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Trouble with BioMart Perl API installation

Dear all, I am trying to install BioMart Perl API (in order to automatize orthologs retrieval in other species for some gene), and I have followed the instructions here. And I'm almost done! Yet, I have the following error when I try to run my example script:

perl apiExample17112015.pl

junk after document element at line 18, column 0, byte 465 at /home/tlorin/perl5/perlbrew/perls/perl-5.20.2/lib/site_perl/5.20.2/x86_64-linux-thread-multi/XML/Parser.pm line 187.

Here is my example script:

# An example script demonstrating the use of BioMart API.
# This perl API representation is only available for configuration versions >=  0.5
use strict;
use lib '/home/tlorin/biomart-perl/lib/';
use BioMart::Initializer;
use BioMart::Query;
use BioMart::QueryRunner;

my $confFile = "../conf/martURLLocation.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='clean';
my $initializer = BioMart::Initializer->new('registryFile'=>$confFile, 'action'=>$action);
my $registry = $initializer->getRegistry;

my $query = BioMart::Query->new('registry'=>$registry,'virtualSchemaName'=>'default');


$query->setDataset("drerio_gene_ensembl");
$query->addFilter("ensembl_gene_id", ["ENSDARG00000003732"]);
$query->addAttribute("ensembl_gene_id");
$query->addAttribute("ensembl_transcript_id");
$query->addAttribute("pformosa_homolog_ensembl_gene");
$query->addAttribute("gmorhua_homolog_ensembl_gene");
$query->addAttribute("amexicanus_homolog_ensembl_gene");
$query->addAttribute("cintestinalis_homolog_ensembl_gene");
$query->addAttribute("lchalumnae_homolog_ensembl_gene");
$query->addAttribute("trubripes_homolog_ensembl_gene");

$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();

I must precise that I am not familiar with Perl and I have no idea of what could happen here. Any idea? Has someone already experienced that?

Thanks a lot for your time!

perl biomart ensembl api
• 3,589 views • link
updated by Ram Ram • written by tlorin tlorin

3 answers

I got it, thanks to @Jean-Karim Heriche:

My xml file was:

because I had pasted what was indicated on the Perl page (when you do a biomart search) at the end of the initial martURLLocation.xml file that was initially only:

<!DOCTYPE MartRegistry>
<MartRegistry>
<MartURLLocation
                    name         = "msd"
                    displayName  = "My BioMart Database"
                    host         = "www.biomart.org"
                    port         = "80"
                    visible      = "1"
                    default      = ""
                     includeDatasets = ""
                    martUser     = ""
>
</MartRegistry>

So I just deleted this first part and it's now working!

<!DOCTYPE MartRegistry>
<MartRegistry>
  <MartURLLocation database="ensembl_mart_82" default="1" displayName="Ensembl Genes 82" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ENSEMBL" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="sequence_mart_82" default="" displayName="Sequence" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_SEQUENCE" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="ontology_mart_82" default="" displayName="Ontology" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ONTOLOGY" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="genomic_features_mart_82" default="" displayName="Genomic features 82" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_GENOMIC" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
  <MartURLLocation database="snp_mart_82" default="" displayName="Ensembl Variation 82" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_SNP" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="regulation_mart_82" default="" displayName="Ensembl Regulation 82" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_FUNCGEN" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="vega_mart_82" default="" displayName="Vega 62" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_VEGA" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
  <MartURLLocation database="pride_mart_1" default="1" displayName="PRIDE (EBI UK)" host="www.ebi.ac.uk" includeDatasets="" martUser="" name="pride" path="/pride/biomart/martservice" port="80" redirect="1" serverVirtualSchema="default" visible="1" />
</MartRegistry>

Thanks again :D

• 1 views • link
updated by Ram Ram • written by tlorin tlorin

As the error message suggests, you have a malformed XML document. My guess is the culprit is martURLLocation.xml. Check that it is valid XML.

Edit: Just checked what EnsEMBL gives as martURLLocation.xml. There's a white line at the top, this usually causes XML parsers to throw an error.

• 1 views • link
written by Jean-Karim Heriche Jean-Karim Heriche

See my answer below, it was indeed a problem with this file but not due to initial blank line. Thanks :D

• 1 views • link
written by tlorin tlorin

Processing Cached Registry: /share/home/software/biomart-perl/conf/cachedRegistries/martURLLocation.xml.cached

Problems with the web server: 302 Found

Gene stable ID Transcript stable ID HGNC symbol
UniProtKB/Swiss-Prot ID

why I got this with nearly the same code?

• 0 views • link
written by mcclintock • mcclintock

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