9985523937

Committed 18 Jul 2024 04:27AM UTC coverage: 93.861% (+0.1%) from 93.75%

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

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81.25

/vhip/predict_interactions.py

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DuhaimeLab / VirusHostInteractionPredictor / 9985523937

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