Merge pull request #875 from uclahs-cds/czhu-fix-variant-peptide-pool

Fix VariantPeptidePool Peptide not recognized correctly during validation
uclahs-cds · May 26, 2024 · b4da46e · b4da46e
2 parents bd98136 + 37d95cc
commit b4da46e
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,6 +10,10 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ## [Unreleased]
 
+## [1.4.1] - 2024-05-26
+
+- Fixed `VariantPepidePool` that old versions of `SeqUtils.molecular_weight` don't handle `SeqRecord` objects. #874
+
 ## [1.4.0] - 2024-03-27
 
 - `--coding-novel-orf` added to `callNoncoding` and `callVariant` to call novel ORF peptides from coding transcripts. #659

diff --git a/moPepGen/__init__.py b/moPepGen/__init__.py
@@ -8,7 +8,7 @@
 from . import constant
 
 
-__version__ = '1.4.0'
+__version__ = '1.4.1'
 
 ## Error messages
 ERROR_INDEX_IN_INTRON = 'The genomic index seems to be in an intron'

diff --git a/moPepGen/aa/VariantPeptidePool.py b/moPepGen/aa/VariantPeptidePool.py
@@ -36,9 +36,9 @@ def add_peptide(self, peptide:AminoAcidSeqRecord,
             min_mw = cleavage_params.min_mw
             min_length = cleavage_params.min_length
             max_length = cleavage_params.max_length
-            if SeqUtils.molecular_weight(peptide, 'protein') < min_mw:
+            if SeqUtils.molecular_weight(peptide.seq, 'protein') < min_mw:
                 return False
-            if len(peptide.seq) < min_length or len(peptide) > max_length:
+            if len(peptide.seq) < min_length or len(peptide.seq) > max_length:
                 return False
             if str(peptide.seq) in canonical_peptides:
                 return False