Can a region be too small to render with bigwig or bam?

On our E. coli Gbrowse we're trying to show published high throughput data using bigwig tracksets. This:

	http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Lrp_Exponential&t=Lrp_Stationary

Seems to work when I am zoomed to >2kbp, but not when I'm at 1kbp.  It times out on the smaller region with the
dreaded pink track display. I get this in the logs

[Sat May 18 10:17:24 2013] [error] [client 74.197.139.252] [Sat May 18 10:17:24 2013] gbrowse: alarm
clock at /usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/RenderPanels.pm line 1508., referer: http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Lrp_Exponential&t=Lrp_Stationary
[Sat May 18 10:17:24 2013] [error] [client 74.197.139.252] [Sat May 18 10:17:24 2013] gbrowse:
RenderPanels error: timeout at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/RenderPanels.pm line 1508., referer: http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Lrp_Exponential&t=Lrp_Stationary
[Sat May 18 10:17:24 2013] [error] [client 74.197.139.252] [Sat May 18 10:17:24 2013] gbrowse: [14887]
rendering error track: Timeout; Try turning off tracks or looking at a smaller region. at
/usr/local/lib/perl/5.14.2/Bio/Graphics/Browser2/Render.pm line 3651., referer: http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/?t=Lrp_Exponential&t=Lrp_Stationary

Counterintuitive!

To see if it's just us, I looked a modencode. I don't see that for what I am guessing is a bigwig track on the C.
elegans gbrowse there (adult spe0 miRNA change), but I do see a problem at 1kb with Young Adult 25dC 46hrs.
It displays this in the pink track messages:

can't locate object method tid via package Bio::DB::Bam::SplitAlignmentPart

Jim
=====================================
Jim Hu
Professor
Dept. of Biochemistry and Biophysics
2128 TAMU

multiple tracks via URL

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new file upload options

Hello,

I have done some work to extend the available file options for uploading custom user tracks that I would like
to make available to the community.

The short list of changes include.
1. BigBed files are now supported via upload and URL. Both region and coverage tracks are generated.
2. Archives (ZIP or TAR) of two or more BigWig files are supported, resulting in a BigWigSet with each file
set up as a subtrack selected by display name.
3. USeq archives are automatically converted to BigWig or BigBed tracks depending on context if support is enabled.

Additionally, uploaded Bam files are no longer sorted automatically but only when the Bam sort flag header
is not set to coordinate. Samtools does not set this flag (you must do it manually), but Picard does.

You may checkout the additions here
https://github.com/tjparnell/GBrowse/tree/new_upload_options
They are sync'ed with the current GBrowse master.

I have tested these on the VBox and Amazon GBrowse virtual machines, as well as in house on Mac OS X. Please let
me know if you find any problems.

Some additional notes:
The archives are extracted through a pipe directly to file to avoid issues with errant and non-sensible
paths that may be stored in the archive.

The USeq format is native to the USeq analysis package developed here at the University of Utah. More
information can be found at http://useq.sourceforge.net, including information about the file
format. It requires the installation of java 1.6+ and the USeq package in a searchable path. It should fail
gracefully if these are not found.

Upload file size limits may need to be increased for FCGI environments to avoid timeout issues. 

Tim

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Re: Why AA seq in CDS track is incorrect?

Hi!

I'm answering to this relatively old post (see
http://gmod.827538.n3.nabble.com/Why-AA-seq-in-CDS-track-is-incorrect-tt4027587.html#a4027660
for the complete thread).

The problem is definitively not a bug in my adapter because it is
reproducible with the internal yeast database provided with the
Gbrowse installation.

Just compare the CDS translation of the two genes YAL009W and YAL008W
(chrI:135,700..137,699).

In my opinion, it looks like a caching problem of the CDS glyph
because if I click to see the details of the CDS, the correct DNA
sequence is shown.
Also, If I zoom out, the CDS glyph shows the correct bar for the
reading frame and also colours it correctly. Zooming in retains the
correct colour for the translated sequence but shows the incorrect
sequence.

How to dig further into it?

--
Regards,
Mathias

> Hi Mathias,
>
> This is almost certainly a bug in your adaptor.  I'd suggest writing
> some command line scripts that repeatedly pull features and their
> sequences out of the database and translate them and run that through
> the perl debugger to see if anything shows up.  Debugging that
> remotely is a pretty daunting task (of course, if you live somewhere
> fun, I might be able to come help in person 
>
> Scott
>
>
> On Wed, Dec 12, 2012 at 4:08 PM, Walter, Mathias <[hidden email]> wrote:
>
> > Hi Scott,
> >
> > I've attached some screenshots.
> >
> > In the first screenshot (cds_6frame.jpg), the topmost red CDS aa is
> > the correct translation of the topmost yellow gene at the reverse
> > strand. I verified this with the details page and with the translated
> > sequence stored in my database. It corresponds to the 6-frame
> > translation too. Hence, it works in general. But looking at the other

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Features on reverse strand

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Personal Genome SNP format or BigBed?

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Download FASTA issue

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Added features on the reverse strand via URL

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Problem with BigWig file

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Need documentation on Gbrowse session handling

Dear Gbrowse list,

I have, with a little desperation, started to search look for documentation on the Gbrowse2 Session
module. In particular, I am 
interested in how to *correctly* initialize and build up a Gbrowse session which is fully authorized for a
user. Let's assume the 
task is to: write a cgi script (in addition to the gbrowse cgi) to initialize a gbrowse session with an
authenticated user, such that in
the next invocation of gbrowse, the user is authenticated and logged in. 

I found by reading through the source code and reverse
engineering a sequence of commands that will *almost* get me there. I am seemingly missing one step only:
- the example code below works in case I already have a Gbrowse session
- the example doesn't work when there is no session at all, because subsequent calls to gbrowse make a new
session which then is not authenticated.

So, what is the correct way to initialize a Gbrowse2 Session programmatically? Am I missing something.

I'd really appreciate your help, because now I am definitely stuck.

Michael Dondrup
Postdoctoral fellow
Sea Lice Research Centre/Department of Informatics
University of Bergen
Thormøhlensgate 55, N-5008 Bergen, 
Norway

#!/usr/bin/env perl

use strict;
use warnings;
use Net::SAML;
use CGI::Fast qw(:standard);

use Bio::Graphics::Browser2;
use Bio::Graphics::Browser2::Render::HTML;

while (my $q = CGI::Fast->new) {
my $username ="valid user"; 
# it's not really important where this comes from,
# the user information is coming from an authentication module using Net::SAML
my $fullname = "Fully Valid";
my $mail = "valid@...";

 if ($username) {

	my $p = "https://url";
	my $myurl = "https://url/gbrowse/lsalmonis/";
	my $htmlhead = <<HTML
<script src="$p/gbrowse2/js/login.js" type="text/javascript"></script>
<script src="$p/gbrowse2/js/controller.js" type="text/javascript"></script>
HTML
;
       ## STEP 1:
        ## get the session and initialize it

        my $session = $render->session;
        $session->lock();
        $session->username($username);
        $session->flush;

	## STEP 2:
        ## authorization handling:
	my $userdb = $render->userdb;
        my $id = $userdb->check_or_add_named_session($session->id,$username);
        $userdb->set_fullname_from_username($username=>$fullname,$mail) if defined $fullname;
        warn "username ".$session->username. " stored in session ".$session->id();
        # now authenticate
        my ($sid, $nonce) = $render->authorize_user($username,$id, 1,undef);
        my $is_authorized = $render->user_authorized_for_source($username);

        ## STEP 3:
        ## prepare for JavaScript invocation
        ## seems like the final step is to invoke login_load_account to make the UI aware of the login

	# convert the login data to json
        my $result = to_json { userOK  => 1,
                sessionid => $id,
                username  => $username,
                message   => 'login ok',
              };
	
	## STEP 5:
        ## print an intermediate web page to invoke javascript 
	print header(-type=>"text/html");
      	print start_html(-head=>$htmlhead);
      	print b("user $username". (($is_authorized)?" is ": "is not ") . "authorized!");
        print script({-type=>'text/javascript'},
<<SCRIPT      
var p = $result;
login_load_account("$myurl",p);
SCRIPT
);
	$session->unlock();
	print end_html();
 }

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What glyph to use for displaying a gene?

I have a gff3 file with gene defined using the parental nesting
described here: http://www.gmod.org/wiki/GFF3
The features include (with indentation representing the nesting):

gene
   mRNA
   transcript
      five_prime_UTR
      CDS
      three_prime_UTR
      exon

My question is: What glyph should be used to properly display this
gene description in gbrowse2?

I've tried transcript, transcript2, processed_transcript, cds.
None of them are showing what I think it should look like.
--

-- 
Wes Barris

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