callAltTranslation: Required flags cause BioPython crash on stop codons

[askolari]

Bug Description
callAltTranslation has an issue that makes it unusable in v1.4.6:

1. Tool requires at least one flag:

   • --selenocysteine-termination OR
   • --w2f-reassignment

2. Without flags: ValueError: At least one of --selenocysteine-termination and --w2f-reassignment must be given.

3. With either flag: Tool crashes after ~1h runtime:

   ValueError: ''*'' is not a valid unambiguous letter for protein

at Bio/SeqUtils/__init__.py:474 in molecular_weight()

Root Cause
Both flags generate peptides containing stop codons (*), which BioPython's
molecular_weight() function cannot handle when checking --min-mw threshold.

Environment

• moPepGen: v1.4.6
• Python: 3.9
• Reference: Ensembl 114
• BioPython: (via moPepGen dependencies)

Expected Behavior
Tool should either:

1. Filter out stop-codon-containing peptides before molecular weight check, OR
2. Skip molecular weight validation for these specific peptide types, OR
3. Make flags truly optional (don't require at least one)

Workaround
Currently none - callAltTranslation is completely unusable.

Steps to Reproduce

moPepGen callAltTranslation \
  --index-dir /path/to/index \
  --reference-source ENSEMBL \
  --output-path output.fasta \
  --selenocysteine-termination \
  --cleavage-rule trypsin \
  --miscleavage 2 \
  --min-length 7 \
  --max-length 25 \
  --min-mw 500.0

Crashes after ~1 hour at peptide validation stage.

[zhuchcn]

I lost control of this repo. Could you open an issue in the repo, please? https://github.com/zhuchcn/package-moPepGen

Also, usually, the error message should print the transcript ID where the error is raised. Can you look find it? Or you can paste the full error message in the new issue.