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Merge pull request #876 from uclahs-cds/czhu-fix-split-fasta
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Fix splitFasta: NovelORF peptides from coding transcripts not recognized correctly
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zhuchcn authored Jun 23, 2024
2 parents b4da46e + 2593943 commit 305ffbb
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Showing 5 changed files with 10 additions and 6 deletions.
4 changes: 4 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -10,6 +10,10 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm

## [Unreleased]

## [1.4.2] - 2024-06-23

- Fixed `splitFasta` that NovelORF peptides coding transcripts not recognized correctly.

## [1.4.1] - 2024-05-26

- Fixed `VariantPepidePool` that old versions of `SeqUtils.molecular_weight` don't handle `SeqRecord` objects. #874
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2 changes: 1 addition & 1 deletion moPepGen/__init__.py
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Expand Up @@ -8,7 +8,7 @@
from . import constant


__version__ = '1.4.1'
__version__ = '1.4.2'

## Error messages
ERROR_INDEX_IN_INTRON = 'The genomic index seems to be in an intron'
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2 changes: 1 addition & 1 deletion moPepGen/aa/VariantPeptideLabel.py
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Expand Up @@ -203,7 +203,7 @@ def from_variant_peptide(peptide:AminoAcidSeqRecord,
info = VariantPeptideInfo(str(variant_id), gene_ids, var_ids, variant_id.index)

if check_source:
if tx_id not in coding_tx:
if variant_id.orf_id is not None:
info.sources.add(constant.SOURCE_NOVEL_ORF, group_map=group_map)

for gene_id, _ids in var_ids.items():
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6 changes: 3 additions & 3 deletions test/unit/test_peptide_pool_splitter.py
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Expand Up @@ -283,7 +283,7 @@ def test_from_variant_peptide_noncoding(self):
infos = VariantPeptideInfo.from_variant_peptide(peptide, tx2gene, coding_tx, label_map)
self.assertIn('NovelORF', infos[0].sources)

peptide = create_aa_record('KHIRJ','ENST0004|1')
peptide = create_aa_record('KHIRJ','ENST0004|ORF1|1')
infos = VariantPeptideInfo.from_variant_peptide(peptide, tx2gene, coding_tx, label_map)
self.assertIn('NovelORF', infos[0].sources)

Expand Down Expand Up @@ -543,7 +543,7 @@ def test_split_database_source_comb_order(self):
peptides_data = [
[
'SSSSSSSR',
'CIRC-ENST0002-E1-E2|1 ENST0005|SE-2100|1'
'CIRC-ENST0002-E1-E2|1 ENST0005|SE-2100|ORF2|1'
]
]
peptides = VariantPeptidePool({create_aa_record(*x) for x in peptides_data})
Expand Down Expand Up @@ -576,7 +576,7 @@ def test_split_database_source_comb_order_case2(self):
peptides_data = [
[
'SSSSFSSR',
'CIRC-ENST0002-E1-E2|1 ENST0005|SE-2100|W2F-5|1'
'CIRC-ENST0002-E1-E2|1 ENST0005|SE-2100|W2F-5|ORF-2|1'
]
]
peptides = VariantPeptidePool({create_aa_record(*x) for x in peptides_data})
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2 changes: 1 addition & 1 deletion test/unit/test_peptide_pool_summarizer.py
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Expand Up @@ -50,7 +50,7 @@ def test_summarize_fasta_source_comb_order(self):
peptides_data = [
[
'SSSSSSSR',
'CIRC-ENST0002-E1-E2|1 ENST0005|SE-2100|1'
'CIRC-ENST0002-E1-E2|1 ENST0005|SE-2100|ORF2|1'
]
]
peptides = VariantPeptidePool({create_aa_record(*x) for x in peptides_data})
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