Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Generate ortholog PDFs when data are unavailable #10

Merged
merged 8 commits into from
Apr 8, 2021
Merged

Generate ortholog PDFs when data are unavailable #10

merged 8 commits into from
Apr 8, 2021

Conversation

Cecilia-Sensalari
Copy link
Collaborator

@Cecilia-Sensalari Cecilia-Sensalari commented Apr 6, 2021 •
edited
Loading

  • 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
Error msg if species pairs missing from ortho DBs
bf9e390 
- 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.
Checkpoint now logs "errors" and not "warnings"
68f309b
Update branch with new PAML installation
d80493f
Minor (remove unnecessary newline)
0ef354e
If missing species pairs, plot incomplete PDF
65e5f6d 
- 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
Copy link
Collaborator Author

Cecilia-Sensalari commented Apr 6, 2021 •
edited
Loading

  • 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
Ortholog PDF has only trios with complete data
ff00d40 
- 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.
Minor (clearer variable name)
5f0a186
Bugfix (check if ortholog peak DB is available)
c947e20
@Cecilia-Sensalari
Copy link
Collaborator Author

  • 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
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

None yet
1 participant
@Cecilia-Sensalari