Adds config option `inferCdsParts` to ProcessedTranscript glyph #872

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vivekkrish commented Mar 22, 2017

Assumes that JSON data for any particular gene feature being processed by JBrowse contains one complete CDS instead of disjointed features. The code in this PR makes use of the exon coordinates and total CDS span to infer the CDS parts.

Set "inferCdsParts": true in the track config to invoke this functionality.

This PR is being added to satisfy a specific use case, where JBrowse-compatible JSON data produced by the InterMine JBrowse REST API represents the CDS feature as a single element, mainly because of the way in which CDSs are loaded into the warehouse.

JBrowse installed at jbrowse.org without this fix: https://jbrowse.org/code/latest-release/?data=https://apps.araport.org/thalemine/service/jbrowse/config/3702&loc=Chr1:22311..32037&tracks=ThaleMine-3702-Gene&tracklist=0&nav=0&overview=0

JBrowse installed at Araport with this fix: https://apps.araport.org/jbrowse?data=https://apps.araport.org/thalemine/service/jbrowse/config/3702&loc=Chr1:22311..32037&tracks=ThaleMine-3702-Gene&tracklist=0&nav=0&overview=0&fullviewlink=0

+ Add option `inferCdsParts` to ProcessedTranscript glyph
Assumes that data being sent to JBrowse contains one complete
CDS instead of disjointed features. Uses the exon coordinates
and total CDS span to infer the CDS parts

Set "inferCdsParts": true in the track config to invoke this function
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cmdcolin Mar 22, 2017

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Looks great. It is also safely behind a feature flag, so I don't really see anything preventing merger

Maybe just fix jshint warning to say "var start" and "var end" here https://github.com/GMOD/jbrowse/pull/872/files#diff-c7233e49f25e7e8afba5a2bba1615f49R106

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cmdcolin commented Mar 22, 2017

Looks great. It is also safely behind a feature flag, so I don't really see anything preventing merger

Maybe just fix jshint warning to say "var start" and "var end" here https://github.com/GMOD/jbrowse/pull/872/files#diff-c7233e49f25e7e8afba5a2bba1615f49R106

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vivekkrish Mar 22, 2017

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Thanks for the review @cmdcolin! I've pushed a fix as suggested. Hopefully this can get merged into the upcoming release.

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vivekkrish commented Mar 22, 2017

Thanks for the review @cmdcolin! I've pushed a fix as suggested. Hopefully this can get merged into the upcoming release.

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cmdcolin Mar 22, 2017

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Cool

I guess one thing to be aware of is since this doesn't materialize the CDS subfeatures (it's sort of a rendering only flag) I'd be aware of possible limitations when combining with other plugins like apollo or featuresequence perhaps, but I think that this is a good fix

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cmdcolin commented Mar 22, 2017

Cool

I guess one thing to be aware of is since this doesn't materialize the CDS subfeatures (it's sort of a rendering only flag) I'd be aware of possible limitations when combining with other plugins like apollo or featuresequence perhaps, but I think that this is a good fix

@cmdcolin cmdcolin merged commit 6488c81 into GMOD:master Mar 22, 2017

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