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

Add multiprocessing #13

Open
wants to merge 9 commits into
base: main
Choose a base branch
from
Open

Add multiprocessing #13

wants to merge 9 commits into from

Conversation

sof202
Copy link
Owner

@sof202 sof202 commented Jan 30, 2025

Description

This pull request will allow for the user to input multiple regions in one run of the script and the script now has built in multiprocessing to assist with this. The wrapper script doesn't lend well to this change, but I don't care about that as it is mainly there as an example of what you can do. With a different wrapper script, one could find all peak regions in dataset A and then feed these positions into the python script (parallelising further across multiple cores for each chromosome for example).

Type of change

  • Bug fix
  • New feature
  • Code refactor
  • Documentation update

Checklist:

  • My code is consistent in style with the rest of ATACPeakCompare
  • I have performed a self-review of my own code
  • I have made corresponding changes to the documentation

I also got rid of the non parsable version as it is kinda useless and
doesn't lend to this new code unless I add additional logic to handle
the different regions considered.
Previously chromosome was being converted to int, which doesn't work
when the chromosome starts with "chr" (standard)
Due to parallelism, the order of inputs isn't necessarily going to be
the order of results. So a bunch of numbers doesn't really give you any
information. Instead, the region is printed alongside the metric.
@sof202 sof202 added the enhancement New feature or request label Jan 30, 2025
@sof202 sof202 linked an issue Jan 30, 2025 that may be closed by this pull request
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
None yet
Development

Successfully merging this pull request may close these issues.

[Enhancement suggestion]: Enable parallelisation for peak comparison
1 participant