terminators update

[nathandunn]

• add sprite for termintator

  • create terminator features with a strand
  • return terminator features with a strand
  • make sure that it returns features with that strand in place

• disallow changing terminator types

• fix width of popup

• remove menu options

• remove server calls

  • fix REST calls

[nathandunn]

Quick question: @jasonjgill / @meiliuCPT / @jrr-cpt

I am assuming that you are wanting to associate a terminator with multiple isoforms?

I have a few questions:

1 - is the relationship to that isoform always going to be the same (I would assume so)., or are there other properties you might try to annotate?
1a - our default relationship between features (isoform being parent and terminator being the child) is part_of . . I'm hoping that is sufficient, but if there is a better SO / GO definition, that is okay.
2 - do you have a png associated with this?

[nathandunn]

3 - should a lookup of "near" isoforms be provided? Say, less than 100 bp (or pick a number)?

[nathandunn]

This is roughly what I'm envisioning, but not sure if its overkill or not. The icons for the terminator might need to be added, as well.

@jasonjgill / @meiliuCPT / @jrr-cpt is this roughly what you were envisioning?

(removed)

[nathandunn]

Sorry, the single entry for transcript should not be there.

The new section would be the "associated transcripts" section, which would be autofilled with upstream isoforms.

[nathandunn]

4 - Would you ever have a set of isoforms for a single gene where some mRNA would correspond to the terminator and some would not or would it always be safe to associate a terminator to all mRNA for a gene?

[nathandunn]

Won't need association data at this point. So, we can get rid of a lot of the association stuff and add the png and be done.

[jasonjgill]

Here is our proposed glyph for transcriptional terminators. Jason. *From:* Nathan Dunn <[email protected]> *Sent:* Friday, January 11, 2019 3:01 PM *To:* GMOD/Apollo <[email protected]> *Cc:* jasonjgill <[email protected]>; Mention <[email protected]> *Subject:* Re: [GMOD/Apollo] terminators should be able to be associated with an mRNA (#1990) Won't need association data at this point. So, we can get rid of a lot of the association stuff and add the png and be done. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_GMOD_Apollo_issues_1990-23issuecomment-2D453654960&d=DwMCaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=ZLRJ7TVhWeImQv2EgrUXoAw_ODAXXUpaAexqogSeRek&m=7OMnFMJz1N5HD8bbdS6nUgcO1-CLEb_dlfoY7vxgde0&s=Gh4lxwZd3Fxa4eklmRQkBAmO_0H-XaU9p0k58FKo8bA&e=>, or mute the thread <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ApBYTj-5FnmGVGmethSRZjdlyR-5FHZyXvdWks5vCPt9gaJpZM4ZUUFl&d=DwMCaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=ZLRJ7TVhWeImQv2EgrUXoAw_ODAXXUpaAexqogSeRek&m=7OMnFMJz1N5HD8bbdS6nUgcO1-CLEb_dlfoY7vxgde0&s=AorhwUZlB9R5-hlPdkCkNw0g3rJyhWyCUvHkBwnNc_E&e=> .

[jasonjgill]

here is our proposed glyph for transcriptional terminators.

since terminators are directional, the glyph should have the ball on top for terminators pointing rightwards (i.e., on the top strand) and be upside-down for terminators on the bottom strand.

[nathandunn]

• add termintator sprint for 16x16 (or close) (should work for data around 200-150 bp)
• add a negative terminator flipped over

Resize command:

convert terminator.png -resize 16.x16 terminator16.png

Not sure how to sure how to use convert to do this, but can pull into another program to do the same http:https://www.imagemagick.org/Usage/resize/#resample

[nathandunn]

@jasonjgill Will the width of a terminator typically be 10-50 bps?

[nathandunn]

Or are you counting the hairpin, etc. (200+ bp) or just a single point for the terminator (at the start for instance)?

Also, if you are going to have an icon and a block, do you want the icon at the downstream end of the block or the upstream?

[jasonjgill]

We annotate these terminators as the hairpin plus the poly-T tail, so the features are usually around 20-25 bp long. I guess it makes the most sense for the glyph to be at the downstream (3') end of the feature,

[nathandunn]

Sprint added successfully. Having trouble detecting strand on this.

[nathandunn]

Adding notes to the top

[jasonjgill]

What is the problem with detecting strand? The tool should assign the terminator to base coordinates and a strand...

[nathandunn]

Its just a problem in the code as its typically used to annotate straddles features. This is a reminder for me for next week. It should be pretty fixable.

…

On Jan 19, 2019, at 7:47 AM, jasonjgill ***@***.***> wrote: What is the problem with detecting strand? The tool should assign the terminator to base coordinates and a strand... — You are receiving this because you were assigned. Reply to this email directly, view it on GitHub <#1990 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAt2qs62PJ2QGYrNBjy7qfIH3DQEEd2wks5vEz4ggaJpZM4ZUUFl>.

[nathandunn]

I'm not going to be able flip the widget as far as I can tell, but I think this is fairly straight-forward, still.

[nathandunn]

• strand on the left, and negative strand on the right

[nathandunn]

the other mode I has was this, but I like itless.:

[nathandunn]

I'm not going to be able flip the widget as far as I can tell, but I think this is fairly straight-forward, still.

[nathandunn]

@jasonjgill I'm going to merge this in for completeness, but we can make changes later as needed.

[jasonjgill]

OK. If it's going to be like an end cap on the feature, maybe I could get rid of the stick in the glyph?

[nathandunn]

@jasonjgill They're pretty easy for me to update in preview (if I understood you correctly).

I think this looks much better this way. Let me know.

[jasonjgill]

That's perfect, thanks!