Add an example of pyfaidx usage#1
Merged
icwells merged 1 commit intoWilsonSayresLab:masterfrom Jul 30, 2018
Merged
Conversation
Collaborator
|
Looks pretty cool. I'm not sure if it will make too much of a difference here (since most of the time is spent analyzing the sequences), but it certainly won't hurt. |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
I just did this for fun, since I saw this module pop up in my activity feed, and you're doing lots of operations on multi-fasta files where I think my pyfaidx module might help out - both in terms of code complexity and computational efficiency, since it uses the samtools indexing strategy to reduce I/O. Feel free to ignore this if you want - just doing this over my morning coffee.