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Refactoring code and fixing cutoff argument handling #4

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Refactoring code and fixing cutoff argument handling #4

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Commits on May 22, 2023

  1. Move generating input for fasta35 into a separate function

    @serzero2007
    serzero2007 committed May 22, 2023
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  2. Fix --cutoff flag type and help message 

    According to the source code the cutoff flag is minimum protein
importance value for it to be included into selected_proteins list.
The previous flag definition was misleading and had incorrect type,
making the flag unusable, because any non-zero integer cutoff value
would result in no protein selected at all.
    @serzero2007
    serzero2007 committed May 22, 2023
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  3. Remove unused fasta35 function

    @serzero2007
    serzero2007 committed May 22, 2023
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  4. Move parsing arguments logic into its own function

    @serzero2007
    serzero2007 committed May 22, 2023
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  5. Remove redundant import

    @serzero2007
    serzero2007 committed May 22, 2023
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  6. Move code for running fasta35 into spawn_fasta35

    @serzero2007
    serzero2007 committed May 22, 2023
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  7. define select_genomes, select_proteins functions

    @serzero2007
    serzero2007 committed May 22, 2023
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  8. Define train_random_forest function

    @serzero2007
    serzero2007 committed May 22, 2023
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  9. Define parse_fasta35_scores function

    @serzero2007
    serzero2007 committed May 22, 2023
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  10. Use len(...) instead of value from args

    @serzero2007
    serzero2007 committed May 22, 2023
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  11. No fail if len(selected_proteins) < num_proteins

    @serzero2007
    serzero2007 committed May 22, 2023
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  12. No fail if len(labels[label]) < args.num_genomes

    @serzero2007
    serzero2007 committed May 22, 2023
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