'X' is not a valid unambiguous letter for protein

[lydiayliu]

I feel like we've seen this error before but I can't believe I'm seeing it again under this circumstance lol

I am trying to use the new lysN enzyme to call noncoding peptides

moPepGen callNoncoding \
    --genome-fasta /hot/project/method/AlgorithmDevelopment/ALGO-000074-moPepGen/ref/GRCh38-EBI-GENCODE34/GRCh38.p13.genome.fa \
    --annotation-gtf /hot/project/method/AlgorithmDevelopment/ALGO-000074-moPepGen/ref/GRCh38-EBI-GENCODE34/gencode.v34.chr_patch_hapl_scaff.annotation.gtf \
    --proteome-fasta /hot/project/method/AlgorithmDevelopment/ALGO-000074-moPepGen/ref/GRCh38-EBI-GENCODE34/gencode.v34.pc_translations.fa \
    --output-path /hot/project/method/AlgorithmDevelopment/ALGO-000074-moPepGen/ref/GRCh38-EBI-GENCODE34/noncoding_peptides/lysn_m0_peptides.fa \
    --cleavage-rule lysn \
    --miscleavage 0 \
    --min-mw 0 \
    --min-tx-length 0 \
    --min-length 0 \
    --max-length 99

Got the following error

[ 2022-08-25 21:44:26 ] moPepGen callNoncoding started
[ 2022-08-25 21:46:08 ] Annotation GTF loaded.
[ 2022-08-25 21:46:09 ] Proteome FASTA loaded.
[ 2022-08-25 21:46:28 ] Genome assembly FASTA loaded.
[ 2022-08-25 21:46:50 ] canonical peptide pool generated.
[ 2022-08-25 21:48:04 ] 5000 transcripts processed.
[ 2022-08-25 21:49:29 ] 10000 transcripts processed.
[ 2022-08-25 21:50:52 ] 15000 transcripts processed.
[ 2022-08-25 21:52:21 ] 20000 transcripts processed.
[ 2022-08-25 21:53:55 ] 25000 transcripts processed.
[ 2022-08-25 21:55:29 ] 30000 transcripts processed.
[ 2022-08-25 21:57:03 ] 35000 transcripts processed.
[ 2022-08-25 21:58:19 ] 40000 transcripts processed.
[ 2022-08-25 21:59:56 ] 45000 transcripts processed.
[ 2022-08-25 22:01:39 ] 50000 transcripts processed.
[ 2022-08-25 22:02:58 ] 55000 transcripts processed.
[ 2022-08-25 22:03:01 ] Exception raised from ENST00000625083.1
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/call_noncoding_peptide.py", line 115, in call_noncoding_peptide
    peptides, orfs = call_noncoding_peptide_main(tx_id, tx_model, genome,
  File "/usr/local/lib/python3.8/site-packages/moPepGen/cli/call_noncoding_peptide.py", line 171, in call_noncoding_peptide_main
    peptides = pgraph.call_variant_peptides(
  File "/usr/local/lib/python3.8/site-packages/moPepGen/svgraph/PeptideVariantGraph.py", line 763, in call_variant_peptides
    self.call_and_stage_unknown_orf(
  File "/usr/local/lib/python3.8/site-packages/moPepGen/svgraph/PeptideVariantGraph.py", line 1028, in call_and_stage_unknown_orf
    traversal.pool.add_miscleaved_sequences(
  File "/usr/local/lib/python3.8/site-packages/moPepGen/svgraph/VariantPeptideDict.py", line 336, in add_miscleaved_sequences
    for seq, metadata in seqs:
  File "/usr/local/lib/python3.8/site-packages/moPepGen/svgraph/VariantPeptideDict.py", line 213, in join_miscleaved_peptides
    is_valid = self.is_valid_seq(seq, blacklist)
  File "/usr/local/lib/python3.8/site-packages/moPepGen/svgraph/VariantPeptideDict.py", line 158, in is_valid_seq
    SeqUtils.molecular_weight(seq, 'protein') >= min_mw
  File "/usr/local/lib/python3.8/site-packages/Bio/SeqUtils/__init__.py", line 379, in molecular_weight
    raise ValueError(
ValueError: 'X' is not a valid unambiguous letter for protein

I'm using mopepgen:0.9.2 as the first releast that introduced lysn

[zhuchcn]

The DNA sequence of the gene has a 'N' in the genome so it is translated to 'X' by biopython.. Should we just skip any peptides that have a 'X'?

[lydiayliu]

Yeah that's do that, it's useless for the search algos anyways. I retried this with version 0.6.0 and didn't have this error. What did you do since then that introduced it between 0.6.0 and 0.9.2?

[zhuchcn]

Nothing that should change this was made since 0.6.0 that I can recall so I have no idea..