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.

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

MRG: add pretty printing option to manysearch command #408

Merged
merged 8 commits into from
Aug 12, 2024
Merged

Conversation

ctb
Copy link
Collaborator

@ctb ctb commented Aug 11, 2024

This PR adds an option-P/--pretty-print to manysearch that uses the code in #380 to produce nice output.

The default is to pretty-print, which is maybe not great if you're generating thousands of results. But it's easy to turn off with -N.

This PR also adjusts manysearch so that the average_abund, median_abund, and std_abund are not present when abundance is not available, which follows practice elsewhere in the code base.

Questions:

  • should we add this to pairwise a la sourmash compare, too?
  • same question for fastgather a la sourmash gather...

Fixes #379
Closes #377 because it adds an explicit test for the output.

TODO:

  • add tests

@ctb ctb changed the title WIP: add pretty printing option to manysearch command MRG: add pretty printing option to manysearch command Aug 11, 2024
@ctb
Copy link
Collaborator Author

ctb commented Aug 12, 2024

@sourmash-bio/devs read for review & merge!

Copy link
Contributor

@bluegenes bluegenes left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

lgtm!

@ctb ctb merged commit 670bb9f into main Aug 12, 2024
1 check passed
@ctb ctb deleted the add_prettyprint branch August 12, 2024 22:21
@ctb ctb mentioned this pull request Aug 13, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

lower manysearch default threshold script to compare mgmanysearch results with manysearch
2 participants