Use tangermeme backend for tomtom #75
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…into tomtom-tangermeme
…into tomtom-tangermeme
avantikalal
changed the title
suragnair
reviewed
Nov 8, 2024
src/grelu/interpret/score.py
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| top_n_matches: int, | ||
| ) -> None: | ||
| """ | ||
| Modified from https://github.com/jmschrei/tfmodisco-lite/blob/main/modiscolite/report.py#L245 |
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can you add the permalink: https://github.com/jmschrei/tfmodisco-lite/blob/3c6e38f/modiscolite/report.py#L245
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also, would it make more sense to put this function and run_modisco in a separate modisco.py file? Does not fit into score.py thematically I feel.
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Makes sense, I'll make both changes.
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suragnair
approved these changes
Nov 8, 2024
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Replaced the TOMTOM executable from the MEME suite with the tomtom reimplementation in tangermeme v0.4. Tomtom no longer has to be installed in the environment to use
run_modisco, which is a major source of user issues.Specific changes:
Dockerfile:run_tomtomfunction ininterpret.motifs. This takes a dictionary of motifs and a meme file, and compares the motifs to the reference motifs in the meme file.run_tomtomintests/test_interpret.py.run_modiscoto userun_tomtomfor the tomtom part if a meme file is provided. This involved creating a new function _add_tomtom_to_modisco_report which is modified from modiscolite.Fully addresses #55