_xls['molecularAttributes|molecularEffects|label'] += "|"+ moleculareffect
#print(dict_to_xls['molecularAttributes|molecularEffects|id'])
else:
formatted=False
else:
try:
varianttype=v.INFO.get('VT')
except Exception:
varianttype='UNKNOWN'
try:
if varianttype == 'SV': continue
except Exception:
pass
try:
num_of_populations=0
if pipeline is not None:
num_of_populations=pipeline["numberOfPopulations"]
source=pipeline["source"]
source_reference=pipeline["sourceReference"]
frequencies=[]
populations=pipeline["populations"]
if num_of_populations != 0:
for population in populations:
dict_per_population={}
allele_frequency=v.INFO.get(population["alleleFrequency"])
allele_count=v.INFO.get(population["alleleCount"])
allele_number=v.INFO.get(population["alleleNumber"])
ac_hom=v.INFO.get(population["alleleCountHomozygous"])
ac_het=v.INFO.get(population["alleleCountHeterozygous"])
if allele_frequency == None:
pass
if isinstance(allele_frequency, tuple):
allele_frequency=list(allele_frequency)
allele_frequency=allele_frequency[0]
else:
allele_frequency = float(allele_frequency)
if allele_frequency == 0.0:
i+=1
pbar.update(1)
continue
if allele_number == None:
pass
elif isinstance(allele_number, tuple):
allele_number=list(allele_number)
allele_number=allele_number[0]
else:
allele_number = int(allele_number)
if allele_count == None:
pass
elif isinstance(allele_count, tuple):
allele_count=list(allele_count)
allele_count=allele_count[0]
else:
allele_count = int(allele_count)
if allele_count == 0:
i+=1
pbar.update(1)
continue
if ac_hom == None:
pass
elif isinstance(ac_hom, tuple):
ac_hom=list(ac_hom)
ac_hom=ac_hom[0]
else:
ac_hom = int(ac_hom)
if ac_het == None:
pass
elif isinstance(ac_het, tuple):
ac_het=list(ac_het)
ac_het=ac_het[0]
else:
ac_het = int(ac_het)
if allele_frequency != 0 or allele_frequency != None:
if allele_count != 0 or allele_count != None:
if ac_hom == None and ac_het != None and allele_count != None:
ac_hom = allele_count - ac_het
elif ac_het == None and ac_hom != None and allele_count != None:
ac_het = allele_count - ac_hom
popu=population["population"]
if allele_frequency != 0 or allele_frequency != None:
dict_per_population["alleleFrequency"]=allele_frequency
if allele_count != None and allele_count != 0:
dict_per_population["alleleCount"]=allele_count
dict_per_population["alleleCountHomozygous"]=ac_hom
dict_per_population["alleleCountHeterozygous"]=ac_het
if allele_number != None and allele_number != 0:
dict_per_population["alleleNumber"]=allele_number
dict_per_population["population"]=popu
if dict_per_population != {} and allele_frequency !=None:
frequencies.append(dict_per_population)
else:
allele_frequency=v.INFO.get('AF')
if allele_frequency == None:
pass
if isinstance(allele_frequency, tuple):
allele_frequency=list(allele_frequency)
allele_frequency=allele_frequency[0]
else:
allele_frequency = float(allele_frequency)
if allele_frequency == 0.0:
i+=1
pbar.update(1)
continue
allele_number=v.INFO.get('AN')
if allele_number == None:
pass
elif isinstance(allele_number, tuple):
allele_number=list(allele_number)
allele_number=allele_number[0]
else:
allele_number = float(allele_number)
allele_count=v.INFO.get('AC')
if allele_count == None:
pass
elif isinstance(allele_count, tuple):
allele_count=list(allele_count)
allele_count=allele_count[0]
else:
allele_count = float(allele_count)
if allele_count == 0.0:
i+=1
pbar.update(1)
continue
ac_hom=v.INFO.get('AC_Hom')
if ac_hom == None:
pass
elif isinstance(ac_hom, tuple):
ac_hom=list(ac_hom)
ac_hom=ac_hom[0]
else:
ac_hom = float(v.INFO.get('AC_Hom'))
ac_het=v.INFO.get('AC_Het')
if ac_het == None:
pass
elif isinstance(ac_het, tuple):
ac_het=list(ac_het)
ac_het=ac_het[0]
else:
ac_het = float(v.INFO.get('AC_Het'))
if allele_frequency is not None:
dict_to_xls['frequencyInPopulations|sourceReference']=pipeline["frequencyInPopulations|sourceReference"]
dict_to_xls['frequencyInPopulations|source']=pipeline["frequencyInPopulations|source"]
dict_to_xls['frequencyInPopulations|frequencies|population']="Total"
dict_to_xls['frequencyInPopulations|frequencies|alleleFrequency']=allele_frequency
if allele_frequency != 0 or allele_frequency != None:
dict_per_population["alleleFrequency"]=allele_frequency
if allele_count != None and allele_count != 0:
dict_per_population["alleleCount"]=allele_count
dict_per_population["alleleCountHomozygous"]=ac_hom
dict_per_population["alleleCountHeterozygous"]=ac_het
if allele_number != None and allele_number != 0:
dict_per_population["alleleNumber"]=allele_number
dict_per_population["population"]=popu
if dict_per_population != {} and allele_frequency !=None:
frequencies.append(dict_per_population)
num_of_populations=1
except Exception as e:
pass
#print(allele_frequency)
#print(v)
try:
ref=v.REF
chrom=v.CHROM
start=v.start
end=v.end
alt=v.ALT
except Exception:
chrom=v.CHROM
start=v.start
ref=v.REF
end=v.INFO.get('END')
alt=v.ALT
if alt != [] and '<' and '>' in alt[0]:
continue
elif alt == []:
alt=['N']
dict_to_xls['variation|alternateBases'] = alt[0]
dict_to_xls['variation|referenceBases'] = ref
try:
dict_to_xls['variation|variantType'] = varianttype
if varianttype is None:
if len(alt[0]) == len(ref):
dict_to_xls['variation|variantType']='SNP'
else:
dict_to_xls['variation|variantType']='INDEL'
except Exception:
dict_to_xls['variation|variantType']='UNKNOWN'
chromos=re.sub(r"</?\[>", "", chrom)
chromos=chromos.replace("chr","")
if 'X' in chrom:
chromos = '23'
elif 'Y' in chrom:
chromos = '24'
if conf.reference_genome == 'GRCh37':
HGVSId='NC_0000'+str(chromos) + '.10' + ':' + 'g.' + str(start) + ref + '>' + alt[0]
dict_to_xls['identifiers|genomicHGVSId'] = HGVSId
elif conf.reference_genome == 'GRCh38':
HGVSId='NC_0000'+str(chromos) + '.11' + ':' + 'g.' + str(start) + ref + '>' + alt[0]
dict_to_xls['identifiers|genomicHGVSId'] = HGVSId
elif conf.reference_genome == 'NCBI36':
HGVSId='NC_0000'+str(chromos) + '.9' + ':' + 'g.' + str(start) + ref + '>' + alt[0]
dict_to_xls['identifiers|genomicHGVSId'] = HGVSId
dict_to_xls['variation|location|interval|start|value'] = int(start)
dict_to_xls['variation|location|interval|start|type']="Number"
dict_to_xls['variation|location|interval|end|value'] = int(end)
dict_to_xls['variation|location|interval|end|type']="Number"
dict_to_xls['variation|location|interval|start|value'] = int(start)
dict_to_xls['variation|location|interval|start|type']="Number"
dict_to_xls['variation|location|interval|end|value'] = int(end)
dict_to_xls['variation|location|interval|end|type']="Number"
dict_to_xls['variation|location|interval|type']="SequenceInterval"
dict_to_xls['variation|location|type']="SequenceLocation"
dict_to_xls['variation|location|sequence_id']="HGVSid:" + str(chrom) + ":g." + str(start) + ref + ">" + alt[0]
dict_to_xls['variantInternalId'] = str(uuid.uuid1())+':' + str(ref) + ':' + str(alt[0])
if conf.case_level_data == True:
if conf.zygosity == False:
j=0
dict_trues={"id": HGVSId, "datasetId": conf.datasetId}
for zygo in v.gt_types:
if zygo==True:
dict_trues[str(j)]="y"
j+=1
else:
j+=1
elif conf.zygosity == True:
j=0
dict_trues={"id": HGVSId, "datasetId": conf.datasetId}
for zygo in v.genotypes:
if zygo[0] == 1 and zygo[1]== 1:
dict_trues[str(j)]="11"
j+=1
elif zygo[0] == 1 and zygo[1]== 0:
dict_trues[str(j)]="10"
j+=1
elif zygo[0] == 0 and zygo[1]== 1:
dict_trues[str(j)]="01"
j+=1
#dict_to_xls['caseLevelData|biosampleId'] = 'hola'
#biosampleids=",".join(biosampleids)
#if dict_to_xls['caseLevelData|biosampleId'] == '':
#continue
k=0
dict_of_properties={}
for kline, vline in dict_to_xls.items():
property_value = kline
valor = vline
if valor:
dict_of_properties[property_value]=valor
elif valor == 0:
dict_of_properties[property_value]=valor
#print(dict_properties)
#print(dict_of_properties)
definitivedict={}
for key, value in dict_properties.items():
if isinstance(value, list):
value_list=[]
item_dict={}
for item in value:
outcome = 0
if isinstance(item, dict):
for ki, vi in item.items():
if isinstance(vi, list):
vi_list=[]
subitem_dict={}
for subitem in vi:
if isinstance(subitem, dict):
for k, v in subitem.items():
if isinstance(v, list):
listitemv=[]
vivdict={}
for itemv in v:
if isinstance(itemv, dict):
#print('ki is {}'.format(ki))
#print('k is {}'.format(k))
#print(itemv)
for kiv, viv in itemv.items():
if isinstance(viv, list):
for itemviv in viv:
if isinstance(itemviv, dict):
for kivi, vivi in itemviv.items():
new_item = ""
new_item = key + "|" + ki + "|" + k + "|" + kiv + "|" + kivi
for propk, propv in dict_of_properties.items():
if propk == new_item:
try:
if 'value' in propk:
vivdict[kiv][kivi]=int(propv)
else:
vivdict[kiv][kivi]=propv
except Exception:
vivdict[kiv]={}
vivdict[kiv][kivi]=propv
elif propk == key + "|" + ki + "|" + k + "|" + kiv:
vivdict[kiv]=propv
else:
new_item = ""
new_item = key + "|" + ki + "|" + k + "|" + kiv
for propk, propv in dict_of_properties.items():
if propk == new_item:
#print(propk)
vivdict[kiv]=propv
if vivdict != {}:
#print(vivdict)
subitem_dict[k]=vivdict
if isinstance(v, dict):
for k1, v1 in v.items():
new_item = ""
new_item = key + "|" + ki + "|" + k + "|" + k1
for propk, propv in dict_of_properties.items():
if propk == new_item:
try:
subitem_dict[k][k1]=propv
except Exception:
subitem_dict[k]={}
subitem_dict[k][k1]=propv
else:
new_item = ""
new_item = key + "|" + ki + "|" + k
for propk, propv in dict_of_properties.items():
if propk == new_item:
try:
if ki == 'clinicalInterpretations':
pass
else:
propv = re.sub(r'\s', '', propv)
respropv = json.loads(propv)
subitem_dict[k]=respropv
except Exception:
subitem_dict[k]=propv
if subitem_dict != {}:
if subitem_dict not in vi_list and subitem_dict != {}:
vi_list.append(subitem_dict)
if ki == 'clinicalInterpretations':
for itemvl in vi_list:
list_to_def=commas(itemvl)
for itemldf in list_to_def:
try:
if itemldf not in item_dict[ki]:
item_dict[ki].append(itemldf)
except Exception:
item_dict[ki]=[]
item_dict[ki].append(itemldf)
elif ki == 'frequencies':
item_dict[ki]=vi_list
else:
item_dict[ki]=vi_list[0]
elif isinstance(vi, dict):
vi_dict={}
for ki1, vi1 in vi.items():
new_item = ""
new_item = key + "|" + ki + "|" + ki1
for propk, propv in dict_of_properties.items():
if propk == new_item:
vi_dict[ki1]=propv
item_dict[ki]=vi_dict
if vi_dict=={}:
del vi_dict
else:
new_item = ""
new_item = key + "|" + ki
for propk, propv in dict_of_properties.items():
if propk == new_item:
if '|' in propv:
outcome +=1
v1_keys=[]
item_dict[ki]=propv
if item_dict != {} and item_dict != [{}]:
if outcome > 0:
if item_dict not in value_list:
value_list.append(item_dict)
if value_list != []:
itemdict={}
definitivedict[key]=[]
v_array=[]
for itemvl in value_list:
for kvl, vvl in itemvl.items():
if isinstance(vvl, str):
if '|' in vvl:
itemv={}
v_array = vvl.split('|')
itemv[kvl]=v_array
v_key = kvl
elif isinstance(vvl, dict):
v1_array=[]
itemdict[kvl]={}
v1_keys = []
for kvl1, vvl1 in vvl.items():
itemdict[kvl][kvl1]={}
if isinstance(vvl1, str) and '|' in vvl1:
vvl1_array = vvl1.split('|')
for vvlitem in vvl1_array:
v1_array.append(vvlitem)
v1_bigkeys = kvl
if kvl1 not in v1_keys:
v1_keys.append(kvl1)
if v1_keys != []:
n=0
list_to_def=[]
half_array_number = len(v1_array)/2
itemdict[v1_bigkeys]={}
while n < int(half_array_number):
newdict={}
newdict[v1_bigkeys]={}
num=int(half_array_number+n)
#print(v_array)
#print(v1_array)
newdict[v_key]=v_array[n]
newdict[v1_bigkeys][v1_keys[0]]=v1_array[n]
newdict[v1_bigkeys][v1_keys[1]]=v1_array[num]
list_to_def.append(newdict)
n +=1
for itemldf in list_to_def:
definitivedict[key].append(itemldf)
elif len(v_array) > 1:
list_to_def=[]
for itva in v_array:
newdict={}
newdict[v_key]=itva
list_to_def.append(newdict)
for itemldf in list_to_def:
definitivedict[key].append(itemldf)
else:
for itemvl in value_list:
definitivedict[key].append(itemvl)
else:
if key == 'caseLevelData' or key=='frequencyInPopulations':
definitivedict[key]=[]
definitivedict[key].append(item_dict)
else:
definitivedict[key]=item_dict
elif isinstance(value, dict):
value_dict={}
for kd, vd in value.items():
if isinstance(vd, list):
vd_list=[]
value_dict[kd]={}
for itemvd in vd:
if isinstance(itemvd, dict):
dict_mol={}
list_mol=[]
for kd1, vd1 in itemvd.items():
new_item = ""
new_item = key + "|" + kd + "|" + kd1
for propk, propv in dict_of_properties.items():
if propk == new_item:
if '|' in propv:
propv_splitted = propv.split('|')
propv_splitted=list(dict.fromkeys(propv_splitted))
t=0
while t < len(propv_splitted):
dict_mol={}
try:
dict_mol[kd1]=propv_splitted[t]
except Exception:
dict_mol[kd1]=propv_splitted[t]
t+=1
list_mol.append(dict_mol)
t=0
u=0
if kd1 == 'label':
try:
if len(list_mol) == 2:
dict_mol_2={}
dict_mol_2['id']=list_mol[t]['id']
dict_mol_2['label']=list_mol[t+1]['label']
try:
value_dict[kd].append(dict_mol_2)
except Exception:
value_dict[kd]=[]
value_dict[kd].append(dict_mol_2)
except Exception:
pass
else:
try:
while u < len(list_mol):
dict_mol_2={}
dict_mol_2['id']=list_mol[t]['id']
indice = int(len(list_mol)/2)
dict_mol_2['label']=list_mol[t+indice]['label']
try:
value_dict[kd].append(dict_mol_2)
except Exception:
value_dict[kd]=[]
value_dict[kd].append(dict_mol_2)
t+=1
u+=2
except Exception:
pass
if value_dict not in vd_list:
vd_list.append(value_dict)
else:
if value_dict == {}:
value_dict[kd]={}
if 'molecularEffects' in kd:
try:
dict_mol[kd1]=propv
value_dict[kd].append(dict_mol)
except Exception:
dict_mol[kd1]=propv
value_dict[kd]=[]
else:
value_dict[kd][kd1]=propv
#print(list_mol)
else:
new_item = ""
new_item = key + "|" + kd
for propk, propv in dict_of_properties.items():
if propk == new_item:
value_dict[kd]=[]
value_dict[kd].append(propv)
value_dict = {ka:va for ka,va in value_dict.items() if va != {}}
if value_dict != {}:
definitivedict[key]=value_dict
else:
new_item = ""
new_item = key + "|" + kd
for propk, propv in dict_of_properties.items():
if propk == new_item:
value_dict[kd]=propv
definitivedict[key]=value_dict