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Remove ambition to add unipressed, add species constraint to mapping #32

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Merged
ladislav-hovan merged 1 commit into from
Jan 7, 2026
Merged

Remove ambition to add unipressed, add species constraint to mapping #32

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2 changes: 0 additions & 2 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -264,8 +264,6 @@ The project is: _in progress_.
## Room for Improvement
Room for improvement:
- Better tests
- Try incorporating unipressed
- Improve overlap computations

To do:
- Support for more species
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2 changes: 1 addition & 1 deletion src/sponge/modules/ppi_retriever/ppi_retriever.py
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Expand Up @@ -108,7 +108,7 @@ def retrieve_ppi(
print ('Checking the conflicts in the UniProt database...')
mapper = ProteinIDMapper(self.protein_url)
uniprot_df = mapper.get_uniprot_mapping('Gene_Name', 'UniProtKB',
ids_to_check).set_index('from')
ids_to_check, taxonomy_id=9606).set_index('from')
p_to_q = {p: q for q,p in zip(diff_df['queryName'],
diff_df['preferredName'])}
# Keep the conflicts where there is a match or where one or both
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