Removed unnecessary flags. Added check for translation beyond utr. Mo…

…ved proximal variants to flags column.

bin/epitopes.py

@@ -19,11 +19,10 @@ def create_epitope_varcode(chrm, start, ref, alt, db, mut_dna, mut_aa, transcrip
         errors += ' Could not infer the effect.'
     else:
         # Retrieve effect type
-        protein_mut = effect.short_description
+        protein_mut = effect.short_description 
         if protein_mut is None:
             errors += ' Could not retrieve AA mutation.'
         elif not protein_mut.startswith('p.'):
-            errors += ' Computed with dictionary method.'
             errors += ' Invalid mutation {}.'.format(protein_mut)
             aa_pos = int(re.findall(r'\d+', mut_aa)[0]) if mut_aa != '' else 0
             cDNA_pos = int(re.findall(r'\d+', mut_dna)[0]) if mut_dna != '' else 0
@@ -63,7 +62,6 @@ def create_epitope_varcode(chrm, start, ref, alt, db, mut_dna, mut_aa, transcrip
                 if effect.mutant_protein_sequence is None or effect.original_protein_sequence is None:
                     errors += ' Could not retrieve protein sequence.'
                 else:
-                    errors += ' Computed with varcode method.'
                     # Type of effect
                     effect_type = type(effect).__name__
                     if 'StopLoss' in effect_type:

bin/variant_effect.py

@@ -11,7 +11,6 @@
 def translate_dna(seq):
     return translate(seq, to_stop=True)
 
-
 def missense_variant(starts, ends, wt_mer, mut_mer, errors, mut_dna, mut_aa, transcript, cDNA_pos, aa_pos, cDNA_dict, AA_dict):
     if 'delins' in mut_dna:
         return errors, wt_mer, mut_mer
@@ -70,9 +69,9 @@ def frameshift_variant(ref, starts, ends, wt_mer, mut_mer, errors, mut_dna, mut_
     wt_mer = [protein_seq[x:y] for x, y in zip(start, end)]
     if 'del' in mut_dna:
         fs = len(ref)
-        mut_cDNA = cDNA_seq[:cDNA_pos - 1] + cDNA_seq[cDNA_pos + fs - 1:]
-        mut_fasta = str(translate_dna(mut_cDNA.replace(' ', '')))
-        mut_mer = [mut_fasta[x:] for x in start]
+        mut_fasta = cDNA_seq[:cDNA_pos - 1] + cDNA_seq[cDNA_pos + fs - 1:]
+        mut_protein = str(translate_dna(mut_fasta.replace(' ', '')))
+        mut_mer = [mut_protein[x:] for x in start]
     elif 'dup' in mut_dna:
         dup_pos = [None, None]
         dup_pos = list(map(int, re.findall(r'\d+', mut_dna))) if mut_dna != '' else 0
@@ -84,6 +83,11 @@ def frameshift_variant(ref, starts, ends, wt_mer, mut_mer, errors, mut_dna, mut_
         mut_fasta = cDNA_seq[:cDNA_pos] + ins_seq + cDNA_seq[cDNA_pos:]
         mut_protein = translate_dna(mut_fasta)
         mut_mer = [mut_protein[x:y] for x, y in zip(start, end)]
+
+    cds_utr_protein = translate(mut_fasta)
+    if "*" in cds_utr_protein and cds_utr_protein[-1] != "*":
+        errors += " Translation goes beyond the 3'-UTR."
+
     return errors, wt_mer, mut_mer
 
 

bin/variants.py

@@ -51,7 +51,7 @@ def proximal_variants(vcf, chromosome, start, end, alt, flanking_bases):
         if entry.start == start and entry.stop == end and entry.alts[0] == alt:
             continue
         else:
-            proximal_variants += f"{entry.chrom}:{entry.pos}-{entry.ref}>{entry.alts[0]}. "
+            proximal_variants += f" {entry.chrom}:{entry.pos}-{entry.ref}>{entry.alts[0]}. "
     return proximal_variants
 
 
@@ -372,6 +372,7 @@ def filter_variants_dna(file, normal_coverage, tumor_coverage, tumor_var_depth,
                 variant.num_callers = len(filtered)
                 variant.status = pass_snp >= num_callers or pass_indel >= num_callers_indel
                 variant.epitopes = variant_epitopes
+                variant.epitopes.flags = proximal_vars
                 variant.dbsnp = avsnp150
                 variant.gnomad = gnomad_AF
                 variant.cosmic = cosmic70