Skip to content

Draft code to standardize frame of motifs#486

Open
gaberbz wants to merge 16 commits into
mainfrom
New_motif_standardization
Open

Draft code to standardize frame of motifs#486
gaberbz wants to merge 16 commits into
mainfrom
New_motif_standardization

Conversation

@gaberbz

@gaberbz gaberbz commented May 26, 2026

Copy link
Copy Markdown
Contributor

To Do

  • Convert motifs to a set of canonical ones based on the gene direction
  • Check that the updated motifs make sense for all loci
  • Change the form entry and schema instructions so that the gene direction is the one entered/edited

Description

Summarize the changes

Fixes: # Link to any relevant issues and/or discussions

Major Changes

  • Edited "check_loci" motif frame determining functions to fit the standard frames used in literature, which is written as a list in the scema file
  • Gene_orientation is now the canonical motif that reference_orientation is based on, and that is reflected in the schema

Minor Changes

-Minor formatting changes in "check_loci"

Checklist

  • All changes are well summarized
  • Check all tests pass
  • Check that the website preview looks good
  • Update the STRchive version in CITATION.cff, format X.Y.Z. If any major changes, increment Y. If only minor changes, increment Z. If the breaking change (rare), increment X.
  • Ask someone to review this PR

@netlify

netlify Bot commented May 26, 2026

Copy link
Copy Markdown

Deploy Preview for strchive ready!

Name Link
🔨 Latest commit a0dd36f
🔍 Latest deploy log https://app.netlify.com/projects/strchive/deploys/6a18c01f5aecf10008f98e27
😎 Deploy Preview https://deploy-preview-486--strchive.netlify.app
📱 Preview on mobile
Toggle QR Code...

QR Code

Use your smartphone camera to open QR code link.

To edit notification comments on pull requests, go to your Netlify project configuration.

@gaberbz gaberbz requested a review from hdashnow May 27, 2026 15:28
@gaberbz gaberbz force-pushed the New_motif_standardization branch from c95eb93 to bd8324a Compare May 28, 2026 16:11
Adding auto generated to reference descriptions and removing from gene descriptions

Editing descriptions to say explicitly say auto generated from gene

Fix formatting

fix formatting

Editing script to derive canonical motifs from schema

fixing

adding canonical_motifs to function call
@gaberbz gaberbz force-pushed the New_motif_standardization branch from 25f20b6 to 862f476 Compare May 28, 2026 16:34
@gaberbz gaberbz marked this pull request as ready for review May 28, 2026 17:09
Comment thread scripts/check-loci.py Outdated
@gaberbz gaberbz requested a review from hdashnow May 28, 2026 22:32
@hdashnow

Copy link
Copy Markdown
Member

This looks good! I'm going to hold off on merging and do it with the lit review.

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.

2 participants