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debug_stringdb #202

Merged
merged 7 commits into from
Jan 15, 2025
Merged

debug_stringdb #202

merged 7 commits into from
Jan 15, 2025

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tabbassidaloii
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@tabbassidaloii tabbassidaloii commented Jan 7, 2025 •
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  • support other species
  • debug when the input is not gene symbol
  • add Ensembl protein ID

Done by @djwetstede taken from the PR #176

Improvements required:

  • the UniProt ID is not correct (it is the gene symbol of the entity queried), could be removed as we have the Ensembl Protein ID
  • the code is very slow which is because of many for loops in lines 69-103

@tabbassidaloii
update codes
fd6be7c 
- support other species
- debug when the input is not gene symbol

Done by @djwetstede taken from the PR #176 (#176)

Improvements required:
- the uniprot id is not correct (it is the gene symbol of entity queried)
- the code is very slow which is because of many for loops in line 69-103
@tabbassidaloii tabbassidaloii changed the title update codes debug_stringdb Jan 8, 2025
@jmillanacosta
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  • Retrieves the Uniprot-TrEMBL protein IDs from the Uniprot REST API for queried and linked gene products (TBD: implement Ensembl Protein/Peptide mappings in BridgeDB)
  • Updated tests

@tabbassidaloii tabbassidaloii merged commit 0301cd8 into main Jan 15, 2025
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@jmillanacosta jmillanacosta jmillanacosta approved these changes

@YojanaGadiya YojanaGadiya Awaiting requested review from YojanaGadiya

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@tabbassidaloii @jmillanacosta @YojanaGadiya