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Add unprocessed transcript glyph #1230

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merged 4 commits into from Oct 26, 2018

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cmdcolin commented Oct 8, 2018

This adds an "unprocessed transcript" glyph with an unprocessedTranscriptColor config variable that distinguishes it from the other transcripts

This code uses the noncodingType config (analogous to transcriptType) to render non-coding features with a gene parent correctly

screenshot-localhost-2018 10 08-15-37-38

This references #1106 although it's not a true pseudogene glyph, it handles unprocessed transcripts like ncRNA, lncRNA, miRNA, etc. Issues like #757 are potentially also relevant but was closed with a workaround

@wafflebot wafflebot bot added the in progress label Oct 8, 2018

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cmdcolin commented Oct 8, 2018

Screenshot of same region on dev branch

screenshot-localhost-2018 10 08-15-50-24

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rbuels commented Oct 8, 2018

oh sweet! code looks good to me so far

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rbuels commented Oct 24, 2018

@cmdcolin you good with me merging this?

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cmdcolin commented Oct 24, 2018

I think it should be ok. Note that I turned off feature type "transcript" automatically being a ProcessedTranscript based on my experience with ncbi gff but I do know that ensembl gff does use transcript for it. Since the addition of transcript being a ProcessedTranscript is sort of recent I don't expect many would rely on that behavior of guessType

@rbuels rbuels added this to the 1.15.5 milestone Oct 26, 2018

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rbuels commented Oct 26, 2018

@cmdcolin ok could you revert that 'transcript' default behavior change as we discussed just now in grooming, then I think it's good to merge

@cmdcolin cmdcolin force-pushed the unprocessed_transcript_glyph branch from d66aa4f to c884b1e Oct 26, 2018

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cmdcolin commented Oct 26, 2018

The 'transcript' type is now back to default and I added some docusaurus documentation :)

@cmdcolin cmdcolin merged commit c4535c6 into dev Oct 26, 2018

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@wafflebot wafflebot bot removed the in progress label Oct 26, 2018

@cmdcolin cmdcolin deleted the unprocessed_transcript_glyph branch Oct 26, 2018

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