Re: [Gmod-ajax] Loading errors for Gene Locus track

[Colin <col...@gm...>]

I'd assert that the track on araport is somehow corrupted. You can see if
you click "View details" on any given feature that it has weird subfeatures
with NaN values.

In this sense, jbrowse is doing it's best here :)

I would just "grep -v" all the lines with NaN before trying to load your
track with flatfile-to-json.

You might also want to perform "delete Array.prototype.values" in the your
javascript console before doing Save track data if you want to fix the
issue of "function() { [values] }" in the exported GFF. Newer jbrowse
versions contain a bugfix for this but older JBrowse versions do not (the
bug was introduced only recently by browsers due to changes in how the
javascript language has evolved over the years...)

-Colin

On Tue, Mar 26, 2019 at 6:05 PM Shabari Subramaniam <sh...@ar...>
wrote:

> Thanks Scott. Here is the link.
>
>
> https://apps.araport.org/jbrowse/?data=arabidopsis&loc=Chr1%3A24330927..24332945&tracks=Araport11_Loci&highlight=
>
> Click on the dropdown on the track label 'Araport11 Gene Locus' and select
> 'Save Track Data'. Then you select 'Whole reference sequence' and  'GFF3'
> as the format option. (Screenshot attached).
>
> Thanks for your help.
>
> Best
> -shabari
>
> On Tue, Mar 26, 2019 at 12:51 PM Scott Cain <sc...@sc...> wrote:
>
>> Hi Shabari,
>>
>> I'm sending this to the JBrowse mailing list too, so others can chime in
>> with suggestions.  The problem is almost certainly with the GFF: it is
>> really screwed up (periods in the type column for all of the child
>> features, NAN for the start coordinates and periods for the end
>> coordinates).  I'd say addressing that will go a long way to fixing any
>> problems. You said you dumped this GFF out of a JBrowse instance.  Can you
>> provide the URL for that instance? Maybe there is something wrong with it.
>>
>> Thanks,
>> Scott
>>
>>
>> On Tue, Mar 26, 2019 at 11:53 AM Shabari Subramaniam <
>> sh...@ar...> wrote:
>>
>>> Hi Scott,
>>> I am getting errors when i try to upload the data from the 'Araport11
>>> Gene Locus' track. I downloaded the data from the Jbrowse track on
>>> Araport11's Jbrowse viewer in gff format. I removed the 'Chr' from the gff
>>> file. The gff file is attached.
>>>
>>> The problem may be the -type is not the right one. The file only has
>>> 'gene' as type so i tried '--type gene' (below) and no type defined. I am
>>> getting the same error (attached). What am i doing wrong? Let me know if
>>> you need access to the machine to check this out.
>>>
>>> [ec2-user@ip-172-31-31-73 JBrowse-1.16.2]$ bin/flatfile-to-json.pl
>>> --gff ./arabidopsis/raw/Araport11\ -\ Gene\ Locus-Chr1-1..30427671.gff3
>>> --tracklabel 'Araport11 Gene Locus' --metadata '{"Source": "Araport11
>>> Release (Jun 2016)", "Description": "Araport11 Protein-coding,
>>> Transposable-element, and Non-coding gene loci", "category": "Araport Data
>>> / Araport11 / Annotation (Jun 2016)"}' --type gene
>>>
>>>
>>> I am not getting this error when i load the 'Araport11 Protein Coding
>>> Genes' track data with --type as exon.
>>>
>>>
>>> Thanks for your help.
>>>
>>> -shabari
>>>
>>> --
>>> ---------------------------------------------------
>>> Sabarinath Subramaniam, Ph.D.
>>> Director of Business Development
>>> Phoenix Bioinformatics
>>> 39221 Paseo Padre Parkway, Ste. J
>>> Fremont, CA 94583, USA
>>> Email: sh...@ar...
>>> SkypeID:  shabarinath
>>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>
>
> --
> ---------------------------------------------------
> Sabarinath Subramaniam, Ph.D.
> Director of Business Development
> Phoenix Bioinformatics
> 39221 Paseo Padre Parkway, Ste. J
> Fremont, CA 94583, USA
> Email: sh...@ar...
> SkypeID:  shabarinath
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