summarizeFasta not cannot find variant

[lydiayliu]

This is my attempt to run CPCG with parser entry instead of GVF entry (too lazy to reparse alllllll the files manually with 0.11.1). Interesting error that we've never seen lol.

    Command output:
      [ 2023-02-01 07:25:34 ] moPepGen summarizeFasta started
      [ 2023-02-01 07:27:15 ] Reference indices loaded.
    
    Command error:
      [ 2023-02-01 07:25:34 ] moPepGen summarizeFasta started
      [ 2023-02-01 07:27:15 ] Reference indices loaded.
      Traceback (most recent call last):
        File "/usr/local/lib/python3.8/site-packages/moPepGen/aa/VariantPeptideLabel.py", line 323, in get_source
          return self.data[gene_id][var_id]
      KeyError: 'ENSG00000231764.10'
      
      The above exception was the direct cause of the following exception:
      
      Traceback (most recent call last):
        File "/usr/local/bin/moPepGen", line 8, in <module>
          sys.exit(main())
        File "/usr/local/lib/python3.8/site-packages/moPepGen/cli/__main__.py", line 89, in main
          args.func(args)
        File "/usr/local/lib/python3.8/site-packages/moPepGen/cli/summarize_fasta.py", line 123, in summarize_fasta
          summarizer.count_peptide_source(anno, args.cleavage_rule)
        File "/usr/local/lib/python3.8/site-packages/moPepGen/aa/PeptidePoolSummarizer.py", line 194, in count_peptide_source
          self.summary_table.add_entry(seq, self.label_map, anno, enzyme)
        File "/usr/local/lib/python3.8/site-packages/moPepGen/aa/PeptidePoolSummarizer.py", line 86, in add_entry
          peptide_labels = VariantPeptideInfo.from_variant_peptide(
        File "/usr/local/lib/python3.8/site-packages/moPepGen/aa/VariantPeptideLabel.py", line 191, in from_variant_peptide
          source = label_map.get_source(gene_id, var_id)
        File "/usr/local/lib/python3.8/site-packages/moPepGen/aa/VariantPeptideLabel.py", line 325, in get_source
          raise err.VariantSourceNotFoundError(gene_id, var_id) from e
      moPepGen.err.VariantSourceNotFoundError: Variant source not found transcript [ENSG00000231764.10] variant [ENSG00000231764.10]. Please verify all GVF files are imported
    
    Work dir:
      work/6a/4493b9fdd44f3a349d40c4f97535da
    
    Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

I actually think this is because the FASTA header of callNoncoding has changed??? When I ran the first 10 samples without the noncoding_peptides.fasta it was perfectly fine.

[lydiayliu]

I reran this with a working directory on /hot/, and here it is
/hot/project/method/AlgorithmDevelopment/ALGO-000074-moPepGen/CPCGENE/processed/noncanonical-database/call-nonCanonicalPeptide/work_pipe/eb/809f9aab0542e1201f86114b5720ab

Still same issue!

[zhuchcn]

I believe this is because the sequence fasta header for noncoding peptides got updated in the last PR so the gene ID is now part of it. And the gene ID is somehow treated as a variant label mistakenly.