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Generate ortholog PDFs when data are unavailable #10

Merged
merged 8 commits into from
Apr 8, 2021

Commits on Apr 2, 2021

  1. Error msg if species pairs missing from ortho DBs

    - check if each pair in the trios is present in
    both databases; if it's missing in one, the script
    will exit.
    - note however that if the ortholog peak DB is not present
    but the Ks list database is complete, the distrbutions
    will still be plotted, all without their modes. This was a
    choice made some time ago that I didn't want to remove.
    cesen committed Apr 2, 2021
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Commits on Apr 6, 2021

  1. Update branch with new PAML installation

    cesen committed Apr 6, 2021
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  2. Minor (remove unnecessary newline)

    cesen committed Apr 6, 2021
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  3. If missing species pairs, plot incomplete PDF

    - Now if one or more species pair is missing,
    the PDF will be generated and the available data
    will be plotted.
    - Checking for missing pairs is now done during
    the main for loop and not before (outside) it.
    - The missing pairs are listed at the end, after
    the for loop.
    - The missing pairs are listed as missing 1) from
    both databases, 2) from only peak DB and 3) from
    only Ks list DB.
    cesen committed Apr 6, 2021
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Commits on Apr 7, 2021

  1. Ortholog PDF has only trios with complete data

    - Every PDF page contains a trio with complete
    data (Ks list and Ks peak estimate).
    - If there are no complete trios for a PDF, the
    file is not generated.
    - More clearly logging when a species pair is
    missing in DBs and the plotting of a trio is
    skipped.
    cesen committed Apr 7, 2021
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  2. Minor (clearer variable name)

    cesen committed Apr 7, 2021
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Commits on Apr 8, 2021

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