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  • Feb 26 2018 23:40
    nathandunn synchronize #1235
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    nathandunn on master

    Fix cvTerm and alternateCvTerm … (compare)

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    pinging build (compare)

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Robert Buels
@rbuels
ok done. events in the GMOD/Apollo repo should appear in the sidebar now
Nathan Dunn
@nathandunn
Please!
Yating Liu
@Yating-L
@nathandunn I removed the gene lines from GFF3 and generated GFF3Tabix track. But there are a few CDS do not show. Is this a known issue? Or it has been solved?
Screen Shot 2018-04-05 at 9.57.24 AM.png
Nathan Dunn
@nathandunn
@Yating-L I’m not sure. If the CDS parent is the exon or the gene instead of the mRNA that could be a problem. Mostly it depends on how its created. Can you send your samples before and after?
I’m assuming this is just for the HTML version?
Yating Liu
@Yating-L
HTMLFeatures, yes
Yating Liu
@Yating-L
@nathandunn here are the gene prediction output file, before and after filtering gene lines
Nathan Dunn
@nathandunn
@Yating-L there are no exons (which is fine). Are you saying that it is not showing some of the specified CDS’s?
Robert Buels
@rbuels
@nathandunn is this the use case you're working on in your gff3tabix pull req so that it works out of the box?
Nathan Dunn
@nathandunn
@rbuels I thiknk so
Yating Liu
@Yating-L
@nathandunn yes, some CDSs are not showing
Nathan Dunn
@nathandunn
@Yating-L this is with the HTMLFeatures?
I’m guess it is
so, the answer to your question is yes @rbuels
Yating Liu
@Yating-L
@nathandunn I think so. I tested on two GFF3. Canvas renders correctly
but HTML missing some subfeatures
Robert Buels
@rbuels
which data store were both tests using? GFF3Tabix?
Yating Liu
@Yating-L
"JBrowse/Store/SeqFeature/GFF3Tabix"
Nathan Dunn
@nathandunn
yeah, they both use the same store. The difference is when the Canvas redners, they just render one on top of another and it works. With HTMLFeatures, you can’t do that with divs and so it blocks the other one out
Yating Liu
@Yating-L
is this solvable?
Robert Buels
@rbuels
is there a reason that you guys can't just use canvasfeatures? i've been hoping since 2013 to deprecate htmlfeatures
is it cause of apollo needing to drag the features around
Nathan Dunn
@nathandunn
@rbuels Part of it is dragging the features, an important feature of Apollo. The other reason is highlighting edges.
Nathan Dunn
@nathandunn
I guess the two questions are: @Yating-L can you use the JSON version? and @rbuels how much work would it be to fix the HTMLFeatures?
Robert Buels
@rbuels
i'm going to work on fixing the htmlfeatures, cause it is already on the 1.14.0 milestone
Nathan Dunn
@nathandunn
A couple of reasons to fix it as well: (1) the more users we have using GFF3Tabix, the fewer users we’ll have to transition with the newer JBrowse, and (2) handling the JBrowse JSON files has been problematic because of the large number of files versus tabix
@rbuels . . .. looking for proper emojis
:fire: :clap: :sparkles:
:rocket:
@rbuels Do you have colin and my half-working attempts?
not sure if they would be helpful or not
Yating Liu
@Yating-L
@nathandunn we want to use tabix because we want to upload jbrowse to CyVerse Data Store. JSON version generates too many files, which takes too long to upload
Nathan Dunn
@nathandunn
thanks @Yating-L . . @rbuels , who is much more capable than I, is going to work on this. Thank you very much @rbuels
Yating Liu
@Yating-L
And HTMLFeatures is useful for our team because they want the dragging features and highlight edge features
Robert Buels
@rbuels
@nathandunn do you have everything in your pull requests?
if not, just tell me what other branches there are and I'll take care of weaving them all together
@nathandunn the only one i see so far is GMOD/jbrowse#996
@Yating-L could you send me the reference sequence that go with those augustus gff3s? i will use those as test data to make sure they display well
using htmlfeatures
or link them here
Yating Liu
@Yating-L
Let me make a folder
Yating Liu
@Yating-L
@rbuels
Thanks a lot!
Scott Cain
@scottcain
I get the appeal of having a single tabix file for a track, but it isn’t clear to me why having hundreds of json files is a problem. Just run rsync (or the equiv for the cloud platform of choice) and all of the files go in place. I do this regularly with JBrowse tracks that are run off of Amazon’s S3 service. It takes a few minutes to do the upload (since it’s transering lots of small files) but once it’s done I never have to think about it again.
Yating Liu
@Yating-L
do you mean download from S3?
how long does it usually take for running rsync? It took me days… @scottcain