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Fix VariantPeptidePool Peptide not recognized correctly during validation #875

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merged 1 commit into from
May 26, 2024

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@zhuchcn zhuchcn commented May 26, 2024

Description

The SeqUtils.molecular_weight function from some older versions of Biopython don't accept SeqRecord as input, causing an error when trying to calculate the molecular weight.

Closes #874

Checklist

  • This PR does NOT contain PHI or germline genetic data. A repo may need to be deleted if such data is uploaded. Disclosing PHI is a major problem.
  • This PR does NOT contain molecular files, compressed files, output files such as images (e.g. .png, .jpeg), .pdf, .RData, .xlsx, .doc, .ppt, or other non-plain-text files. To automatically exclude such files using a .gitignore file, see here for example.
  • I have read the code review guidelines and the code review best practice on GitHub check-list.
  • The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].
  • I have added the major changes included in this pull request to the CHANGELOG.md under the next release version or unreleased, and updated the date.
  • All test cases passed locally.

@zhuchcn zhuchcn merged commit b4da46e into main May 26, 2024
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@zhuchcn zhuchcn deleted the czhu-fix-variant-peptide-pool branch May 26, 2024 18:28
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callNovelORF & callAltTrans error: ':' is not a valid unambiguous letter for protein
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