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[Stacked PR] GVF file finder#41

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khetherin wants to merge 11 commits into
EBIvariation:mainfrom
khetherin:ftp_file_finder
Open

[Stacked PR] GVF file finder#41
khetherin wants to merge 11 commits into
EBIvariation:mainfrom
khetherin:ftp_file_finder

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@khetherin khetherin commented May 29, 2026

A stacked PR (to be reviewed after minor refactor in #40 has been merged) & seeking early feedback.
This PR traverses a file directory structure and finds the GVF files in line with Step 2 of the Strategy (EVA-4147). This will find either all the GVFs in one study accession or all the GVFs in the top directory depending on input parameters.

  • hpc_file_finder.py: traverses a directory and returns a dictionary{study_accession: [gvf_files]}. Supports filtering by study_accession.
  • tests/hpc_dir: a test folder

Currently this is only for a local directory and has the HPC directory traversal has not been added yet (but this can be implemented in another ticket if this is merged or addressed later on in this ticket).

TODO: add config for HPC, parsing HPC config, add/switch to traversing the HPC, unit tests
Merge after #40

@khetherin khetherin requested a review from tcezard May 29, 2026 14:32
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