Hi Syed,
I am still struggling with getting the pairwise genomic alignments
between mouse and human.
I changed my query in order to get only a short stretch starting with
only 10000 bases of the human chromosome:
$query->setDataset("compara_mart_blastznet_hsap_mmus");
$query->addFilter("hsap_dnafrag_end", ["10000000"]);
$query->addFilter("hsap_chro", ["1"]);
$query->addFilter("hsap_dnafrag_start", ["9990000"]);
$query->addAttribute("pairwise_genomic_alignments");
The same query takes me a few seconds on EnsMart (the whole results),
but with my script it even did not even finish after over night.
Thanks,
Matthias
-----Original Message-----
From: Syed Haider [mailto:[EMAIL PROTECTED]
Sent: Friday, August 24, 2007 6:38 PM
To: Wahl, Matthias
Cc: [email protected]
Subject: RE: [mart-dev] Biomart - pairwise_genomic_alignments
Hi Matthias
Are you retrieving the whole results set or just a subset (using some
filters) ? The results you see on EnsMart are first 10 results only.
cheers
syed
On Fri, 2007-08-24 at 16:22 -0500, Wahl, Matthias wrote:
> Hi Syed,
>
> Thank you very much for the quick answer. I removed the three lines
> and the program is executing, however it runs forever (it is running
> more than one hour now without finishing), but the same query over the
> EnsMart web page is done in a few seconds.
>
> Thanks,
>
> Matthias
> -----Original Message-----
> From: Syed Haider [mailto:[EMAIL PROTECTED]
> Sent: Friday, August 24, 2007 2:36 PM
> To: Wahl, Matthias
> Cc: [email protected]
> Subject: Re: [mart-dev] Biomart - pairwise_genomic_alignments
>
>
> Hi Matthias
> I have tested your code all you need to do is to remove the following
> three lines which are only for retrieving count
> $query->count(1);
> $query_runner->execute($query);
> print $query_runner->getCount();
>
> Count, in case of Genomic sequence data has some problem, which we
> will address soon. In addition, the two sections (one for count and
> one for data retrievel are mutually exclusive - you can execute only
> one at a
> time.)
>
> hope this will get you going with your work for now.
>
> cheers
> syed
>
>
> On Fri, 2007-08-24 at 12:43 -0500, Wahl, Matthias wrote:
> > Hi All,
> >
> > I am trying to retrieve pairwise genomic alignments from EnsMart
> > using
>
> > the script below (taken from the web page), but all I get the
> > following error message:
> >
> > Unimplemented method 'BioMart::Dataset::GenomicSequence::getCount'
> >
> > Does anyone know what I am doing wrong?
> > Thanks,
> >
> > Matthias
> >
> >
> >
> >
> > my $action='cached';
> > my $initializer =
> > BioMart::Initializer->new('registryFile'=>$confFile,
> > 'action'=>$action);
> > my $registry = $initializer->getRegistry;
> >
> > my $query =
> >
BioMart::Query->new('registry'=>$registry,'virtualSchemaName'=>'defaul
> > t');
> >
> >
> > $query->setDataset("compara_mart_blastznet_hsap_mmus");
> > $query->addFilter("mmus_dnafrag_start", ["1"]);
> > $query->addFilter("mmus_chro", ["1"]);
> > $query->addFilter("mmus_dnafrag_end", ["10000000"]);
> > $query->addAttribute("pairwise_genomic_alignments");
> >
> > my $query_runner = BioMart::QueryRunner->new();
> > ############################## GET COUNT
> > ############################ $query->count(1);
> > $query_runner->execute($query); print $query_runner->getCount();
> >
#####################################################################
> >
> >
> > ############################## GET RESULTS
##########################
> > # to obtain unique rows only
> > # $query_runner->uniqueRowsOnly(1);
> >
> > $query_runner->execute($query);
> > $query_runner->printHeader();
> > $query_runner->printResults();
> > $query_runner->printFooter();
> >
#####################################################################
> >
> > Matthias Wahl, PhD
> > Stowers Institute for Medical Research
> > 1000 E. 50th Street
> > Kansas City, MO 64110
> > Phone: 816-926-4302
> > Fax: 816-926-2044
> > E-mail : [EMAIL PROTECTED]
> > http://www.stowers-institute.org/
> >
