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Add TRANSFAC ↔ JASPAR motif format converters#358

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cokelaer merged 2 commits intomainfrom
copilot/meme-motif-conversion
Mar 7, 2026
Merged

Add TRANSFAC ↔ JASPAR motif format converters#358
cokelaer merged 2 commits intomainfrom
copilot/meme-motif-conversion

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Copilot AI commented Mar 6, 2026 •
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Implements bidirectional conversion between TRANSFAC and JASPAR transcription factor binding motif formats, addressing the MEME motif conversion use case via biopython's Bio.motifs module.

Changes

  • bioconvert/core/extensions.py: Register jaspar (*.jaspar) and transfac (*.transfac, *.tf) format extensions
  • bioconvert/transfac2jaspar.py: New TRANSFAC2JASPAR converter; preserves AC/ID metadata fields as matrix_id/name in JASPAR output
  • bioconvert/jaspar2transfac.py: New JASPAR2TRANSFAC converter
  • test/data/transfac/, test/data/jaspar/: Sample motif files (2-motif sets: AGL3, RUNX1) used as fixtures

Usage

from bioconvert.transfac2jaspar import TRANSFAC2JASPAR
from bioconvert.jaspar2transfac import JASPAR2TRANSFAC

TRANSFAC2JASPAR("motifs.transfac", "motifs.jaspar")()
JASPAR2TRANSFAC("motifs.jaspar", "motifs.transfac")()

Both converters are auto-discovered by the registry and available via the CLI. Only dependency is biopython.

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

  • meme-suite.org
    • Triggering command: /home/REDACTED/work/_temp/ghcca-node/node/bin/node /home/REDACTED/work/_temp/ghcca-node/node/bin/node --enable-source-maps /home/REDACTED/work/_temp/copilot-developer-action-main/dist/index.js (dns block)

If you need me to access, download, or install something from one of these locations, you can either:

Original prompt

This section details on the original issue you should resolve

<issue_title>meme motif conversion</issue_title>
<issue_description>https://meme-suite.org/meme/doc/motif_conversion.html</issue_description>

Comments on the Issue (you are @copilot in this section)

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@cokelaer
Add TRANSFAC and JASPAR motif format converters
520e1df 
Co-authored-by: cokelaer <778821+cokelaer@users.noreply.github.com>
Copilot AI changed the title [WIP] Add functionality for meme motif conversion Add TRANSFAC ↔ JASPAR motif format converters Mar 6, 2026
@cokelaer cokelaer marked this pull request as ready for review March 7, 2026 21:03
@cokelaer cokelaer merged commit e0441f7 into main Mar 7, 2026
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meme motif conversion

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