[Gmod-help] Problem with GMOD Gbrowse

[Lincoln Stein]

Hello,

This is a low priority bug, but it will be fixed within a few weeks. You can
increase its priority by entering a bug report in the bug tracking system.

Lincoln

On Tue, Jun 1, 2010 at 11:14 AM, Aurélien BERNARD <
arbernard at clermont.inra.fr> wrote:

>  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> 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.pmline 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
>>
>>
>
>
> --
> 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>
>
>
>
> --
> 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>
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