Allow overriding start/stop characters for highlighting in refseq track #657

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erasche commented Nov 18, 2015

Originally only Ms were highlighted, instead of highlighting things which are actually starts. E.g. TTG, even though it is a recognised start codon in table 1, translates to L by default. The built in highlighter was not aware of the distinction and thus didn't highlight it as a possible start codon.

Configuration options are supplied to allow users to override this setting, just like they can with the codonTable setting.

Here I have set "codonStarts": ["AAA"], in my trackList.json file:
snapshot1

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cmdcolin Nov 19, 2015

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This is pretty cool. Alternatively I suppose that you could specify something like this?

.translatedSequence td.aminoAcid_k {
    background-color: #00FF00;
}

I think the javascript config variable solution here is a bit better though

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cmdcolin commented Nov 19, 2015

This is pretty cool. Alternatively I suppose that you could specify something like this?

.translatedSequence td.aminoAcid_k {
    background-color: #00FF00;
}

I think the javascript config variable solution here is a bit better though

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erasche Nov 19, 2015

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I discarded the CSS solution as it doesn't account for cases where only two codons translate to the same amino acid, but only one codes for a start. E.g. TTA vs TTG in table 1 both translate as L, but only TTG is a start.. Otherwise that would've been a much easier to solution, and wouldn't have required touching upstream.

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erasche commented Nov 19, 2015

I discarded the CSS solution as it doesn't account for cases where only two codons translate to the same amino acid, but only one codes for a start. E.g. TTA vs TTG in table 1 both translate as L, but only TTG is a start.. Otherwise that would've been a much easier to solution, and wouldn't have required touching upstream.

Allow overriding start/stop characters for highlighting
Originally only Ms were highlighted, instead of highlighting things which are actually starts.
E.g. TTG, even though it is a recognised start codon in table 1, it translates to L by default.
The built in highlighter was not aware of the distinction and thus didn't highlight it as a possible
start codon.

Configuration options are supplied to allow users to override this setting, just like they can with .
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erasche Dec 4, 2015

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Rebased against master.

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erasche commented Dec 4, 2015

Rebased against master.

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erasche Dec 8, 2015

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Pinging jbrowse devs. Do I need to do anything else for this PR?

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erasche commented Dec 8, 2015

Pinging jbrowse devs. Do I need to do anything else for this PR?

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Looks pretty good to me!

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cmdcolin commented Dec 8, 2015

Looks pretty good to me!

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Who do I ping/email for a merge @cmdcolin? Is there a formal process I need to go through or ... ?

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erasche commented Dec 8, 2015

Who do I ping/email for a merge @cmdcolin? Is there a formal process I need to go through or ... ?

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I think it'll be ok if we go ahead :). It looks like there are no backwards incompatible changes and code looks good.

Thanks for the awesome work btw.

I actually still want to add this type of sequence track back into apollo at some point to make it easy for annotators to spot start/stop codons

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cmdcolin commented Dec 8, 2015

I think it'll be ok if we go ahead :). It looks like there are no backwards incompatible changes and code looks good.

Thanks for the awesome work btw.

I actually still want to add this type of sequence track back into apollo at some point to make it easy for annotators to spot start/stop codons

cmdcolin added a commit that referenced this pull request Dec 8, 2015

Merge pull request #657 from erasche/extra-starts
Allow overriding start/stop characters for highlighting in refseq track

@cmdcolin cmdcolin merged commit bec318c into GMOD:master Dec 8, 2015

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@cmdcolin ah, thanks. :) yeah, I'd love to see this sort of thing back in Apollo. We use table 11 and all my users are used to Artemis' stop/start codon display, so I'd be more than happy to help implement that.

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erasche commented Dec 8, 2015

@cmdcolin ah, thanks. :) yeah, I'd love to see this sort of thing back in Apollo. We use table 11 and all my users are used to Artemis' stop/start codon display, so I'd be more than happy to help implement that.

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yep. oh, also master branch build is broken but not due to this PR...that is due to Bio::SamTools 1.4.2 latest release seems to fail their own tests...

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cmdcolin commented Dec 8, 2015

yep. oh, also master branch build is broken but not due to this PR...that is due to Bio::SamTools 1.4.2 latest release seems to fail their own tests...

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Oh, yikes. Ok, good to know.

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erasche commented Dec 8, 2015

Oh, yikes. Ok, good to know.

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ya. looks like it was released today http://search.cpan.org/~lds/Bio-SamTools/ :)

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cmdcolin commented Dec 8, 2015

ya. looks like it was released today http://search.cpan.org/~lds/Bio-SamTools/ :)

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enuggetry Dec 8, 2015

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Thanks for that, Eric. Made it into the release.

On Tue, Dec 8, 2015 at 11:44 AM, Colin Diesh notifications@github.com
wrote:

ya. looks like it was released today
http://search.cpan.org/~lds/Bio-SamTools/ :)


Reply to this email directly or view it on GitHub
#657 (comment).

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enuggetry commented Dec 8, 2015

Thanks for that, Eric. Made it into the release.

On Tue, Dec 8, 2015 at 11:44 AM, Colin Diesh notifications@github.com
wrote:

ya. looks like it was released today
http://search.cpan.org/~lds/Bio-SamTools/ :)


Reply to this email directly or view it on GitHub
#657 (comment).

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