GMOD/jbrowse

JBrowse 1 maintenance and issues

Andrew Duncan

@agduncan94

I'm thinking the calls to undefined might be caused by that console log

Warren Francis

@wrf

yeah I can now see the feature

Andrew Duncan

@agduncan94

are you able to find the 'same_sense' field?

Warren Francis

@wrf

I see the value, but there is no name tag with it

the "Parent" menu has 14 items, and its buried in those with the other things I gave it

like accession= and description=

should it be something like feature.get(parent.same_sense)?

Andrew Duncan

@agduncan94

that could work if same_sense is directly within the parent

Warren Francis

@wrf

what is the right syntax for that?

this is definitely not it:
feature.get('parent').get('same_sense')==0

Andrew Duncan

@agduncan94

I think the get is a custom function and not the typical javascript one for objects, I think it might be something more like feature.get('parent')['same_sense']

So feature.get('parent') grabs the object, and then ['same_sense'] grabs the value for the key same_sense in the object

Warren Francis

@wrf

it is the 7th item in the array, could I also use [7] ?

Andrew Duncan

@agduncan94

I think it is 0 index, so the 7th item would be 6. However I don't know think there is any sorting for javascript objects so you cannot be sure that it is always in the 7th spot

Warren Francis

@wrf

so feature.get('parent') should return an array?

Andrew Duncan

@agduncan94

I'm not sure. The [] notation works for objects as well, you could also do feature.get('parent).same_sense I think

Helena Rasche

@erasche

https://ebi-webcomponents.github.io/nightingale/#/ is being presented now at BioHackathon, might be interesting for some folks here

Andrew Duncan

@agduncan94

@wrf are you able to send the parent object?

Warren Francis

@wrf

feature.get('parent')['same_sense'] does not seem to work, the track does not load

what do you mean send the parent object?

Andrew Duncan

@agduncan94

like the object being printed to the firefox console from the console.log(feature) line

Warren Francis

@wrf

console.log(feature.get('Parent')) seems to make an error

Andrew Duncan

@agduncan94

Looking at the JBrowse code, it looks like the get function does something like return this.data[ name.toLowerCase() ];

so that explains why that doesn't work

Warren Francis

@wrf

console.log(this.feature.get('parent')); return feature.get('parent')==1 ?'#253494' : '#fe6f4f'; makes all features the "else" color" and does not display anything in the log

here is what the features show in the console:

(8) […]

0: 1

1: 8114035

2: 8114122

3: -1

4: 76.3

5: "scaffold_0013"

6: "blastx"

7: "match_part"

_parent: (14) […]

0: 0

1: 8114035

2: 8115179

3: -1

4: "Q3E7K8"

5: "Polyubiquitin 12"

6: "Em_i100k_d5.18488.5.UBQ12_ARATH.76"

7: "0"

8: 76.3

9: "scaffold_0013"

10: "blastx"

11: Array [ (8) […], (8) […] ]

12: "UBQ12_ARATH 153 224 -"

13: "protein_match"

_parent: undefined

_uniqueID: "30,15"

that 7:"0" is the one I want

Andrew Duncan

@agduncan94

this is what is returned by console.log(feature) ?

Warren Francis

@wrf

yes, it goes on further, but those are the relevant lines it appears

in another one, it has 7:"1"

Andrew Duncan

@agduncan94

Ok I think I'm understanding more now. Since it is an NClist it doesn't seem to work the same way as the tracks I've worked with. Can you change the console log to console.log(feature._parent) and see if it prints out the parent

If so I think feature._parent[7] may get the feature you want

Warren Francis

@wrf

yep, I'm seeing it now

return feature._parent.get('same_sense')==1 ?'#253494' : '#fe6f4f'; }" works totally correct

thanks heaps for your help!

Andrew Duncan

@agduncan94

awesome :)

no problem

Warren Francis

@wrf

the whole idea was to view transcripts that had antisense protein matches, which was probably an indicator of transcripts that were fused in the UTRs

now it's much easier to find

thanks again

Scott Cain

@scottcain

Is there a style config option for adjusting the height of the connector in Alignment2 tracks? I don’t see anything in the documentation, but I haven’t dived into the code either :-)

Scott Cain

@scottcain

I would have thought connectorThickness would change the connector thickness in Alignments2 but it does not appear to have any effect.

Colin Diesh

@cmdcolin

thats hardcoded i think

could make it use connectorThickness probably tho

code here https://github.com/GMOD/jbrowse/blob/master/src/JBrowse/View/FeatureGlyph/Alignment.js#L134

Scott Cain

@scottcain

That explains why I couldn’t find it, as it’s not explicit (I have been reading code for a little while trying to figure out where it was set). No rush to change it, as it’s a pretty minor aesthetic change.

Scott Cain

@scottcain

I have no idea who this guy is (I think he might be an undergrad at Texas A&M) but in this twitter thread, he mentions JBrowse, posts a picture of a screenshot that mentions Chado and Sybil (GMOD synteny viewer) and a video where Galaxy is on a screen. He’s like a GMOD poster child. https://twitter.com/jackmharlan/status/1176925846277410818

Robert Buels

@rbuels

@scottcain what are the top GBrowse Syn instances out there

Scott Cain

@scottcain

WormBase. That’s the only one I can think of at the moment: https://wormbase.org/tools/synteny/mercator/
I’ll ask around to see if I can stir up any more.

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