Functionmotifs #116
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Functionmotifs #116
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…are being applied properly.
christinehc
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Dec 12, 2023
changelog: - kmers can now be scored by probability score subtracting the observed kmers in a supplied background set, family set, or combining both background and family - note: some column headers have changed, which may affect downstream analysis (e.g. integration with #115, #116) - to handle user-supplied background files, new rules have been created to count background kmers and combine background kmer counts into a background matrix. The appropriate files for the new workflow have been created. - extensive changes have been made to `snekmer.score` to accommodate the new changes, including: - `snekmer.score.score` now has 3 distinct formulae to compute probability scores according to the desired scoring method - `snekmer.score.feature_class_probabilities` now also integrates the scoring method - the main scoring rule itself has been significantly altered as follows" - all references to the old and not-working "background subtraction" (e.g. separating sequences by "sample" or "background" labels) have been removed - extraneous kmer probability scores for every family are no longer calculated; only the family in question's kmer profile is scored - scoring method now integrated
christinehc
added a commit
that referenced
this pull request
Dec 12, 2023
changelog: - kmers can now be scored by probability score subtracting the observed kmers in a supplied background set, family set, or combining both background and family - note: some column headers have changed, which may affect downstream analysis (e.g. integration with #115, #116) - to handle user-supplied background files, new rules have been created to count background kmers and combine background kmer counts into a background matrix. The appropriate files for the new workflow have been created. - extensive changes have been made to `snekmer.score` to accommodate the new changes, including: - `snekmer.score.score` now has 3 distinct formulae to compute probability scores according to the desired scoring method - `snekmer.score.feature_class_probabilities` now also integrates the scoring method - the main scoring rule itself has been significantly altered as follows" - all references to the old and not-working "background subtraction" (e.g. separating sequences by "sample" or "background" labels) have been removed - extraneous kmer probability scores for every family are no longer calculated; only the family in question's kmer profile is scored - scoring method now integrated
christinehc
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Jan 23, 2024
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Overall Comments
- Code is very well documented IMO, great job on that front :)
- I've added (very minor) comments re:code changes.
- I think the function motifs capability would strongly benefit from an example notebook or demo going through results and the interpretation thereof. We can also potentially work on a template for a summary report.
- We need a docs page, as well as general updates to the docs, to reflect the function motifs workflow.
| @@ -52,7 +52,7 @@ jobs: | |||
| - shell: bash -l {0} | |||
| run: mamba install -y -c conda-forge snakemake==7.0 tabulate==0.8.10 | |||
| - shell: bash -l {0} | |||
| run: pip install -e git+https://github.com/PNNL-CompBio/Snekmer@kmer-association#egg=snekmer | |||
| run: pip install -e git+https://github.com/PNNL-CompBio/Snekmer@functionmotifs#egg=snekmer | |||
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I see why this was changed for local testing, but once we merge in the PR, this should be changed to not point to the functionmotifs branch anymore
snekmer/rules/motif.smk
Outdated
| @@ -0,0 +1,209 @@ | |||
| """model.smk: Module for supervised kmer-based annotation models. | |||
changelog: - RTD pages now include notebook-formatted pages with the learn/apply and motif demos. - Formatted notebooks for compatibility with sphinx notebook formatting. - Cleaned up notebooks, e.g. removing extraneous import statements
changelog: - removed ~HEAD notebook file - moved learn/apply and motif tutorial notebooks to docs folders to add them into sphinx documentation - created symlinks for the above notebooks so that notebooks are still accessible from the resources directory
christinehc
requested changes
Mar 13, 2024
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I would additionally love to see a (minor) deep dive on the results for the two different families, i.e. comparing the highest-scoring kmers for the two families, or brief analysis of the top N kmers. Extra points if there is some sequence motif we can use as an example that makes sense for each given family.
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Add Motif mode for identification of functionally relevant sequence motifs