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Generate ortholog PDFs when data are unavailable #10

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merged 8 commits into from
Apr 8, 2021

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Cecilia-Sensalari
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@Cecilia-Sensalari Cecilia-Sensalari commented Apr 6, 2021

  • Add new checkpoint: if species pairs are missing from the DBs, the script will exit with informative error message.
  • Better logging
    image

cesen added 5 commits April 2, 2021 15:44
- 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.
- 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.
@Cecilia-Sensalari
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Cecilia-Sensalari commented Apr 6, 2021

  • The PDF file is generated also when ortholog data are missing
  • All ortholog distributions that do have data are plotted
  • The list of missing species pair now has also a section of species missing from both databases

image

cesen added 3 commits April 7, 2021 15:38
- 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.
@Cecilia-Sensalari
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  • A PDF file is now generated only when at least one of its trios has complete ortholog data
  • Improved logging of warning messages about data not yet available ("Skipping...")

image

@Cecilia-Sensalari Cecilia-Sensalari changed the title Checkpoint species pairs in plotting orthologs Generating ortholog PDFs when data are missing Apr 8, 2021
@Cecilia-Sensalari Cecilia-Sensalari changed the title Generating ortholog PDFs when data are missing Generate ortholog PDFs when data are unavailable Apr 8, 2021
@Cecilia-Sensalari Cecilia-Sensalari merged commit 0113723 into master Apr 8, 2021
@Cecilia-Sensalari Cecilia-Sensalari deleted the plot_orthologs branch April 8, 2021 09:23
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