Dear Junjun,
Problem exists even with the code generated by BioMart (attached).
When I'm trying to retrieve protein sequences for 10-20 genes everything is
ok. But not for more.
Dear Paweł,
>
> Could you please send me your perl code so I can test it over here? It's
> likely just a temporary issue, may be at that time the server was quite
> busy.
>
> Best regards,
> Junjun
>
>
>
> ------------------------------
> *From:* [email protected] [mailto:[email protected]] *On
> Behalf Of *Pawel Labaj
> *Sent:* Tuesday, June 16, 2009 8:34 AM
> *To:* [email protected]
> *Subject:* [mart-dev] problems with executing query through Perl API
>
> Dear BioMart Team,
>
> Recently I have problems with executing some types of the queries under
> Perl BioMart API.
> For queries such as retrieving orthologues/paralogues there are no
> problems. (EnsEMBL database)
>
> They start when I'm trying sth bigger like transcripts and peptide
> sequences of genes.
> After retrieving between 20-70 rows (peptide sequence, gene id and
> transcripts id) I receive a message:
>
> "Problems with the web server: 500 read timeout"
>
> Some time ago with the same code I had no problems.
>
> Best wishes,
> --
> Paweł Łabaj
>
> Chair of Bioinformatics
> Department of Biotechnology
> Boku University Vienna
> A-1190 Muthgasse 18
> Austria, Europe
>
>
--
Paweł Łabaj
Chair of Bioinformatics
Department of Biotechnology
Boku University Vienna
A-1190 Muthgasse 18
Austria, Europe
# An example script demonstrating the use of BioMart API.
# This perl API representation is only available for configuration versions >= 0.5
use strict;
use BioMart::Initializer;
use BioMart::Query;
use BioMart::QueryRunner;
my $confFile = "/bi/common/src/BioMart/biomart-perl/conf/apiExampleRegistry.xml";
#
# NB: change action to 'clean' if you wish to start a fresh configuration
# and to 'cached' if you want to skip configuration step on subsequent runs from the same registry
#
my $action='cached';
my $initializer = BioMart::Initializer->new('registryFile'=>$confFile, 'action'=>$action);
my $registry = $initializer->getRegistry;
my $query = BioMart::Query->new('registry'=>$registry,'virtualSchemaName'=>'default');
$query->setDataset("ggallus_gene_ensembl");
$query->addFilter("ensembl_gene_id", ["ENSGALG00000011244", "ENSGALG00000001532", "ENSGALG00000008481", "ENSGALG00000017507", "ENSGALG00000002555", "ENSGALG00000011968", "ENSGALG00000000589", "ENSGALG00000007303", "ENSGALG00000019144", "ENSGALG00000010032", "ENSGALG00000006609", "ENSGALG00000009208", "ENSGALG00000013838", "ENSGALG00000010692", "ENSGALG00000015623", "ENSGALG00000004986", "ENSGALG00000000760", "ENSGALG00000007891", "ENSGALG00000014509", "ENSGALG00000011358", "ENSGALG00000014389", "ENSGALG00000004097", "ENSGALG00000020388", "ENSGALG00000019547", "ENSGALG00000002546", "ENSGALG00000002931", "ENSGALG00000011455", "ENSGALG00000016829", "ENSGALG00000015142", "ENSGALG00000001883", "ENSGALG00000013579", "ENSGALG00000015972", "ENSGALG00000023070", "ENSGALG00000012415", "ENSGALG00000014256", "ENSGALG00000021589", "ENSGALG00000011469", "ENSGALG00000008473", "ENSGALG00000004661", "ENSGALG00000024481", "ENSGALG00000016791", "ENSGALG00000021620", "ENSGALG00000017301", "ENSGALG00000003476", "ENSGALG00000000044", "ENSGALG00000008973", "ENSGALG00000009637", "ENSGALG00000015746", "ENSGALG00000004293", "ENSGALG00000005519", "ENSGALG00000017247", "ENSGALG00000015028", "ENSGALG00000020390", "ENSGALG00000023517", "ENSGALG00000021490", "ENSGALG00000005102", "ENSGALG00000006715", "ENSGALG00000005907", "ENSGALG00000006594", "ENSGALG00000017239", "ENSGALG00000000545", "ENSGALG00000016071", "ENSGALG00000012308", "ENSGALG00000011193", "ENSGALG00000014582", "ENSGALG00000006498", "ENSGALG00000011696", "ENSGALG00000017041", "ENSGALG00000021238", "ENSGALG00000000560", "ENSGALG00000006382", "ENSGALG00000006346", "ENSGALG00000021016", "ENSGALG00000004732", "ENSGALG00000021577", "ENSGALG00000014008", "ENSGALG00000015958", "ENSGALG00000011347", "ENSGALG00000016678", "ENSGALG00000006409", "ENSGALG00000004463", "ENSGALG00000003161", "ENSGALG00000010399", "ENSGALG00000002024", "ENSGALG00000001361", "ENSGALG00000000251", "ENSGALG00000002613", "ENSGALG00000003433", "ENSGALG00000006876", "ENSGALG00000002553", "ENSGALG00000017381", "ENSGALG00000016523", "ENSGALG00000007837", "ENSGALG00000011152", "ENSGALG00000017334", "ENSGALG00000011813", "ENSGALG00000011509", "ENSGALG00000000761", "ENSGALG00000000569", "ENSGALG00000021314", "ENSGALG00000005534", "ENSGALG00000005116", "ENSGALG00000016478", "ENSGALG00000019233", "ENSGALG00000011921", "ENSGALG00000017046", "ENSGALG00000006000", "ENSGALG00000008286", "ENSGALG00000003389", "ENSGALG00000024484", "ENSGALG00000005694", "ENSGALG00000006613", "ENSGALG00000000771", "ENSGALG00000016677", "ENSGALG00000007914", "ENSGALG00000001071", "ENSGALG00000007785", "ENSGALG00000001370", "ENSGALG00000003479", "ENSGALG00000012504", "ENSGALG00000008664", "ENSGALG00000021559", "ENSGALG00000012798", "ENSGALG00000015030", "ENSGALG00000006097", "ENSGALG00000021313", "ENSGALG00000012417", "ENSGALG00000016256", "ENSGALG00000014014", "ENSGALG00000007102", "ENSGALG00000006403", "ENSGALG00000007807", "ENSGALG00000008359", "ENSGALG00000003118", "ENSGALG00000007814", "ENSGALG00000019061", "ENSGALG00000006995", "ENSGALG00000003196", "ENSGALG00000009095", "ENSGALG00000014908", "ENSGALG00000022098", "ENSGALG00000009724", "ENSGALG00000008418", "ENSGALG00000001884", "ENSGALG00000004893", "ENSGALG00000008272", "ENSGALG00000010718", "ENSGALG00000017172", "ENSGALG00000004438", "ENSGALG00000015058", "ENSGALG00000005503", "ENSGALG00000010597", "ENSGALG00000003014", "ENSGALG00000005427", "ENSGALG00000003103", "ENSGALG00000000850", "ENSGALG00000006441", "ENSGALG00000016491", "ENSGALG00000016800", "ENSGALG00000023605", "ENSGALG00000013697", "ENSGALG00000020956", "ENSGALG00000003933", "ENSGALG00000012193", "ENSGALG00000005985", "ENSGALG00000015347", "ENSGALG00000000548", "ENSGALG00000000608", "ENSGALG00000000498", "ENSGALG00000006507", "ENSGALG00000001150", "ENSGALG00000012185", "ENSGALG00000002075", "ENSGALG00000011149", "ENSGALG00000006206", "ENSGALG00000015677", "ENSGALG00000003742", "ENSGALG00000006998", "ENSGALG00000020389", "ENSGALG00000013200", "ENSGALG00000004361", "ENSGALG00000004050", "ENSGALG00000008551", "ENSGALG00000007471", "ENSGALG00000016160", "ENSGALG00000006318", "ENSGALG00000017343", "ENSGALG00000020151", "ENSGALG00000007620", "ENSGALG00000013925", "ENSGALG00000011826", "ENSGALG00000007906", "ENSGALG00000004533", "ENSGALG00000005730", "ENSGALG00000001009", "ENSGALG00000009546", "ENSGALG00000012671", "ENSGALG00000013773", "ENSGALG00000001250", "ENSGALG00000005688", "ENSGALG00000005675", "ENSGALG00000011485", "ENSGALG00000010969", "ENSGALG00000007910", "ENSGALG00000002958", "ENSGALG00000005892", "ENSGALG00000006009", "ENSGALG00000013674", "ENSGALG00000012899", "ENSGALG00000016035", "ENSGALG00000013869", "ENSGALG00000005628", "ENSGALG00000017715", "ENSGALG00000002913"]);
$query->addAttribute("peptide");
$query->addAttribute("ensembl_gene_id");
$query->addAttribute("ensembl_transcript_id");
$query->formatter("TSV");
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();
#####################################################################
