[Gmod-help] Problem with GMOD Gbrowse

Tue Jun 1 11:14:59 EDT 2010

Hello GMOD Team and Dr Stein,

I'm really sorry to bother you again with my problem but I have no news 
from you since my first answer to Dr Stein's question.

This answer was:

     "When I put two GFF file with a sequence in the directory I can 
access both of them with Gbrowse and features are correctly displayed.
     I can also get every information about a given feature (apart the 
sequence).

     However the sequence for supernumerary GFF does not exist in 
Gbrowse and error messages appears.

     Tell me if you need more precision or sample files."

It has been three weeks since I am waiting for a solution to the problem 
of malfunctioning of the module memory.pm.

Can I expect to have a solution within a reasonable time or should I 
change my tactics and consider to use a MySQL database instead of flat 
GFF files ?

Thank you very much for your help,

Best regards,

Aurélien

Le 11/05/2010 15:42, Lincoln Stein a écrit :
> I have not seen this problem before, but if I can reproduce it locally 
> it should be easy to fix. Can I ask whether the basic display of 
> features is broken as well, or is it just the error messages and the 
> inability to access sequence that is problematic?
>
> Lincoln
>
> On Tue, May 11, 2010 at 3:33 AM, Aurélien BERNARD 
> <arbernard at clermont.inra.fr <mailto:arbernard at clermont.inra.fr>> wrote:
>
>     Hello GMOD support team,
>
>     First of all I will present myself:
>
>     My name is Aurélien Bernard, I'm a software engineer in a french
>     laboratory called INRA (National Institute for Agricultural Research)
>     I currently work in the development team of a wheat annotation
>     pipeline that generate GFF files (TriAnnot pipeline:
>     http://urgi.versailles.inra.fr/projects/TriAnnot/index.php).
>
>     We have decided to use Gbrowse (1.70) to allow our users to
>     visualize their results.
>     Please note that Gbrowse is installed on a server of the INRA
>     bioinformatic platform (URGI) and used by several INRA laboratories.
>     Therefore we can't decide which version to use or when to update
>     Gbrowse.
>
>     Since the beginning of my work with Gbrowse I have created a
>     custom configuration file, written some Perl functions to exploit
>     popup balloons (on hover and on click) and developed a simple
>     plugin for our proper use.
>     On URGI's advice we have chosen the following adaptor:
>
>     db_adaptor = Bio::DB::SeqFeature::Store
>
>     However, when they used a MySQL database we have decided to load
>     GFF files into memory:
>
>     db_args = -adaptor memory
>     -dir '/home/projects/triannot/GFF/'
>
>     This choice can be explained by the fact that our pipeline stores
>     GFF result files into a particular directory where our users can
>     download them (or Gbrowse can read them) for a short period of
>     time (Old files are automatically deleted after one or two weeks).
>
>     Everything goes well on the different GFF files I have tested
>     separately.
>     But, if I try to put several GFF files (each of these files
>     contains a sequence in fasta format in its bottom part) in the
>     same directory then everything goes wrong:
>
>     - My apache error file becomes full of error messages
>     - It becomes impossible to access to the sequence of each
>     supernumerary GFF file
>
>     Example of error message:
>
>     [Mon May 03 17:02:43 2010] [error] [client 127.0.0.1] print() on
>     closed filehandle GEN3 at
>     [Mon May 03 17:02:43 2010] [error] [client 127.0.0.1]
>     \t/usr/local/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store/memory.pm
>     <http://memory.pm> line 598, <GEN5> line 888 (#1)
>
>     This problems seems to be directly related to our choice of
>     db_args so I give a look to the correspondant BioPerl module
>     (memory.pm <http://memory.pm>).
>
>     Line 598 is included in a function with a strange comment line:
>
>     # this is ugly
>     sub _insert_sequence {
>         my $self = shift;
>         my ($seqid,$seq,$offset) = @_;
>         my $dna_fh = $self->private_fasta_file or return;
>         if ($offset == 0) { # start of the sequence
>            print $dna_fh ">$seqid\n";
>         }
>         print $dna_fh $seq,"\n";
>     }
>
>     Does a Gbrowse user already encounter this problem ?
>
>     Do you have a solution to make it work better ?
>
>
>     I thank you in advance for your help !!
>
>     Best regards,
>
>     Aurélien
>
>     -- 
>     Aurélien Bernard
>
>     Software engineer
>
>     INRA (Institut National de la Recherche Agronomique)
>     UMR INRA-UBP 1095
>     Génétique, Diversité et Ecophysiologie des Céréales
>     234, Avenue du Brézet
>     63100 Clermont-Ferrand
>     FRANCE
>
>     Tel: +33 (0)4.73.62.43.37
>
>
>
>
> -- 
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <Renata.Musa at oicr.on.ca 
> <mailto:Renata.Musa at oicr.on.ca>>

-- 
Aurélien Bernard

Software engineer

INRA (Institut National de la Recherche Agronomique)
UMR INRA-UBP 1095
Génétique, Diversité et Ecophysiologie des Céréales
234, Avenue du Brézet
63100 Clermont-Ferrand
FRANCE

Tel: +33 (0)4.73.62.43.37

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