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Fix splitFasta #898

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merged 6 commits into from
Feb 20, 2025
Merged

Fix splitFasta #898

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fed5113
fix (splitFasta): variant peptide not split correclty if derived from…
zhuchcn Feb 19, 2025
f18f0ba
fix (splitFasta): update to combine variants for fusino if downstream…
zhuchcn Feb 19, 2025
9927f5b
fix (CICD): update pypi.yaml to use the latest version of our github …
zhuchcn Feb 19, 2025
f290975
test (CICD): test the latest action
zhuchcn Feb 20, 2025
51357ba
fix (CICD): syntax error
zhuchcn Feb 20, 2025
dda2f7b
fix (CICD): update to main pypi
zhuchcn Feb 20, 2025
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4 changes: 2 additions & 2 deletions .github/workflows/pypi.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ jobs:
uses: actions/checkout@v2

- name: Build distribution
uses: uclahs-cds/tool-pypi-publish-action/build-distribution@58e64514405eafe4f8c40130001cbd4d62acdf5c
uses: uclahs-cds/tool-pypi-publish-action/build-distribution@8a59b1548652d33f0a224775805d9a39767f0605
with:
package-name: mopepgen

Expand All @@ -35,7 +35,7 @@ jobs:
uses: actions/checkout@v2

- name: Publish to PyPI
uses: uclahs-cds/tool-pypi-publish-action/publish-to-pypi@58e64514405eafe4f8c40130001cbd4d62acdf5c
uses: uclahs-cds/tool-pypi-publish-action/publish-to-pypi@8a59b1548652d33f0a224775805d9a39767f0605
with:
package-name: mopepgen
url: https://upload.pypi.org/legacy/
6 changes: 6 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -10,6 +10,12 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm

## [Unreleased]

## [1.4.5] - 2025-02-19

### Fixed

- Variant peptide not split correclty if it is derived from fusion that the upstream and downstream are the same gene. #897

## [1.4.4] - 2025-02-11

### Fixed
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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__ = '1.4.4'
__version__ = '1.4.5'

## Error messages
ERROR_INDEX_IN_INTRON = 'The genomic index seems to be in an intron'
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9 changes: 7 additions & 2 deletions moPepGen/aa/VariantPeptideLabel.py
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Expand Up @@ -189,9 +189,14 @@ def from_variant_peptide(peptide:AminoAcidSeqRecord,
var_ids = {
first_gene_id: variant_id.first_variants
+ [variant_id.fusion_id] \
+ variant_id.peptide_variants,
second_gene_id: variant_id.second_variants
+ variant_id.peptide_variants
}
if second_gene_id != first_gene_id:
var_ids[second_gene_id] = variant_id.second_variants
else:
var_ids[first_gene_id] = list(set(
var_ids[first_gene_id] + variant_id.second_variants
))
tx_id = first_tx_id

elif isinstance(variant_id, pi.BaseVariantPeptideIdentifier):
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