Hi Matthias
I am slightly lost now... The following query does work on my end and
finishes in couple of seconds.
$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");
however with out any filters, I just started it and now waiting for the
results to finish. I expect it to take substantial time given I am not
using any filters.
Please let me know if there is something I am missing.
I will keep you posted about performance on my end.
cheers
syed
On Sat, 2007-08-25 at 13:48 -0500, Wahl, Matthias wrote:
> Hy Syed,
>
> I thought I am filtering for human chromosome 1, bases 9990000 to 10000000 by
> adding the following:
>
>
> > $query->addFilter("hsap_dnafrag_end", ["10000000"]);
> > $query->addFilter("hsap_chro", ["1"]);
> > $query->addFilter("hsap_dnafrag_start", ["9990000"]);
>
> Thanks,
>
> Matthias
>
>
> -----Original Message-----
> From: Syed Haider [mailto:[EMAIL PROTECTED]
> Sent: Sat 8/25/2007 2:19 PM
> To: Wahl, Matthias
> Cc: [email protected]
> Subject: RE: [mart-dev] Biomart - pairwise_genomic_alignments
>
> Hi Matthias,
> could you confirm if thats your query
>
> $query->setDataset("compara_mart_blastznet_hsap_mmus");
> $query->addAttribute("pairwise_genomic_alignments");
>
> and no filters at all ?
>
> cheers
> syed
>
>
> On Sat, 2007-08-25 at 11:03 -0500, Wahl, Matthias wrote:
> > 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/
> > > >
>
>
