DuhaimeLab / VirusHostInteractionPredictor

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• gh-readonly-queue/main/pr-127-78a990b30993070e9893f12067490f344d32d454
• TAAI_TCAI
• build/python-3.13
• compute_pair_CUB_features
• dependabot/pip/biopython-1.85
• dependabot/pip/python-dev-0732576d46
• dependabot/pip/python-dev-18acf35fe3
• dependabot/pip/python-dev-19516c84a5
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• dependabot/pip/python-dev-86ba1c6dd5
• dependabot/pip/python-dev-b895837ea7
• dependabot/pip/python-dev-be0bcff883
• dependabot/pip/python-dev-d789a6fb1a
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• dependabot/pip/python-dev-fa19925471
• dependabot/pip/python-prod-51c51656ea
• dependabot/pip/scikit-learn-1.6.0
• gh-readonly-queue/main/pr-100-09eda588f2b76305a6256ebeb90dd83ce653630b
• gh-readonly-queue/main/pr-102-8ad1600110291f6dd92b8e1fbab53986a788fd12
• gh-readonly-queue/main/pr-104-d402b895415b203af7805f57b80b846a89e3362c
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• gh-readonly-queue/main/pr-162-60c088d395e3104f615c405a813ecc3e0fd3b4f1
• gh-readonly-queue/main/pr-163-383e977d1197f9ab7d3b1a17f3f6212993c2fee6
• gh-readonly-queue/main/pr-164-9875e6a81e42e7bec9aaac7e4fb54acb69219feb
• gh-readonly-queue/main/pr-167-d206fe866ebb41fc8bfdd068a6a5915f89cfe592
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• gh-readonly-queue/main/pr-170-0dc60e1bea00fa5dc541489e15db00f890f819d3
• gh-readonly-queue/main/pr-171-3d6113ee7eb7309b57f88819bcfe446c1b6f1fdf
• gh-readonly-queue/main/pr-175-5d95a843fc1225c909fd097295a7335639dfeb11
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• gh-readonly-queue/main/pr-186-e214bb1ce3c2793c56e10a3e0c61259635d91496
• gh-readonly-queue/main/pr-67-a10efe063f508399001f78adaa5400afd887c5fa
• gh-readonly-queue/main/pr-76-3dcff9e80540508d469e69b8fa85e8e78415017e
• gh-readonly-queue/main/pr-82-7aecf9afdde2eecfdf6854b1e042076ba32ea4c8
• gh-readonly-queue/main/pr-83-bf4a512b2d88d57b6dbaf4af69606ccddbd97922
• gh-readonly-queue/main/pr-84-7aecf9afdde2eecfdf6854b1e042076ba32ea4c8
• gh-readonly-queue/main/pr-85-4a7a2448f8a9b4dca23660ad25e329826897026e
• gh-readonly-queue/main/pr-88-353b84c9ab93f40860c7e232bab93f476b88b1b4
• gh-readonly-queue/main/pr-90-40f8bc548caf095d0c3db625124ed332dd0ee0b3
• gh-readonly-queue/main/pr-92-858508a0550e79478da4e2152943f7b1c6a027b3
• gh-readonly-queue/main/pr-93-21ad5e5ae9f22c662e639838ea24da5a4afd049a
• gh-readonly-queue/main/pr-94-f6c64c26f094d2e22f571ea1d360ef8507775b01
• gh-readonly-queue/main/pr-96-57845b3a18fd19e60585294d12398b5d7d870222
• gh-readonly-queue/main/pr-98-e8aee2b5b8ef77b4b09499ebc902e81bb47827e8
• main
• tRNA_counts_frq
• update_example

Build # 9985523937

Build Type

push

github

Committed by web-flow

Commit Message

Incorporate genes files (#127)

This pull request is all about setting up for incorporating methods and
classes from gene_features.py into the main pipeline. To do this, we
need the infrastructure to take in annotated genes files. I hope this
isn't too much all at once (a lot of the changes are just renaming and
uploading things)!

-----------------------
- add arguments, docstrings, and class variables for GENE
files/directories/extensions in ComputeFeatures and PredictInteractions
classes
- write list_gene_files() function (analogous to list_genome_files) and
add method to do_setup()
------------------------
- distinguish all current instances of GENOME files/directories mentions
in ComputeFeatures and PredictInteractions classes
- adjust get_headers() docstrings to specify genome files - so far, no
need for a gene file - specific get headers function
- upload example and testing annotated genes files, rename folders
------------------------
- update test_ComputeFeatures.py, test_PredictInteractions.py to reflect
name changes and test new gene file listing function
- update example.ipynb to include changes and use needed arguments

Run Details

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