gmod-ajax — JBrowse list

Re: [Gmod-ajax] minimal gff

[Mitch S. <mit...@be...>]

Giles Velarde wrote:
> Speaking of which, I ran into another performance issue, this time 
> inside prepare-refseqs.pl. It has to do with preparing refseqs for 
> several 1000s of GFF files. When I looked into it I saw that the 
> refSeqs.js was being opened, parsed, appended to, and closed for every 
> GFF. As this file got larger this opening and appending step got more 
> expensive.
>
> I submit a patch that fixes it for me.

The patch looks good to me; I was just about to apply it, but I wanted 
to ask some questions first.

How are your GFF files organized?  Do you have a GFF file per organism, 
per refseq, or something else?  How many organisms do you have, and how 
many refseqs do they have?  Do your JBrowse instances have sequence data?

If you're using GFF files with prepare-refseqs.pl then one option is to 
create one GFF file per organism with all of the sequence-region lines 
in it (and nothing else).  Running prepare-refseqs.pl on that file 
should be pretty fast.

Did you write that patch before you started making per-organism JBrowse 
instances?

> I must say I have had to continually fight the temptation to cut 
> through the middleman and just generate the JSons directly! So, I do 
> indeed see advantages in your suggestion. Of course, you would need to 
> defensively validate other people's SQL results, which is never fun. 
> Alternatively, a simple abstracted/documented programmatic API for 
> generating the JSON might be a good way, e.g. :
>
> my $jbrowse = new JBrowseConfig ( $jsonConfigurations );
> my $track = $jbrowse->addTrack({ name => "contig01", etc. } );
>
> foreach my $feature ($myCustomFeatureImplementationList)
> {
>     $jbrowse->addFeature( $feature->toJSon() );
> }
>
> $jbrowse->generate_refseqs();
> $jbrowse->generate_jsons();
> $jbrowse->generate_names();
>
> Looking at the bin scripts, you're nearly there right now.

A simple API for generating the JSON has been the goal, but yeah, it 
should probably be simpler/documented.  If anyone is interested in using 
that API, feel free to speak up about your use case and how you want the 
API to work.

Regards,
Mitch

Re: [Gmod-ajax] Change shebang

[Mitch S. <mit...@be...>]

Martin A. Hansen wrote:
> generate-json.pl <http://generate-json.pl>
> generate-names.pl <http://generate-names.pl>
> gff-to-json.pl <http://gff-to-json.pl>
> prepare-refseqs.pl <http://prepare-refseqs.pl>
>
> all have a hardcoded path to #!/usr/bin/perl which means that the 
> scripts will run on the system's perl and not on my locally installed 
> perl - which has the required Bioperl installed.
>
> Please consider changing the shebang to #!/usr/bin/env perl

Done.

http://github.com/jbrowse/jbrowse/commit/79ab79e07be80e480d1d20609813226cc1655131

Also, you appear to have an old version of JBrowse; the names of the 
scripts in the bin/ directory changed a while back.  Did you download it 
recently?  If so, from where?

Regards,
Mitch

[Gmod-ajax] More regarding letters of support for JBrowse/GMOD helpdesk grant

[Ian H. <ih...@be...>]

Hi all,

Here are a few details related to our request for letters of support for
the JBrowse renewal:

1. The title of the proposal is "Enhancing the GBrowse Genome Annotation
Browser".

2. The main aims of the grant are
-- to support the GMOD help desk
-- to develop the main core of JBrowse
-- to develop tools for migrating GBrowse to JBrowse
-- to develop JBrowse_syn, a JBrowse-based synteny browser

3. The co-PIs are Lincoln Stein, Todd Vision, Sheldon McKay & myself;
key personnel include Dave Clements (GMOD helpdesk) & Mitch Skinner
(JBrowse)

4. The preferred format for support letters is PDF (or image) with
signature. Please email directly to me <ih...@be...>

5. We need the letters ideally this week.

Thanks!
Ian

Re: [Gmod-ajax] Loading GFF trouble

[Shankar A. S. <sha...@gm...>]

Hi Martin,

I've had similar issues when using flatfile-to-json.pl. I have since
switched to using biodb-to-json.pl with a conf file to load features.
If you add "Name=" key value pairs to your feature attributes, these
will be displayed as labels under your feature (see demo).
You will also find that the full chromosome-length feature, and 7
seven others, disappear when you use biodb-to-json.pl

Shankar

On Mon, Oct 19, 2009 at 7:52 AM, Martin A. Hansen <ma...@ma...> wrote:
> Right, that did the trick.
>
> But clicking on a feature shows ID undefined? and strand is shown as either
> 1 or -1.
>
> Also, I have a feature that is full chromosome length (2.8M) and 7 that are
> 0.5M. Strange?
>
>
>
>
> Martin
>
> On Mon, Oct 19, 2009 at 1:27 PM, Colin Davenport <col...@ho...>
> wrote:
>>
>> Hi Martin,
>>
>> I had a similar problem.
>>
>> I think this should help : you need to modify the GFF header
>> and add a line
>>
>> ##sequence-region scf1117875581239 1 719819
>>
>> Source was this tutorial
>>
>> http://gmod.org/wiki/JBrowse_Tutorial#Moving_work_to_the_client
>>
>> Hope that helps
>>
>> Colin
>>
>>
>>
>>
>>
>> ________________________________
>> Date: Mon, 19 Oct 2009 12:33:24 +0200
>> From: ma...@ma...
>> To: gmo...@li...
>> Subject: [Gmod-ajax] Loading GFF trouble
>>
>> Hello,
>>
>>
>> I am trying to visualize some Bowtie hits of small sequences mapped to a
>> bacterial genome.
>>
>> I have Apache and Jbrowse up and running.
>>
>> I have loaded the genome sequence using prepare-refseqs.pl from the www
>> root - and it is visible in Jbrowse.
>>
>> Now, loading some GFF3 data gives trouble:
>>
>> bin/flatfile-to-json.pl -gff /Users/maasha/DATA/Assembly/foo.gff
>> --tracklabel test1 --key 'human readable test'
>>
>> working on seq S.aur_COL
>> Didn't find a segment with name S.aur_COL
>> Use of uninitialized value in string eq at bin/flatfile-to-json.pl line
>> 178, <GEN2> line 24.
>>
>>
>> The GFF data looks like this (may be malformatted?):
>>
>> ##gff-version 3
>> S.aur_COL       BOWTIE  .       2474533 2474567 1       +       .
>> ID=5_BWCOjxwXsN1/1
>> S.aur_COL       BOWTIE  .       1980530 1980564 3       +       .
>> ID=7_NZCOjxwXsN1/1
>> S.aur_COL       BOWTIE  .       2115669 2115703 3       +       .
>> ID=7_NZCOjxwXsN1/1
>> S.aur_COL       BOWTIE  .       2232159 2232193 3       +       .
>> ID=7_NZCOjxwXsN1/1
>> S.aur_COL       BOWTIE  .       530658  530692  3       -       .
>> ID=7_NZCOjxwXsN1/1
>> S.aur_COL       BOWTIE  .       574288  574322  3       -       .
>> ID=7_NZCOjxwXsN1/1
>> S.aur_COL       BOWTIE  .       579500  579534  3       -       .
>> ID=7_NZCOjxwXsN1/1
>> S.aur_COL       BOWTIE  .       2721172 2721206 1       +       .
>> ID=3_2VCOjxwXsN1/1
>> S.aur_COL       BOWTIE  .       575753  575787  3       +       .
>> ID=1_GbCOjxwXsN1/1
>>
>>
>> refseq.js looks like this:
>>
>>
>> refSeqs =
>> [
>>    {
>>       "length" : 2809422,
>>       "name" : "S.aur_COL",
>>       "seqDir" : "data/seq/S.aur_COL",
>>       "start" : 0,
>>       "end" : 2809422,
>>       "seqChunkSize" : 20000
>>    }
>> ]
>>
>> I cannot tell what version or revision my Jbrowse installation is (how do
>> I find out?).
>>
>> So what is this segment error? And how do I resolve it?
>>
>>
>>
>> Cheers,
>>
>>
>>
>> Martin
>>
>>
>> ________________________________
>> So gehst du mir nicht vor die Tür! Herbsttrends entdecken
>
> ------------------------------------------------------------------------------
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> is the only developer event you need to attend this year. Jumpstart your
> developing skills, take BlackBerry mobile applications to market and stay
> ahead of the curve. Join us from November 9 - 12, 2009. Register now!
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>

[Gmod-ajax] Out-of-memory crash

[Martin A. H. <ma...@ma...>]

I was trying to upload 2.3M features from a GFF file and Perl crashed out:

perl(1734) malloc: *** mmap(size=16777216) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
Out of memory!

So Jbrowse doesn't handle tracks with a bit of data?




Martin

Re: [Gmod-ajax] Loading GFF trouble

[Martin A. H. <ma...@ma...>]

Right, that did the trick.

But clicking on a feature shows ID undefined? and strand is shown as either
1 or -1.

Also, I have a feature that is full chromosome length (2.8M) and 7 that are
0.5M. Strange?




Martin

On Mon, Oct 19, 2009 at 1:27 PM, Colin Davenport <col...@ho...>wrote:

>  Hi Martin,
>
> I had a similar problem.
>
> I think this should help : you need to modify the GFF header
> and add a line
>
> ##sequence-region scf1117875581239 1 719819
>
> Source was this tutorial
>
> http://gmod.org/wiki/JBrowse_Tutorial#Moving_work_to_the_client
>
> Hope that helps
>
> Colin
>
>
>
>
>
> ------------------------------
> Date: Mon, 19 Oct 2009 12:33:24 +0200
> From: ma...@ma...
> To: gmo...@li...
> Subject: [Gmod-ajax] Loading GFF trouble
>
>
> Hello,
>
>
> I am trying to visualize some Bowtie hits of small sequences mapped to a
> bacterial genome.
>
> I have Apache and Jbrowse up and running.
>
> I have loaded the genome sequence using prepare-refseqs.pl from the www
> root - and it is visible in Jbrowse.
>
> Now, loading some GFF3 data gives trouble:
>
> bin/flatfile-to-json.pl -gff /Users/maasha/DATA/Assembly/foo.gff
> --tracklabel test1 --key 'human readable test'
>
> working on seq S.aur_COL
> Didn't find a segment with name S.aur_COL
> Use of uninitialized value in string eq at bin/flatfile-to-json.pl line
> 178, <GEN2> line 24.
>
>
> The GFF data looks like this (may be malformatted?):
>
> ##gff-version 3
> S.aur_COL       BOWTIE  .       2474533 2474567 1       +       .
> ID=5_BWCOjxwXsN1/1
> S.aur_COL       BOWTIE  .       1980530 1980564 3       +       .
> ID=7_NZCOjxwXsN1/1
> S.aur_COL       BOWTIE  .       2115669 2115703 3       +       .
> ID=7_NZCOjxwXsN1/1
> S.aur_COL       BOWTIE  .       2232159 2232193 3       +       .
> ID=7_NZCOjxwXsN1/1
> S.aur_COL       BOWTIE  .       530658  530692  3       -       .
> ID=7_NZCOjxwXsN1/1
> S.aur_COL       BOWTIE  .       574288  574322  3       -       .
> ID=7_NZCOjxwXsN1/1
> S.aur_COL       BOWTIE  .       579500  579534  3       -       .
> ID=7_NZCOjxwXsN1/1
> S.aur_COL       BOWTIE  .       2721172 2721206 1       +       .
> ID=3_2VCOjxwXsN1/1
> S.aur_COL       BOWTIE  .       575753  575787  3       +       .
> ID=1_GbCOjxwXsN1/1
>
>
> refseq.js looks like this:
>
>
> refSeqs =
> [
>    {
>       "length" : 2809422,
>       "name" : "S.aur_COL",
>       "seqDir" : "data/seq/S.aur_COL",
>       "start" : 0,
>       "end" : 2809422,
>       "seqChunkSize" : 20000
>    }
> ]
>
> I cannot tell what version or revision my Jbrowse installation is (how do I
> find out?).
>
> So what is this segment error? And how do I resolve it?
>
>
>
> Cheers,
>
>
>
> Martin
>
>
> ------------------------------
> So gehst du mir nicht vor die Tür! Herbsttrends entdecken<http://redirect.gimas.net/?n=M0910Herbstmode_WW>
>

Re: [Gmod-ajax] Loading GFF trouble

[Colin D. <col...@ho...>]

Hi Martin,

I had a similar problem.

I think this should help : you need to modify the GFF header
and add a line
##sequence-region scf1117875581239 1 719819
Source was this tutorial

http://gmod.org/wiki/JBrowse_Tutorial#Moving_work_to_the_client

Hope that helps

Colin





Date: Mon, 19 Oct 2009 12:33:24 +0200
From: ma...@ma...
To: gmo...@li...
Subject: [Gmod-ajax] Loading GFF trouble

Hello,


I am trying to visualize some Bowtie hits of small sequences mapped to a bacterial genome.

I have Apache and Jbrowse up and running.

I have loaded the genome sequence using prepare-refseqs.pl from the www root - and it is visible in Jbrowse.


Now, loading some GFF3 data gives trouble:

bin/flatfile-to-json.pl -gff /Users/maasha/DATA/Assembly/foo.gff --tracklabel test1 --key 'human readable test'
working on seq S.aur_COLDidn't find a segment with name S.aur_COL
Use of uninitialized value in string eq at bin/flatfile-to-json.pl line 178, <GEN2> line 24.


The GFF data looks like this (may be malformatted?):


##gff-version 3S.aur_COL       BOWTIE  .       2474533 2474567 1       +       .       ID=5_BWCOjxwXsN1/1
S.aur_COL       BOWTIE  .       1980530 1980564 3       +       .       ID=7_NZCOjxwXsN1/1S.aur_COL       BOWTIE  .       2115669 2115703 3       +       .       ID=7_NZCOjxwXsN1/1
S.aur_COL       BOWTIE  .       2232159 2232193 3       +       .       ID=7_NZCOjxwXsN1/1S.aur_COL       BOWTIE  .       530658  530692  3       -       .       ID=7_NZCOjxwXsN1/1
S.aur_COL       BOWTIE  .       574288  574322  3       -       .       ID=7_NZCOjxwXsN1/1S.aur_COL       BOWTIE  .       579500  579534  3       -       .       ID=7_NZCOjxwXsN1/1
S.aur_COL       BOWTIE  .       2721172 2721206 1       +       .       ID=3_2VCOjxwXsN1/1S.aur_COL       BOWTIE  .       575753  575787  3       +       .       ID=1_GbCOjxwXsN1/1


refseq.js looks like this:


refSeqs = [
   {      "length" : 2809422,
      "name" : "S.aur_COL",      "seqDir" : "data/seq/S.aur_COL",
      "start" : 0,      "end" : 2809422,
      "seqChunkSize" : 20000   }
]
I cannot tell what version or revision my Jbrowse installation is (how do I find out?).

So what is this segment error? And how do I resolve it?




Cheers,



Martin

 		 	   		  
_________________________________________________________________
http://redirect.gimas.net/?n=M0910xHerbstmode2_WW
So gehst du mir nicht vor die Tür! Herbsttrends entdecken

[Gmod-ajax] Loading GFF trouble

[Martin A. H. <ma...@ma...>]

Hello,


I am trying to visualize some Bowtie hits of small sequences mapped to a
bacterial genome.

I have Apache and Jbrowse up and running.

I have loaded the genome sequence using prepare-refseqs.pl from the www root
- and it is visible in Jbrowse.

Now, loading some GFF3 data gives trouble:

bin/flatfile-to-json.pl -gff /Users/maasha/DATA/Assembly/foo.gff
--tracklabel test1 --key 'human readable test'

working on seq S.aur_COL
Didn't find a segment with name S.aur_COL
Use of uninitialized value in string eq at bin/flatfile-to-json.pl line 178,
<GEN2> line 24.


The GFF data looks like this (may be malformatted?):

##gff-version 3
S.aur_COL       BOWTIE  .       2474533 2474567 1       +       .
ID=5_BWCOjxwXsN1/1
S.aur_COL       BOWTIE  .       1980530 1980564 3       +       .
ID=7_NZCOjxwXsN1/1
S.aur_COL       BOWTIE  .       2115669 2115703 3       +       .
ID=7_NZCOjxwXsN1/1
S.aur_COL       BOWTIE  .       2232159 2232193 3       +       .
ID=7_NZCOjxwXsN1/1
S.aur_COL       BOWTIE  .       530658  530692  3       -       .
ID=7_NZCOjxwXsN1/1
S.aur_COL       BOWTIE  .       574288  574322  3       -       .
ID=7_NZCOjxwXsN1/1
S.aur_COL       BOWTIE  .       579500  579534  3       -       .
ID=7_NZCOjxwXsN1/1
S.aur_COL       BOWTIE  .       2721172 2721206 1       +       .
ID=3_2VCOjxwXsN1/1
S.aur_COL       BOWTIE  .       575753  575787  3       +       .
ID=1_GbCOjxwXsN1/1


refseq.js looks like this:


refSeqs =
[
   {
      "length" : 2809422,
      "name" : "S.aur_COL",
      "seqDir" : "data/seq/S.aur_COL",
      "start" : 0,
      "end" : 2809422,
      "seqChunkSize" : 20000
   }
]

I cannot tell what version or revision my Jbrowse installation is (how do I
find out?).

So what is this segment error? And how do I resolve it?



Cheers,



Martin

Re: [Gmod-ajax] minimal gff

[Giles V. <gv...@sa...>]

Apologies for the boilerplate that got inserted in the middle of my  
last email, which is where I dragged the attachment into.
Regards,
Giles

On 18 Oct 2009, at 16:47, Giles Velarde wrote:

>
> On 16 Oct 2009, at 04:45, Mitch Skinner wrote:
>
>> I was talking about this thread:
>>
>> http://www.nabble.com/getting-JBrowse-to-run-off-a-Chado-database-where-feature.name-field-is-not-used-td25491225.html
>>
>> That thread ended a little inconclusively, I thought; Scott had  
>> suggested a database change ("set feature.name =  
>> feature.uniquename") and then Giles started working on genedb->gff- 
>> >jbrowse rather than straight genedb->jbrowse.
>
>
> Mitch, Scott,
>
> Many thanks for looking into this.
>
> Yes, sorry about not ending that thread. Mitch summed it up quite  
> well. I did modify try the modifications as you suggested, Scott,  
> and this did get the script to go a bit further, but then it got  
> stuck somewhere a little further down the line. At the same time we  
> are developing considerable infrastructure around GFF, and so  
> decided to look at that too, and this yielded tangible results more  
> easily.
>
> Scott, thanks for you offer to look into it. It doesn't look like  
> we'll need to be using that adapter for now, mainly because the GFF  
> middle-ware approach is working fine for us and producing all those  
> auto-exported GFF files can have other unforeseen uses. But if  
> you're keen on expanding the scope of the adapter, I could point you  
> to our public read-only snapshot for further testing and would be  
> happy to help you with it.
>
>
>> And then performance became an issue; it sounds like Giles solved  
>> it in his case, but in general I hope to avoid making people do as  
>> much work as he has done.
>>
>
> Speaking of which, I ran into another performance issue, this time  
> inside prepare-refseqs.pl. It has to do with preparing refseqs for  
> several 1000s of GFF files. When I looked into it I saw that the  
> refSeqs.js was being opened, parsed, appended to, and closed for  
> every GFF. As this file got larger this opening and appending step  
> got more expensive.
>
> I submit a patch that fixes it for me.
>
> -- 
> The Wellcome Trust Sanger Institute is operated by Genome  
> ResearchLimited, a charity registered in England with number 1021457  
> and acompany registered in England with number 2742969, whose  
> registeredoffice is 215 Euston Road, London, NW1 2BE.
> <0001-quick-fix-to-help-generate-larger-refseqs.patch>In order not  
> to change any original functionality, I have added a couple of new  
> parameters:
>
> -gffs, which allows you to supply a comma-separated list of files
> -gfffolder, which allows you to supply a folder with gff files in  
> there (it does not check to see if they really are GFFs)
>
> This allows prepare-refseqs.pl to process more than one GFF file at  
> once, which was a serious bottleneck for me. As before, I am not  
> expecting you to necessarily apply the patch. It's just for you to  
> see how I got around the problem. I am sure you can come up with a  
> more elegant way! :-)
>
>
>
> Oh, and another optimization I have had to do is deploy an instance  
> of JBrowse per organism. biodb-to-json.pl seems to fall over when  
> the refseqs file gets too large. This happens to help keep the  
> chromosome/contig-picking drop-down box populated with a sensible  
> amount of choices, and it seems to make sense to me to have a  
> separate page per organism.
>
>
>> Part of the reason I was thinking about having an sql-to-json.pl  
>> (that would take an sql query as a parameter) is this site-specific  
>> variation in chado usage.  I'm not sure how much of it there is,  
>> though.
>>
>> Other reasons were:
>> * allowing other kinds of queries than the ones supported by  
>> Bio::DasI
>> * not having to write Bio::DB::Das::UCSC (unless someone has  
>> already written this?)
>> * not having the bio object intermediate (when I profiled a BED- 
>> >json conversion, the biggest CPU user was  
>> Bio::Root::RootI::_rearrange)
>>
>
> I must say I have had to continually fight the temptation to cut  
> through the middleman and just generate the JSons directly! So, I do  
> indeed see advantages in your suggestion. Of course, you would need  
> to defensively validate other people's SQL results, which is never  
> fun. Alternatively, a simple abstracted/documented programmatic API  
> for generating the JSON might be a good way, e.g. :
>
> my $jbrowse = new JBrowseConfig ( $jsonConfigurations );
> my $track = $jbrowse->addTrack({ name => "contig01", etc. } );
>
> foreach my $feature ($myCustomFeatureImplementationList)
> {
> 	$jbrowse->addFeature( $feature->toJSon() );
> }
>
> $jbrowse->generate_refseqs();
> $jbrowse->generate_jsons();
> $jbrowse->generate_names();
>
> Looking at the bin scripts, you're nearly there right now.
>
>
>> On the other hand, you could argue (as Chris Mungall did to me  
>> today) that it would be better to work on improving the middleware  
>> rather than trying to avoid it.  And then there's the reasons that  
>> people have wanted middleware in the past (not writing m*n mappings  
>> between m data sources and n consumers, but m+n mappings to/from  
>> the middleware).  I think that would be an interesting discussion  
>> to have; each of those m*n mappings can be simpler than the  
>> mappings to and from the middleware, and also take advantage of  
>> unique features of the source and destination.
>>
>
> If by middleware, if this includes parsing formats like GFF, then I  
> would tend to agree with him. It's easier for me to justify my time  
> developing around standards, because of the potential for reuse. The  
> minimal GFF really does seem like a good solution for us: they're  
> still valid files, and they take an order of magnitude's less time  
> to produce (because we have so much annotation in our db).
>
> Thanks again, guys. I really appreciate you're willingness to help.  
> In our particular case we have some rather phenomenal scaling  
> issues, so it was never going to be easy, so rest assured I'll be in  
> touch again if/when I run into more interesting eventualities.
>
> Kind Regards,
> Giles
>
>> Mitch
>>
>> Scott Cain wrote:
>>> Hi Mitch and Giles,
>>>
>>> I must have missed the conversation about Bio::DB::Das::Chado; what
>>> were the nature of the problems?  I can't say I'm terribly surprised
>>> that there were problems, since GeneDB has been using Chado for a  
>>> long
>>> time and so Chado and the gbrowse adaptor have no doubt evolved away
>>> from the way GeneDB is using it.
>>>
>>> Anyway, is there anything I can do?
>>>
>>> Scott
>>>
>>>
>>> On Thu, Oct 15, 2009 at 7:21 PM, Mitch Skinner
>>> <mit...@be...> wrote:
>>>
>>>> Giles Velarde wrote:
>>>>
>>>>> Yes I am using this to pull data out of GeneDB here at Sanger,  
>>>>> which
>>>>> is a Chado database. I have put it up here :
>>>>>
>>>>> http://github.com/gv1/chado2miniGFF
>>>>>
>>>>> It's mostly SQLs, inside light Python wrapper.
>>>>>
>>>>> We usually use Artemis to bulk-export GFF, but in this case we  
>>>>> don't
>>>>> need all the annotations for the time being, and even if we do   
>>>>> use
>>>>> some in the future ( for use in extraData) the approach would be  
>>>>> to
>>>>> selectively put them in.
>>>>>
>>>> Given the difficulty you had with Bio::DB::Das::Chado, and given  
>>>> that
>>>> I'd like to be able to generate jbrowse json from the UCSC database
>>>> (and, potentially, other databases) I've been kicking around the  
>>>> idea of
>>>> having something like an sql-to-json.pl.  You could give it a  
>>>> database
>>>> connection and an sql query (and probably some perl callbacks for
>>>> munging the results) and it would generate jbrowse json for you.
>>>>
>>>> Simple cases would be really easy; the jbrowse json is already  
>>>> sort of
>>>> tabular.  I'm not sure yet about how to deal with subfeatures  
>>>> though,
>>>> given that different databases deal with those quite differently.
>>>>
>>>> FWIW,
>>>> Mitch
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Come build with us! The BlackBerry(R) Developer Conference in SF,  
>>>> CA
>>>> is the only developer event you need to attend this year.  
>>>> Jumpstart your
>>>> developing skills, take BlackBerry mobile applications to market  
>>>> and stay
>>>> ahead of the curve. Join us from November 9 - 12, 2009. Register  
>>>> now!
>>>> http://p.sf.net/sfu/devconference
>>>> _______________________________________________
>>>> Gmod-ajax mailing list
>>>> Gmo...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>
>>>>
>>>
>>>
>>>
>>>
>>
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry(R) Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart  
> your
> developing skills, take BlackBerry mobile applications to market and  
> stay
> ahead of the curve. Join us from November 9 - 12, 2009. Register now!
> http://p.sf.net/sfu/devconference_______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

Re: [Gmod-ajax] minimal gff

[Giles V. <gv...@sa...>]

On 16 Oct 2009, at 04:45, Mitch Skinner wrote:

> I was talking about this thread:
>
> http://www.nabble.com/getting-JBrowse-to-run-off-a-Chado-database-where-feature.name-field-is-not-used-td25491225.html
>
> That thread ended a little inconclusively, I thought; Scott had  
> suggested a database change ("set feature.name =  
> feature.uniquename") and then Giles started working on genedb->gff- 
> >jbrowse rather than straight genedb->jbrowse.


Mitch, Scott,

Many thanks for looking into this.

Yes, sorry about not ending that thread. Mitch summed it up quite  
well. I did modify try the modifications as you suggested, Scott, and  
this did get the script to go a bit further, but then it got stuck  
somewhere a little further down the line. At the same time we are  
developing considerable infrastructure around GFF, and so decided to  
look at that too, and this yielded tangible results more easily.

Scott, thanks for you offer to look into it. It doesn't look like  
we'll need to be using that adapter for now, mainly because the GFF  
middle-ware approach is working fine for us and producing all those  
auto-exported GFF files can have other unforeseen uses. But if you're  
keen on expanding the scope of the adapter, I could point you to our  
public read-only snapshot for further testing and would be happy to  
help you with it.


> And then performance became an issue; it sounds like Giles solved it  
> in his case, but in general I hope to avoid making people do as much  
> work as he has done.
>

Speaking of which, I ran into another performance issue, this time  
inside prepare-refseqs.pl. It has to do with preparing refseqs for  
several 1000s of GFF files. When I looked into it I saw that the  
refSeqs.js was being opened, parsed, appended to, and closed for every  
GFF. As this file got larger this opening and appending step got more  
expensive.

I submit a patch that fixes it for me. 


-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

[Gmod-ajax] Change shebang

[Martin A. H. <ma...@ma...>]

Hello Jbrowsers,


I am working on getting Jbrowse to work on my system.

One annoying thing I notice is the Perl scripts in the bin/ dir:

generate-json.pl
generate-names.pl
gff-to-json.pl
prepare-refseqs.pl

all have a hardcoded path to #!/usr/bin/perl which means that the scripts
will run on the system's perl and not on my locally installed perl - which
has the required Bioperl installed.

Please consider changing the shebang to #!/usr/bin/env perl

Also, I believe that 'use warnings;' in all scripts and modules to invoke
warnings locally allowing more fine grained control are better than calling
perl with -w invoking warnings globally.


Best regards,



Martin

Re: [Gmod-ajax] Letters of support for JBrowse?

[Ian H. <ih...@be...>]

I completely neglected to mention that the JBrowse renewal will also
provide funding support for the high-quality GMOD Help Desk service that
we have all come to know and love... yet another reason to write!

Also, in another subproject of the same grant, we plan to develop a
JBrowse version of the GBrowse_syn synteny viewer developed by Sheldon
McKay, so you can browse syntenic regions of homologous genomes
side-by-side.

Again, anything you can write would be very helpful in keeping JBrowse
going.

Best wishes,
Ian


> Dear JBrowse users and lurkers,
> 
> We are currently applying for renewal of our JBrowse funding from NIH.
> Although we were funded last time around, our budget was significantly
> cut. It's a testament to Mitch's talents that we were still able to
> develop something useful, but it's also true that features had to be
> dropped from our initial plan because NIH cut the budget by ~15%.
> 
> This is all by way of leading up to a plea for letters of support. If
> we're to get continued funding, and support JBrowse to meet all the
> requests that you have justifiably demanded, it's absolutely critical
> that we demonstrate an overwhelming demand for JBrowse from the user
> community -- that means you.
> 
> Please, please, please would you consider writing a letter of support
> for JBrowse this week? We would like to avoid templated form letters,
> but some good points to mention would be:
> 
> -- your research (an indication of the diversity of JBrowse-assisted
> investigations would be extremely helpful)
> 
> -- why you chose JBrowse over other genome browsers (and why you love it...)
> 
> -- how you would benefit from further development of JBrowse (one of the
> pillars of our proposal is to make JBrowse more extensible, so that many
> of the requested features can be implemented in a decentralized way, so
> feel free to go nuts and list the features you would like to implement)
> 
> Some of the things we propose to add to JBrowse:
> -- scalability (SNPs, nextgen sequencing data, facilities to search and
> display hundreds/thousands of annotation tracks)
> -- parallelism (cloud deployment)
> -- extensibility (custom tracks/glyphs/features/menus/etc)
> -- portability (all desktop browsers, plus iPhone and Android)
> -- tagging, commenting, GUI-assisted track editing, more wiki-like
> features (track upload, integration with MediaWiki/EcoliWiki/etc), and
> other social networking-like features
> 
> We need letters of support by the end of the week (Friday October 23rd).
> I know these things can seem like a hassle but it really won't take long
> -- about the same time as it would take to write a help email to this
> list. And, again, it's absolutely critical if we are to secure continued
> funding for the project.
> 
> 
> Thanks!
> Ian
> 

[Gmod-ajax] Letters of support for JBrowse?

[Ian H. <ih...@be...>]

Dear JBrowse users and lurkers,

We are currently applying for renewal of our JBrowse funding from NIH.
Although we were funded last time around, our budget was significantly
cut. It's a testament to Mitch's talents that we were still able to
develop something useful, but it's also true that features had to be
dropped from our initial plan because NIH cut the budget by ~15%.

This is all by way of leading up to a plea for letters of support. If
we're to get continued funding, and support JBrowse to meet all the
requests that you have justifiably demanded, it's absolutely critical
that we demonstrate an overwhelming demand for JBrowse from the user
community -- that means you.

Please, please, please would you consider writing a letter of support
for JBrowse this week? We would like to avoid templated form letters,
but some good points to mention would be:

-- your research (an indication of the diversity of JBrowse-assisted
investigations would be extremely helpful)

-- why you chose JBrowse over other genome browsers (and why you love it...)

-- how you would benefit from further development of JBrowse (one of the
pillars of our proposal is to make JBrowse more extensible, so that many
of the requested features can be implemented in a decentralized way, so
feel free to go nuts and list the features you would like to implement)

Some of the things we propose to add to JBrowse:
-- scalability (SNPs, nextgen sequencing data, facilities to search and
display hundreds/thousands of annotation tracks)
-- parallelism (cloud deployment)
-- extensibility (custom tracks/glyphs/features/menus/etc)
-- portability (all desktop browsers, plus iPhone and Android)
-- tagging, commenting, GUI-assisted track editing, more wiki-like
features (track upload, integration with MediaWiki/EcoliWiki/etc), and
other social networking-like features

We need letters of support by the end of the week (Friday October 23rd).
I know these things can seem like a hassle but it really won't take long
-- about the same time as it would take to write a help email to this
list. And, again, it's absolutely critical if we are to secure continued
funding for the project.


Thanks!
Ian

Re: [Gmod-ajax] multiple tracks for same feature using conf file specification

[Shankar A. S. <sha...@gm...>]

Hi Mitch,

Thanks for your suggestions, I went with option 1 for displaying the
two sets of genes.

Also, I found that biodb-to-json.pl parses attributes in a gff3 file
while I couldn't get the flatfile-to-json to do that
I was processing a set of alignments that contain "Target=contigxxx"
key-value pairs in the attribute column.
biodb-to-json.pl renders the name of the Target sequence, whereas this
doesn't happen with flatfile-to-json.pl

Shankar

On Thu, Oct 15, 2009 at 7:12 PM, Mitch Skinner
<mit...@be...> wrote:
> Shankar Ajay Subramanian wrote:
>>
>> I was hoping you could help me out with a question on the conf file.
>> Is there a way to specify two separate tracks in the conf file for
>> "gene" features that are read from two different gff3 files (for
>> instance, predicted genes and known genes)?
>>
>
> I don't think there's currently a way to do exactly what you're asking for,
> but I have a few ideas that hopefully get you where you want to go.
>
> 1. You could use a different conf file for different gff3 files (or
> different sets of gff3 files).
>
> You could set up two different conf files using the
> Bio::DB::SeqFeature::Store::memory adaptor (see the
> docs/tutorial/conf_files/volvox.json for an example using this method).  One
> conf file would be for (say) predicted genes, and the other would be for
> (say) known genes.  Each conf file would have a track definition with the
> same "feature": ["gene"] setting, but different "track", "key", and other
> settings.
>
> 2.  You could use flatfile-to-json.pl to process your gff3 files.
>
> Regards,
> Mitch
>
>

Re: [Gmod-ajax] minimal gff

[Mitch S. <mit...@be...>]

I was talking about this thread:

http://www.nabble.com/getting-JBrowse-to-run-off-a-Chado-database-where-feature.name-field-is-not-used-td25491225.html

That thread ended a little inconclusively, I thought; Scott had 
suggested a database change ("set feature.name = feature.uniquename") 
and then Giles started working on genedb->gff->jbrowse rather than 
straight genedb->jbrowse.  And then performance became an issue; it 
sounds like Giles solved it in his case, but in general I hope to avoid 
making people do as much work as he has done.

Part of the reason I was thinking about having an sql-to-json.pl (that 
would take an sql query as a parameter) is this site-specific variation 
in chado usage.  I'm not sure how much of it there is, though.

Other reasons were:
* allowing other kinds of queries than the ones supported by Bio::DasI
* not having to write Bio::DB::Das::UCSC (unless someone has already 
written this?)
* not having the bio object intermediate (when I profiled a BED->json 
conversion, the biggest CPU user was Bio::Root::RootI::_rearrange)

On the other hand, you could argue (as Chris Mungall did to me today) 
that it would be better to work on improving the middleware rather than 
trying to avoid it.  And then there's the reasons that people have 
wanted middleware in the past (not writing m*n mappings between m data 
sources and n consumers, but m+n mappings to/from the middleware).  I 
think that would be an interesting discussion to have; each of those m*n 
mappings can be simpler than the mappings to and from the middleware, 
and also take advantage of unique features of the source and destination.

Mitch

Scott Cain wrote:
> Hi Mitch and Giles,
>
> I must have missed the conversation about Bio::DB::Das::Chado; what
> were the nature of the problems?  I can't say I'm terribly surprised
> that there were problems, since GeneDB has been using Chado for a long
> time and so Chado and the gbrowse adaptor have no doubt evolved away
> from the way GeneDB is using it.
>
> Anyway, is there anything I can do?
>
> Scott
>
>
> On Thu, Oct 15, 2009 at 7:21 PM, Mitch Skinner
> <mit...@be...> wrote:
>   
>> Giles Velarde wrote:
>>     
>>> Yes I am using this to pull data out of GeneDB here at Sanger, which
>>> is a Chado database. I have put it up here :
>>>
>>> http://github.com/gv1/chado2miniGFF
>>>
>>> It's mostly SQLs, inside light Python wrapper.
>>>
>>> We usually use Artemis to bulk-export GFF, but in this case we don't
>>> need all the annotations for the time being, and even if we do  use
>>> some in the future ( for use in extraData) the approach would be to
>>> selectively put them in.
>>>       
>> Given the difficulty you had with Bio::DB::Das::Chado, and given that
>> I'd like to be able to generate jbrowse json from the UCSC database
>> (and, potentially, other databases) I've been kicking around the idea of
>> having something like an sql-to-json.pl.  You could give it a database
>> connection and an sql query (and probably some perl callbacks for
>> munging the results) and it would generate jbrowse json for you.
>>
>> Simple cases would be really easy; the jbrowse json is already sort of
>> tabular.  I'm not sure yet about how to deal with subfeatures though,
>> given that different databases deal with those quite differently.
>>
>> FWIW,
>> Mitch
>>
>> ------------------------------------------------------------------------------
>> Come build with us! The BlackBerry(R) Developer Conference in SF, CA
>> is the only developer event you need to attend this year. Jumpstart your
>> developing skills, take BlackBerry mobile applications to market and stay
>> ahead of the curve. Join us from November 9 - 12, 2009. Register now!
>> http://p.sf.net/sfu/devconference
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>>     
>
>
>
>   

Re: [Gmod-ajax] minimal gff

[Scott C. <sc...@sc...>]

Hi Mitch and Giles,

I must have missed the conversation about Bio::DB::Das::Chado; what
were the nature of the problems?  I can't say I'm terribly surprised
that there were problems, since GeneDB has been using Chado for a long
time and so Chado and the gbrowse adaptor have no doubt evolved away
from the way GeneDB is using it.

Anyway, is there anything I can do?

Scott


On Thu, Oct 15, 2009 at 7:21 PM, Mitch Skinner
<mit...@be...> wrote:
> Giles Velarde wrote:
>> Yes I am using this to pull data out of GeneDB here at Sanger, which
>> is a Chado database. I have put it up here :
>>
>> http://github.com/gv1/chado2miniGFF
>>
>> It's mostly SQLs, inside light Python wrapper.
>>
>> We usually use Artemis to bulk-export GFF, but in this case we don't
>> need all the annotations for the time being, and even if we do  use
>> some in the future ( for use in extraData) the approach would be to
>> selectively put them in.
>
> Given the difficulty you had with Bio::DB::Das::Chado, and given that
> I'd like to be able to generate jbrowse json from the UCSC database
> (and, potentially, other databases) I've been kicking around the idea of
> having something like an sql-to-json.pl.  You could give it a database
> connection and an sql query (and probably some perl callbacks for
> munging the results) and it would generate jbrowse json for you.
>
> Simple cases would be really easy; the jbrowse json is already sort of
> tabular.  I'm not sure yet about how to deal with subfeatures though,
> given that different databases deal with those quite differently.
>
> FWIW,
> Mitch
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry(R) Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart your
> developing skills, take BlackBerry mobile applications to market and stay
> ahead of the curve. Join us from November 9 - 12, 2009. Register now!
> http://p.sf.net/sfu/devconference
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

[Gmod-ajax] Subfeature were not shown

[Motokazu I. <m.i...@is...>]

I want to show exon-intron strucutre of mRNA. mRNA shape (gray arrow)
can successfully be shown, but subfeatures (UTR and CDS) weren't shown
on on it. Any subfeature-*.json file weren't created under data/tracks
directory. Could you give me some advices ?

GFF3 file and config file are belows.

** GFF3 file

chr22 hg18_refGene gene 49288242 49293001 . - . ID=gene:NM_033200;
Name=gene:NM_033200;Note=NM_033200
chr22 hg18_refGene mRNA 49288242 49293001 . - . ID=mRNA:NM_033200.1;
Name=mRNA:NM_033200.1; Parent=gene:NM_033200; Index=1
chr22 hg18_refGene five_prime_UTR 49292971 49293001 . - .
ID=five_prime_UTR:NM_033200.1.1; Name=five_prime_UTR:NM_033200.1.1;
Parent=mRNA:NM_033200.1
chr22 hg18_refGene CDS 49292877 49292970 . - 0 ID=CDS:NM_033200.1.2;
Name=CDS:NM_033200.1.2; Parent=mRNA:NM_033200.1


** conf file

{
"description": "ucsc tracks",
"db_adaptor": "Bio::DB::SeqFeature::Store",
"db_args": { "-adaptor": "memory",
"-dir": "stage/ucsc" },
"TRACK DEFAULTS": {
"class": "feature",
"autocomplete": "all"
},
"tracks": [
{
"track": "ucsc_gene",
"key": "ucsc Gene Span",
"feature": ["gene"],
"autocomplete": "all",
"class": "feature2",
"category": "Gene Model features",
"urlTemplate": "http://flybase.org/cgi-bin/fbidq.html?{load_id}",
"extraData": {"load_id": "sub {shift->attributes(\"load_id\");}"}
},
{
"track": "ucsc_mRNA",
"feature": ["mRNA"],
"autocomplete": "alias",
"subfeatures": true,
"key": "ucsc mRNA",
"class": "transcript",
"subfeature_classes": {
"CDS": "transcript-CDS",
"five_prime_UTR": "transcript-five_prime_UTR",
"three_prime_UTR": "transcript-three_prime_UTR"
},
"arrowheadClass": "transcript-arrowhead",
"clientConfig": {
"histScale":5
},
"urlTemplate":
"http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term={load_id}",
"extraData": {"load_id": "sub {shift->attributes(\"load_id\");}"}
},
{
"track": "ucsc_snp",
"feature": ["point_mutation"],
"key": "ucsc Mutation: point mutation",
"class": "feature",
"category": "Mapped features"
}
]
}


-- 
Osaka University
Graduate School of Information Science and Technology
Motokazu Ishikawa
E-mail: m.i...@is...
Web:    http://www-mats.ist.osaka-u.ac.jp/

Re: [Gmod-ajax] minimal gff

[Mitch S. <mit...@be...>]

Giles Velarde wrote:
> Yes I am using this to pull data out of GeneDB here at Sanger, which 
> is a Chado database. I have put it up here : 
>
> http://github.com/gv1/chado2miniGFF
>
> It's mostly SQLs, inside light Python wrapper. 
>
> We usually use Artemis to bulk-export GFF, but in this case we don't 
> need all the annotations for the time being, and even if we do  use 
> some in the future ( for use in extraData) the approach would be to 
> selectively put them in. 

Given the difficulty you had with Bio::DB::Das::Chado, and given that 
I'd like to be able to generate jbrowse json from the UCSC database 
(and, potentially, other databases) I've been kicking around the idea of 
having something like an sql-to-json.pl.  You could give it a database 
connection and an sql query (and probably some perl callbacks for 
munging the results) and it would generate jbrowse json for you.

Simple cases would be really easy; the jbrowse json is already sort of 
tabular.  I'm not sure yet about how to deal with subfeatures though, 
given that different databases deal with those quite differently.

FWIW,
Mitch

Re: [Gmod-ajax] multiple tracks for same feature using conf file specification

[Mitch S. <mit...@be...>]

Shankar Ajay Subramanian wrote:
> I was hoping you could help me out with a question on the conf file.
> Is there a way to specify two separate tracks in the conf file for
> "gene" features that are read from two different gff3 files (for
> instance, predicted genes and known genes)?
>   

I don't think there's currently a way to do exactly what you're asking 
for, but I have a few ideas that hopefully get you where you want to go.

1. You could use a different conf file for different gff3 files (or 
different sets of gff3 files).

You could set up two different conf files using the 
Bio::DB::SeqFeature::Store::memory adaptor (see the 
docs/tutorial/conf_files/volvox.json for an example using this method).  
One conf file would be for (say) predicted genes, and the other would be 
for (say) known genes.  Each conf file would have a track definition 
with the same "feature": ["gene"] setting, but different "track", "key", 
and other settings.

2.  You could use flatfile-to-json.pl to process your gff3 files.

Regards,
Mitch

[Gmod-ajax] multiple tracks for same feature using conf file specification

[Shankar A. S. <sha...@gm...>]

Hi Mitch,

I was hoping you could help me out with a question on the conf file.
Is there a way to specify two separate tracks in the conf file for
"gene" features that are read from two different gff3 files (for
instance, predicted genes and known genes)?

Thanks,
Shankar

Re: [Gmod-ajax] minimal gff

[Giles V. <gv...@sa...>]

On 15 Oct 2009, at 02:28, Mitch Skinner wrote:

> This is cool, sorry for the slow reply on my part.  I wasn't sure  
> about "Derives_from" that you mentioned in your first email.  I'm  
> not aware of any reason jbrowse would use that, but I don't know the  
> Bio::DB::SeqFeature::Store code in detail, which would be the place  
> to look to answer this question definitively.
>

I completely forgot about Derives_from when I was working on it, and  
have stuck relevant upward relationships (derives_from and part_of)  
into the Parent qualifier for the time being.

> Also, if the user is using the "extraData" jbrowse option, then  
> whatever is being extracted from the perl objects that way would be  
> relevant, although I suppose the user already knows if that's the  
> case.
>

I do use that, but only pulling the Name, so that's fine for me.

> Out of curiosity, are you generating GFF from a chado database, or  
> is it another schema?
>

Yes I am using this to pull data out of GeneDB here at Sanger, which  
is a Chado database. I have put it up here :

	http://github.com/gv1/chado2miniGFF

It's mostly SQLs, inside light Python wrapper.

We usually use Artemis to bulk-export GFF, but in this case we don't  
need all the annotations for the time being, and even if we do  use  
some in the future ( for use in extraData) the approach would be to  
selectively put them in.

Regards,
Giles


> Regards,
> Mitch
>
> On 10/14/2009 04:19 PM, Giles Velarde wrote:
>>
>> Further to this question I decided to investigate. Adapting the SQL  
>> code from one of the Chado views (gff3view), to generate a custom  
>> mini-GFF exporter without any annotations. A typical set of lines  
>> looks like this:
>>
>> Lbr.chr1 chado gene 1272 4166 . - . ID=3775871;Name=LbrM01_V2.0010
>> Lbr.chr1 chado exon 1272 4166 . - .  
>> ID=3775872;Name=LbrM01_V2.0010:exon:1;Parent=LbrM01_V2.0010:mRNA
>> Lbr.chr1 chado mRNA 1272 4166 . - .  
>> ID=3775873;Name=LbrM01_V2.0010:mRNA;Parent=LbrM01_V2.0010
>>
>> and JBrowse appears to handle this fine for my purposes. I haven't  
>> done any benchmarks, but it's significantly faster than exporting  
>> the complete GFF. In terms of size alone I am it's gone from 60M to  
>> 36M for the same dataset.
>>
>> If anyone would like to know more on this topic please feel free to  
>> get in touch.
>>
>> Regards,
>> Giles
>>
>>
>>
>>
>> On 14 Oct 2009, at 16:48, Giles Velarde wrote:
>>
>>> Hi,
>>>
>>> I am looking to possibly speed up the generation of GFFs for  
>>> consumption by the JBrowse prepare scripts, and wanted to check  
>>> with you first to see what attributes (tags in the last column)  
>>> are absolutely necessary for JBbrowse. I am guessing :
>>>
>>> - ID
>>> - Name
>>> - Parent
>>> - Derives_from
>>>
>>>
>>> would that be correct?
>>>
>>> Regards,
>>> Giles
>>
>>
>> -- The Wellcome Trust Sanger Institute is operated by Genome  
>> Research Limited, a charity registered in England with number  
>> 1021457 and a compa ny registered in England with number 2742969,  
>> whose registered office is 2 15 Euston Road, London, NW1 2BE. 
>>
>> ------------------------------------------------------------------------------
>> Come build with us! The BlackBerry(R) Developer Conference in SF, CA
>> is the only developer event you need to attend this year. Jumpstart  
>> your
>> developing skills, take BlackBerry mobile applications to market  
>> and stay
>> ahead of the curve. Join us from November 9 - 12, 2009. Register now!
>> http://p.sf.net/sfu/devconference
>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>




-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

Re: [Gmod-ajax] minimal gff

[Mitch S. <mit...@be...>]

This is cool, sorry for the slow reply on my part.  I wasn't sure about 
"Derives_from" that you mentioned in your first email.  I'm not aware of 
any reason jbrowse would use that, but I don't know the 
Bio::DB::SeqFeature::Store code in detail, which would be the place to 
look to answer this question definitively.

Also, if the user is using the "extraData" jbrowse option, then whatever 
is being extracted from the perl objects that way would be relevant, 
although I suppose the user already knows if that's the case.

Out of curiosity, are you generating GFF from a chado database, or is it 
another schema?

Regards,
Mitch

On 10/14/2009 04:19 PM, Giles Velarde wrote:
> Further to this question I decided to investigate. Adapting the SQL 
> code from one of the Chado views (gff3view), to generate a custom 
> mini-GFF exporter without any annotations. A typical set of lines 
> looks like this:
>
> Lbr.chr1 chado gene 1272 4166 . - . ID=3775871;Name=LbrM01_V2.0010
> Lbr.chr1 chado exon 1272 4166 . - . 
> ID=3775872;Name=LbrM01_V2.0010:exon:1;Parent=LbrM01_V2.0010:mRNA
> Lbr.chr1 chado mRNA 1272 4166 . - . 
> ID=3775873;Name=LbrM01_V2.0010:mRNA;Parent=LbrM01_V2.0010
>
> and JBrowse appears to handle this fine for my purposes. I haven't 
> done any benchmarks, but it's significantly faster than exporting the 
> complete GFF. In terms of size alone I am it's gone from 60M to 36M 
> for the same dataset.
>
> If anyone would like to know more on this topic please feel free to 
> get in touch.
>
> Regards,
> Giles
>
>
>
>
> On 14 Oct 2009, at 16:48, Giles Velarde wrote:
>
>> Hi,
>>
>> I am looking to possibly speed up the generation of GFFs for 
>> consumption by the JBrowse prepare scripts, and wanted to check with 
>> you first to see what attributes (tags in the last column) are 
>> absolutely necessary for JBbrowse. I am guessing :
>>
>> - ID
>> - Name
>> - Parent
>> - Derives_from
>>
>> would that be correct?
>>
>> Regards,
>> Giles
>
>
> -- The Wellcome Trust Sanger Institute is operated by Genome Research 
> Limited, a charity registered in England with number 1021457 and a 
> compa ny registered in England with number 2742969, whose registered 
> office is 2 15 Euston Road, London, NW1 2BE.
>
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry(R) Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart your
> developing skills, take BlackBerry mobile applications to market and stay
> ahead of the curve. Join us from November 9 - 12, 2009. Register now!
> http://p.sf.net/sfu/devconference
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>    

Re: [Gmod-ajax] minimal gff

[Giles V. <gv...@sa...>]

Further to this question I decided to investigate. Adapting the SQL  
code from one of the Chado views (gff3view), to generate a custom mini- 
GFF exporter without any annotations. A typical set of lines looks  
like this:

Lbr.chr1	chado	gene	1272	4166	.	-	.	ID=3775871;Name=LbrM01_V2.0010
Lbr.chr1	chado	exon	1272	4166	.	-	.	 
ID=3775872;Name=LbrM01_V2.0010:exon:1;Parent=LbrM01_V2.0010:mRNA
Lbr.chr1	chado	mRNA	1272	4166	.	-	.	 
ID=3775873;Name=LbrM01_V2.0010:mRNA;Parent=LbrM01_V2.0010

and JBrowse appears to handle this fine for my purposes. I haven't  
done any benchmarks, but it's significantly faster than exporting the  
complete GFF. In terms of size alone I am it's gone from 60M to 36M  
for the same dataset.

If anyone would like to know more on this topic please feel free to  
get in touch.

Regards,
Giles




On 14 Oct 2009, at 16:48, Giles Velarde wrote:

> Hi,
>
> I am looking to possibly speed up the generation of GFFs for  
> consumption by the JBrowse prepare scripts, and wanted to check with  
> you first to see what attributes (tags in the last column) are  
> absolutely necessary for JBbrowse. I am guessing :
>
> - ID
> - Name
> - Parent
> - Derives_from
>
> would that be correct?
>
> Regards,
> Giles




-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

[Gmod-ajax] minimal gff

[Giles V. <gv...@sa...>]

Hi,

I am looking to possibly speed up the generation of GFFs for  
consumption by the JBrowse prepare scripts, and wanted to check with  
you first to see what attributes (tags in the last column) are  
absolutely necessary for JBbrowse. I am guessing :

- ID
- Name
- Parent
- Derives_from

would that be correct?

Regards,
Giles


-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

Re: [Gmod-ajax] jbrowse download

[Mitch S. <mit...@be...>]

On 10/12/2009 05:13 AM, colin davenport wrote:
> I am trying to get jbrowse off github, yet the download button is not working.
> Is there another place to get the code from ?
>    

Yeah, the download link isn't working for me either right now.  But I 
did just try this:

http://github.com/jbrowse/jbrowse/zipball/master

and it worked for me.  If I recall correctly, you can also substitute 
"tarball" in place of "zipball" if you prefer that format.

If it continues to be a problem, we'll probably set up some kind of 
backup mechanism on jbrowse.org.

Thanks for the heads-up,
Mitch