Sorry forgot to post what I did before! For those of your who use the
Biomart APIs and want to get results back into a Perl data structures,
here is the approach I use:
If using the Perl API:
use BioMart::Initializer;
use BioMart::Query;
use BioMart::QueryRunner;
my $bm_initializer = BioMart::Initializer->new(
registryFile => "/path/to/myRegistry.xml",
action => 'update',
);
my $bm_query = BioMart::Query->new(
registry => $bm_initializer->getRegistry(),
virtualSchemaName => 'default'
);
$bm_query->setDataset('my_dataset');
$bm_query->addFilter('attr1', ['Q6LTE1']);
$bm_query->addAttribute('attr2');
$bm_query->addAttribute('attr3');
$bm_query->formatter('TSV');
my $bm_query_runner=BioMart::QueryRunner->new();
$bm_query_runner->uniqueRowsOnly(1);
$bm_query_runner->execute($bm_query);
open(RESULTS, '+>', \my $results) or die "$!\n";
$bm_query_runner->printResults(\*RESULTS);
seek(RESULTS, 0, 0);
while (<RESULTS>) {
chomp;
my @row_fields = split /\t/;
# build up a data structure or processed your fields here...
}
close(RESULTS);
Using the REST API:
use LWP::UserAgent ();
my $query_xml = <<XML;
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query virtualSchemaName="default" formatter="TSV" header="0"
uniqueRows="1" count="" datasetConfigVersion="0.7">
<Dataset name="my_dataset" interface="default">
<Filter name="attr1" value="Q6LTE1"/>
<Attribute name="attr2" />
<Attribute name="attr3" />
</Dataset>
</Query>
XML
my $ua = LWP::UserAgent->new();
my $response = $ua->post('http://myserver.mydomain:9002/biomart/martservice',
[ query => $query_xml ]);
if ($response->is_success and $response->decoded_content !~
/BioMart::Exception/i) {
open(RESULTS, '<', \$response->decoded_content) or die "$!\n";
while (<RESULTS>) {
chomp;
my @row_fields = split /\t/;
# build up a data structure or processed your fields here...
}
close(RESULTS);
}
else {
die $response->decoded_content, "\n";
}
On Thu, Jun 10, 2010 at 12:03 AM, Syed Haider <[email protected]> wrote:
> Hi Leandro,
>
> The datastructures representation of results is not returned by the API. If
> you are feeling adventurous please feel free to look into the
> lib/BioMart/Formatter/ directory for the appropriate formatter that you are
> interested in.
>
>
> Best
> Syed
>
>
>
> On 09/06/2010 17:51, Leandro Hermida wrote:
>>
>> Hi,
>>
>> I was wondering if there is a way using the Perl API to get results in a
>> Perl data structure and, if possible, row by row. For example each row
>> returned as an array or arrayref. It seems inefficient to take
>> printResults() and have to break everything up again when I know somewhere
>> in the Perl API it was doing the reverse...
>>
>> thanks,
>> Leandro
>>
>>
>
