developing an update to polya_umi.py script#12
Merged
Conversation
1) fuzzy_polya_umi.py - simply switches adapter matching from regex to sw search using parasail. Does not correct UMI errors 2) corrected_polya_umi.py - finds candidate UMI region using both 3' adapter and polyA region as anchors. Attempts substituion and indel correction of UMI region to extract the "correct" umi 3) find_longest_polyA.py, find_3prime_adapter.py, extract_and_correct_umi_test.py and full_polya_umi_extraction_test.py are test scripts for the individual key parts of the corrected_polya_umi.py script
Collaborator
|
Hi @as2110, code looks good, but why are the scripts in /dev and not integrated into the pipelines? |
Contributor
Author
|
The corrected_polya_umi.py can be moved up a directory if you are happy with the code/tests and I can update the pipeline count script to utlise this. |
polyA complementing fixed to to use last 300 bp for polyA. New umi extract and tagging script n_polya_umi.py added. Dev scripts used to develop and test individual aspects in dev. Pipeline count updated to use umi script and updated minimap2 params for speed.
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
fuzzy_polya_umi.py - simply switches adapter matching from regex to sw search using parasail. Does not correct UMI errors
corrected_polya_umi.py - finds candidate UMI region using both 3' adapter and polyA region as anchors. Attempts substitution and indel correction of UMI region to extract the "correct" umi
find_longest_polyA.py, find_3prime_adapter.py, extract_and_correct_umi_test.py and full_polya_umi_extraction_test.py are test scripts for the individual key parts of the corrected_polya_umi.py script