Thread unique synteny regions along main chromosome

[twalsh-ebi]

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Description

This PR would update the way the synteny view handles data, obtaining a unique set of synteny regions in the main chromosome, and then ordering these in such a way that they are 'threaded' along it.

It would also update the info box shown when a chromosome lacks synteny regions in the selected other species.

Views affected

This PR changes code used in all synteny views.

However, most synteny views should be essentially unaffected.

It is intended to fix issues with the Human self-synteny view, mainly due to challenges working with syntenic regions that may connect different regions of the same genome, possibly even two regions of the same chromosome.

Synteny views affected

Example of synteny view affected by this PR:

• Human self-synteny: sandbox vs staging

Example image of Human self-synteny view for chromosome 1 on sandbox:

Example image of Human self-synteny view for chromosome 1 on staging:

Synteny views unaffected

The following synteny examples should be consistent between sandbox and staging, though the rendering order of highlighted regions or the placement of other chromosomes in the synteny view may differ in some cases.

Vertebrates

• Mouse vs Rat: sandbox vs staging
• Zebrafish vs Medaka: sandbox vs staging
• Human vs Chimpanzee: sandbox vs staging

Example image of Human vs Chimpanzee synteny view for chromosome 2 on sandbox:

Example image of Human vs Chimpanzee synteny view for chromosome 2 on staging:

Plants

• Rice vs Rye: sandbox vs staging
• Potato vs Tomato: sandbox vs staging
• Maize vs Sorghum: sandbox vs staging

Metazoa

• C. elegans vs C. briggsae: sandbox vs staging
• A. gambiae vs A. aegypti: sandbox vs staging
• A. mellifera vs S. invicta : sandbox vs staging

Possible complications

None expected, though further checks are needed.

Merge conflicts

None detected

Related JIRA Issues (EBI developers only)

• ENSCOMPARASW-7059