Skip to content

added new parallelized phylotyping script and its description txt#5

Open
arnaoutleen wants to merge 1 commit into
jgolob:mainfrom
arnaoutleen:feature/parallelized_phylotyping_script
Open

added new parallelized phylotyping script and its description txt#5
arnaoutleen wants to merge 1 commit into
jgolob:mainfrom
arnaoutleen:feature/parallelized_phylotyping_script

Conversation

@arnaoutleen

Copy link
Copy Markdown

As discussed in team meeting, leen tried to parallelize and speed up Jonathan's phylotypes.py script, by:

  • parallelizing the pairwise distances calculations over the different workers / threads
  • distributing the "groups" to calculate onto the workers based on total # of SVs in each "worker" such that we're trying to approximate all of the workers finishing at the same time
  • add in an sqlite cache to continue calculating distances if something breaks in the middle

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.

1 participant