Merge pull request #677 from uclahs-cds/czhu-fix-filter-fasta

fix (filterFasta): noncoding peptide ID updated

moPepGen/aa/VariantPeptideLabel.py

@@ -258,6 +258,8 @@ def get_transcript_ids(self) -> List[str]:
             return [variant_id.first_tx_id, variant_id.second_tx_id]
         if isinstance(variant_id, pi.BaseVariantPeptideIdentifier):
             return [variant_id.transcript_id]
+        if isinstance(variant_id, pi.NoncodingPeptideIdentifier):
+            return [variant_id.transcript_id]
         raise ValueError('Variant ID unrecognized')
 
     def __str__(self) -> str:

test/files/peptides/noncoding.fasta

@@ -1,34 +1,34 @@
->ENST00000624155.2|16
-KEESPVVSWRLEPEDGTAL
->ENST00000624155.2|4
-AAGAVFLALSAQLLQARLMK
->ENST00000624155.2|3
+>ENST00000624155.2|ENSG00000279973.2|ORF2|5
+MKEESPVVSWRLEPEDGTAL
+>ENST00000624155.2|ENSG00000279973.2|ORF4|2
+METAAQQEQ
+>ENST00000624155.2|ENSG00000279973.2|ORF1|4
 MAAGAVFLALSAQLLQARLMK
->ENST00000624155.2|10
+>ENST00000624155.2|ENSG00000279973.2|ORF1|2
+LMKEESPVVSWR
+>ENST00000624155.2|ENSG00000279973.2|ORF4|1
 ETAAQQEQ
->ENST00000624155.2|1
-MAAGAVFLALSAQLLQAR
->ENST00000624155.2|22
-EESPVVSWR
->ENST00000624155.2|23
-EESPVVSWRLEPEDGTAL
->ENST00000624155.2|21
+>ENST00000624155.2|ENSG00000279973.2|ORF1|1
 LMKEESPVVSWRLEPEDGTAL
->ENST00000624155.2|14
+>ENST00000624155.2|ENSG00000279973.2|ORF2|6
 KEESPVVSWR
->ENST00000624155.2|7
-MAQLCDSSSAVVAATVMETAAQQEQ
->ENST00000624155.2|13
+>ENST00000624155.2|ENSG00000279973.2|ORF2|1
+LEPEDGTAL
+>ENST00000624155.2|ENSG00000279973.2|ORF2|3
+EESPVVSWR
+>ENST00000624155.2|ENSG00000279973.2|ORF2|4
+KEESPVVSWRLEPEDGTAL
+>ENST00000624155.2|ENSG00000279973.2|ORF2|7
 MKEESPVVSWR
->ENST00000624155.2|9
-METAAQQEQ
->ENST00000624155.2|8
-AQLCDSSSAVVAATVMETAAQQEQ
->ENST00000624155.2|20
-LMKEESPVVSWR
->ENST00000624155.2|15
-MKEESPVVSWRLEPEDGTAL
->ENST00000624155.2|2
+>ENST00000624155.2|ENSG00000279973.2|ORF1|3
+AAGAVFLALSAQLLQARLMK
+>ENST00000624155.2|ENSG00000279973.2|ORF1|5
 AAGAVFLALSAQLLQAR
->ENST00000624155.2|24
-LEPEDGTAL
+>ENST00000624155.2|ENSG00000279973.2|ORF1|6
+MAAGAVFLALSAQLLQAR
+>ENST00000624155.2|ENSG00000279973.2|ORF2|2
+EESPVVSWRLEPEDGTAL
+>ENST00000624155.2|ENSG00000279973.2|ORF3|2
+MAQLCDSSSAVVAATVMETAAQQEQ
+>ENST00000624155.2|ENSG00000279973.2|ORF3|1
+AQLCDSSSAVVAATVMETAAQQEQ