[Gmod-help] Problem with GMOD Gbrowse

[Aurélien BERNARD]

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 
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).

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

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