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David Messina | 2 Apr 2007 04:54
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Re: installation bioperl

We need more information to be able to help you. Could you please  
show us the actual output you see when trying to install Bioperl?

Also, we need to know:

- what operating system you have
- what version of Bioperl you are trying to install

See

http://www.bioperl.org/wiki/HOWTO:Beginners#Getting_Assistance

and please read the rest of the document, too.

Dave
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Ambrose | 2 Apr 2007 12:09
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bioperl and kegg(out of memory problem )

Hello All,
             I have some problems parsing KEGG using bioperl. I get out of memory problem.I current have 1G RAM.Can some
tell me why this is happening and how it can be solved.It is beacuse the objects passed to bioiperl are so big
or what?

best regrads
Ambrose

 
---------------------------------
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Check out "Tonight's Picks" on Yahoo! TV.
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Chris Fields | 2 Apr 2007 14:43
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Re: bioperl and kegg(out of memory problem )

This doesn't really explain much beyond stating you are having  
problems.  You need to post some code (to the mail list!) and let us  
know what version of BioPerl you are using.

chris

On Apr 2, 2007, at 5:09 AM, Ambrose wrote:

> Hello All,
>              I have some problems parsing KEGG using bioperl. I get  
> out of memory problem.I current have 1G RAM.Can some tell me why  
> this is happening and how it can be solved.It is beacuse the  
> objects passed to bioiperl are so big or what?
>
> best regrads
> Ambrose
>
>
> ---------------------------------
> TV dinner still cooling?
> Check out "Tonight's Picks" on Yahoo! TV.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l <at> lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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Ambrose | 2 Apr 2007 15:56
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Re: bioperl and kegg(out of memory problem )


Hello ALL,

I have the code below,which parses my kegg files.A host of the files are parsed and the information is
inserted into my databases but unfortunate after the program runs for some hours it stops showing the
message out of memory.I assume that this happens because the bioperl object is too big.Please just check
the code below

best regards Ambrose

#!/usr/local/ActivePerl/bin/perl
#
#

use strict;
use Bio::SeqIO;
use Bio::FASTASequence;
use DBI;
use Benchmark  qw(:all) ;

my($ko,$prosite,$ncbigi,$ncbigeneid,$pfam,$uniprot,$ecn1,$pathway_id1,$pathway_name1,$ec_num);
my(%dblink_KO,%dblink_Pfam,%dblink_PROSITE,%dblink_NCBIGI,%dblink_NCBIGENEID,%dblink_UniProt);
my(%pathway_name,%pathway_id,%ecnumbers,%crc64,%ntseq,%aaseq);
my(  <at> kg_id);
my $db="gbdb";
my $host="localhost";
my $userid="root";
my $passwd="ubuntu";
my $connectionInfo="dbi:mysql:$db;"."mysql_socket=/var/run/mysqld/mysqld.sock";
my ($t1,$t2);
(Continue reading)

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Eric Just | 2 Apr 2007 16:12
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Can't locate object method "seq_start" via package "Bio::DB::GenBank"

Hello,

I am getting this error while running a bioperl script that I had been using
in bioperl 1.4.  On upgradeing to bioperl 1.5.2 I get the following fatal
error

Can't locate object method "seq_start" via package "Bio::DB::GenBank"

My script is as follows:

use Bio::DB::GenBank;
use Bio::DB::Query::GenBank;

my $gb = new Bio::DB::GenBank();

my $query = Bio::DB::Query::GenBank->new(
      -query   =>'txid44689[Organism:noexp]',
      -reldate => 60,
      -db      => 'nucleotide'

);

my $in = $gb->get_Stream_by_query($query);

while ( my $seq = $in->next_seq()) {
      print "do something";
      #....
}

I noticed that seq_start is created in the begin block of
(Continue reading)

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Eric Just | 2 Apr 2007 16:15
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Re: Can't locate object method "seq_start" via package "Bio::DB::GenBank"

Sorry about that.

As soon as I sent the email I found my problem ( an old NCBIHelper in my
inheritance path ).   There is no bug here.

Eric

On 4/2/07, Eric Just <e-just <at> northwestern.edu> wrote:
>
> Hello,
>
> I am getting this error while running a bioperl script that I had been
> using in bioperl 1.4.  On upgradeing to bioperl 1.5.2 I get the following
> fatal error
>
> Can't locate object method "seq_start" via package "Bio::DB::GenBank"
>
> My script is as follows:
>
>
> use Bio::DB::GenBank;
> use Bio::DB::Query::GenBank;
>
> my $gb = new Bio::DB::GenBank();
>
> my $query = Bio::DB::Query::GenBank->new(
>       -query   =>'txid44689[Organism:noexp]',
>       -reldate => 60,
>       -db      => 'nucleotide'
>
(Continue reading)

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Chris Fields | 2 Apr 2007 17:32
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Re: bioperl and kegg(out of memory problem )

Ambrose,

Data is persisting in your hashes (in particular DBLink objects),  
which is eating away at your memory.  If I take a sample KEGG gene  
file and simply parse it:

while (my $seq = $io->next_seq) {
     print $seq->accession,"\n";
}

there are no memory issues, but if I store the data in hashes  
declared outside the loop:

my(%dblink_KO,%dblink_Pfam,%dblink_PROSITE,%dblink_NCBIGI,% 
dblink_NCBIGENEID,%dblink_UniProt);
my(%pathway_name,%pathway_id,%ecnumbers,%crc64,%ntseq,%aaseq);

while (my $seq = $io->next_seq) {
     # store Bio::Seq data in hashes
}

I see problems with only one genome file with KEGG records.  You'll  
definitely run into memory issues if you are parsing many genome  
files, which you appear to be:

my(%dblink_KO,%dblink_Pfam,%dblink_PROSITE,%dblink_NCBIGI,% 
dblink_NCBIGENEID,%dblink_UniProt);
my(%pathway_name,%pathway_id,%ecnumbers,%crc64,%ntseq,%aaseq);

for my $genomefile ( <at> genomelist) {
(Continue reading)

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David Messina | 2 Apr 2007 18:19
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Re: installation bioperl

Hi Fahmi,

Please include the list on the reply so that others can comment, too.

Yes, it appears the machine you are installing on does not have an  
internet connection. You probably will want to resolve that problem  
before dealing with Bioperl. Alternatively, you could simply install  
and use Bioperl  on the machine which does have an internet connection.

If you really need to get Bioperl installed on that machine, however,  
probably the easiest way would be to find a machine that does have an  
internet connection, install CPAN::Mini, and use it to make a local  
mirror of CPAN. You could then copy that local mirror over to the  
machine without the internet connection and point that machine's cpan  
at the local mirror (read the CPAN documentation to find out how to  
do this). Also, the BioPerl install instructions list several  
external packages that you will need to use some parts of Bioperl  
(e.g. GD). Again, you can download those distributions using the  
machine with the internet connection and copy them over.

Dave

On Apr 2, 2007, at 9:22 AM, fahmi derbali wrote:

> thank you for answer. I will give you the maximum of informations  
> inorder to be able to diagnostic the problem:
>
> i use the linux mandriva 2006
> i'm traying to install bioperl-1.5.2_102.tar.gz which i obtained  
> from the url:
(Continue reading)

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Chris Fields | 2 Apr 2007 20:10
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Fwd: BLAST beta, URLAPI, and BioPerl (RemoteBlast users)

This may be of interest to anyone using RemoteBlast.

For anyone who uses RemoteBlast, the new changes to NCBI's BLAST  
interface shouldn't affect anything (Scott tested it out).  If there  
are any abnormalities with RemoteBlast queries over the next few  
weeks let us know.

chris

Begin forwarded message:

> From: "Mcginnis, Scott \(NIH/NLM/NCBI\) [E]"  
> <mcginnis <at> ncbi.nlm.nih.gov>
> Date: April 2, 2007 12:53:33 PM CDT
> To: "Chris Fields" <cjfields <at> uiuc.edu>
> Subject: RE: BLAST beta, URLAPI, and BioPerl
>
> Hi Chris:
>
> We are ready to make the new pages the defaults come April 16th. An  
> announcement is going out shortly. There are some very minor  
> changes to the URL API and I have listed them below. IT will be  
> part of the announcements. Please note we actually tested BioPerl  
> and it seems to me fine with the new pages. If you have a news on  
> your site or a mailing list you might want to pass this on.
>
> A Note About URLAPI
>
> The new BLAST pages support URLAPI, a protocol that scripts and
> programs use to run BLAST searches and retrieve results over
(Continue reading)

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Stéphane Téletchéa | 3 Apr 2007 14:28
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Re: Packaging bioperl for Fedora

Alex Lancaster a écrit :
> Hello bioperl,
> 
> I'm new to the bioperl world, having just started a research position
> in which I need to manage a large bioperl-based codebase.  To this
> end, I'm working on packaging bioperl as an official Fedora Package
> (formerly "Fedora Extras") and I'm currently wading through and
> packaging the long laundry list of Perl dependencies (then I'm going
> to try and do the same for biopython).  You can see my some of my
> progress (including links to the reviews) here:
> 
> http://fedoraproject.org/wiki/AlexLancaster
> 
> Several issues have arisen during the packaging that I hope the
>

Nice, i was on my way to do it :-)
I'm a Mandriva packager and have been kindly "spushed" for maintaining 
the bioperl package for Mandriva.

You can have a look at the work already done by Mandriva at the addresses:
http://svn.mandriva.com/cgi-bin/viewvc.cgi/packages/cooker/perl-bioperl/current/
http://svn.mandriva.com/cgi-bin/viewvc.cgi/packages/cooker/perl-bioperl-run/current/

(Happy users of Mandriva do 'urpmi perl-bioperl, et voilà :-).

Feel free to contact me if you need more input for dependencies, since 
they are quite a lot.

Cheers,
(Continue reading)

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Gmane