Jfw polya

VariantValidator/modules/utils.py

@@ -485,7 +485,7 @@ def pro_delins_info(prot_ref_seq, prot_var_seq, in_frame=False):
             return info
 
 
-def translate(ed_seq, cds_start, modified_aa=None, tolerate_no_stop_cds=False, polyadenylate=False):
+def translate(ed_seq, cds_start, modified_aa=None, tolerate_no_stop_cds=False):
     """
     Translate c. reference sequences, including those that have been modified
     must have the CDS in the specified position
@@ -512,10 +512,6 @@ def translate(ed_seq, cds_start, modified_aa=None, tolerate_no_stop_cds=False, p
         use_dict = PROT_TRANSLATION_DICT
         stops = ['TAA', 'TAG', 'TGA']
 
-    # Add Polyadenylation stop codon completing bases to relevant transcripts
-    if polyadenylate is True:
-        coding_sequence = f"{coding_sequence}A"
-
     # Translate
     if len(coding_sequence) % 3:
         last_codon_end = int(len(coding_sequence)/3) * 3
@@ -529,7 +525,13 @@ def translate(ed_seq, cds_start, modified_aa=None, tolerate_no_stop_cds=False, p
             break
     if translation[-1] != '*':
         if not tolerate_no_stop_cds:
-            raise IndexError('No stop CDS')
+            # Add Polyadenylation stop codon completing bases to relevant
+            # transcripts
+            spare_end = len(coding_sequence) % 3
+            if spare_end and coding_sequence[-spare_end:] in ['T','TA']:
+                translation.append('*')
+            else:
+                raise IndexError('No stop CDS')
         translation.append('X')
 
     return "".join(translation)

VariantValidator/modules/vvMixinInit.py

@@ -15,7 +15,6 @@
 import vvhgvs.normalizer
 from vvhgvs.location import AAPosition, Interval
 from vvhgvs.edit import AARefAlt, AAExt, Dup
-from vvhgvs.utils import unusual_transcripts
 from Bio.Seq import Seq
 
 import re
@@ -460,23 +459,16 @@ def _remake_unc(prot,nucleotide_not_equal=False):
         else:
             modified_aa = None
 
-        # Add Polyadenylation stop codon completing bases to relevant transcripts
-        require_A = unusual_transcripts.polyadnylate()
-        if hgvs_transcript.ac in require_A:
-            polyadenylate = True
-        else:
-            polyadenylate = False
-
         # Translate the reference and variant proteins
         try:
-            prot_ref_seq = utils.translate(ref_seq, cds_start, modified_aa, polyadenylate=polyadenylate)
+            prot_ref_seq = utils.translate(ref_seq, cds_start, modified_aa)
         except IndexError:
             import traceback
             traceback.print_exc()
             hgvs_transcript_to_hgvs_protein['error'] = \
                 'ProteinTranslationError: Cannot generate a protein without an identifiable in-' +\
                 'frame Termination codon in the reference mRNA sequence, this transcript may be ' +\
-                'subject to non-sense mediated decay'
+                'subject to non-stop mediated decay'
             hgvs_transcript_to_hgvs_protein['hgvs_protein'] = _tot_unc(associated_protein_accession)
             return hgvs_transcript_to_hgvs_protein
         except KeyError:
@@ -491,12 +483,12 @@ def _remake_unc(prot,nucleotide_not_equal=False):
 
 
         try:
-            prot_var_seq = utils.translate(var_seq, cds_start, modified_aa, polyadenylate=polyadenylate)
+            prot_var_seq = utils.translate(var_seq, cds_start, modified_aa)
         except IndexError:
             hgvs_transcript_to_hgvs_protein['error'] = \
                 'ProteinTranslationError: Cannot generate a protein without an identifiable in-' +\
                 'frame Termination codon in the variant mRNA sequence, this transcript may be ' +\
-                'subject to nonstop decay'
+                'subject to non-stop decay'
             hgvs_protein = _tot_unc(associated_protein_accession)
             hgvs_transcript_to_hgvs_protein['hgvs_protein'] = hgvs_protein
             return hgvs_transcript_to_hgvs_protein

batch/.gitignore

@@ -0,0 +1,4 @@
+# Ignore all files and subdirectories
+*
+# But make an exception for just this .gitignore file
+!.gitignore