chore: removing symbols from QTL study identifiers #971
+128
−74
Conversation
This file contains 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
DSuveges
commented
Jan 14, 2025
| @@ -1,17 +1,17 @@ | |||
| molecular_trait_id gene_id cs_id variant rsid cs_size pip pvalue beta se z cs_min_r2 region | |||
| RBP7.14208.3.3..1 ENSG00000162444 RBP7.14208.3.3..1_L1 chr1_10000458_T_C rs3003377 22 0.0170703689724805 1.33564e-10 0.139135 0.0215922 6.45120520807609 0.649351082174683 chr1:8997206-10997206 | |||
There was a problem hiding this comment.
The sample files were changed to provide a more complete representation of the issues caused by the special characters in the studyId.
DSuveges
changed the title
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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Outdated suggestions cannot be applied.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.
Context
When concatenating various fields of QTL studies to generate the study identifier, there is an unexpected side effect: the resulting string might contain special characters that interfere with using study identifiers as URLs. To resolve this problem, upon ingestion, study id string is lower cased, and all non-alphanumeric (plus
_and-) characters are replaced with underscores.