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EGA-archive · Oct 17, 2024 · d9028cd · d9028cd
1 parent b63f534
commit d9028cd
Showing 1 changed file with 3 additions and 5 deletions.
diff --git a/genomicVariations_vcf.py b/genomicVariations_vcf.py
@@ -97,15 +97,13 @@ def generate(dict_properties):
         print(vcf_filename)
         vcf = VCF(vcf_filename)
         vcf.set_samples([])
-        vcf.set_index(index_path="files/vcf/files_to_read/pop11_sub2_chr1.vcf.bgz.tbi")
+
         #my_target_list = vcf.samples
         count=0
 
 
         pbar = tqdm(total = num_rows)
 
-        r=0
-
         for v in vcf:
             #print(v)
 
@@ -813,8 +811,8 @@ def generate(dict_properties):
             try:
                 definitivedict["frequencyInPopulations"][0]["frequencies"][0]["alleleCount"]=allele_count
                 definitivedict["frequencyInPopulations"][0]["frequencies"][0]["alleleNumber"]=allele_number
-                #definitivedict["frequencyInPopulations"][0]["frequencies"][0]["alleleCountHomozygous"]=ac_hom
-                #definitivedict["frequencyInPopulations"][0]["frequencies"][0]["alleleCountHeterozygous"]=ac_het
+                definitivedict["frequencyInPopulations"][0]["frequencies"][0]["alleleCountHomozygous"]=ac_hom
+                definitivedict["frequencyInPopulations"][0]["frequencies"][0]["alleleCountHeterozygous"]=ac_het
             except Exception:
                 pass
             total_dict.append(definitivedict)