allowing non AF vcf

EGA-archive · Nov 8, 2024 · 162a1bc · 162a1bc
1 parent bd2ce68
commit 162a1bc
Showing 1 changed file with 26 additions and 24 deletions.
diff --git a/genomicVariations_vcf.py b/genomicVariations_vcf.py
@@ -138,9 +138,7 @@ def generate(dict_properties):
             try:
                 allele_frequency=v.INFO.get('AF')
                 if allele_frequency == None:
-                    i+=1
-                    pbar.update(1)
-                    continue
+                    pass
                 if isinstance(allele_frequency, tuple):
                     allele_frequency=list(allele_frequency)
                     allele_frequency=allele_frequency[0]
@@ -152,48 +150,48 @@ def generate(dict_properties):
                     continue
                 allele_number=v.INFO.get('AN')
                 if allele_number == None:
-                    i+=1
-                    continue
+                    pass
                 elif isinstance(allele_number, tuple):
                     allele_number=list(allele_number)
                     allele_number[0]
                 else:
                     allele_number = float(allele_number)
                 allele_count=v.INFO.get('AC')
                 if allele_count == None:
-                    i+=1
-                    pbar.update(1)
-                    continue
+                    pass
                 elif isinstance(allele_count, tuple):
                     allele_count=list(allele_count)
-                    allele_count[0]
+                    allele_count=allele_count[0]
                 else:
                     allele_count = float(allele_count)
-                ac_hom=v.INFO.get('AC_Hom')
-                if ac_hom == None:
+                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[0]
+                    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:
-                    i+=1
-                    continue
+                    pass
                 elif isinstance(ac_het, tuple):
                     ac_het=list(ac_het)
-                    ac_het[0]
+                    ac_het=ac_het[0]
                 else:
                     ac_het = float(v.INFO.get('AC_Het'))
-                dict_to_xls['frequencyInPopulations|sourceReference']=pipeline["frequencyInPopulations|sourceReference"]
-                dict_to_xls['frequencyInPopulations|source']=pipeline["frequencyInPopulations|source"]
-                dict_to_xls['frequencyInPopulations|frequencies|population']=conf.datasetId
-                dict_to_xls['frequencyInPopulations|frequencies|alleleFrequency']=allele_frequency
+                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']=conf.datasetId
+                    dict_to_xls['frequencyInPopulations|frequencies|alleleFrequency']=allele_frequency
             except Exception as e:
-                continue
+                pass
             #print(allele_frequency)
 
             #print(v)
@@ -614,10 +612,14 @@ def generate(dict_properties):
             GenomicVariations(**definitivedict)
             definitivedict["datasetId"]=conf.datasetId
             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
+                if allele_count:
+                    definitivedict["frequencyInPopulations"][0]["frequencies"][0]["alleleCount"]=allele_count
+                if allele_number:
+                    definitivedict["frequencyInPopulations"][0]["frequencies"][0]["alleleNumber"]=allele_number
+                if ac_hom:
+                    definitivedict["frequencyInPopulations"][0]["frequencies"][0]["alleleCountHomozygous"]=ac_hom
+                if ac_het:
+                    definitivedict["frequencyInPopulations"][0]["frequencies"][0]["alleleCountHeterozygous"]=ac_het
             except Exception:
                 pass
             total_dict.append(definitivedict)