Hi Syed, Since none of the BioMart APIs actually return results in a data structure (it only returns formatted files like TSV, etc) I was trying to be helpful and show other developers on this forum how they can go about populating a Perl data structure from the results returned by BioMart.
It's not obvious after reading the docs and when you get started how you need to do this, one initially expects in the APIs that there would be for e.g. in the Perl API some method call ->getResults() which returns an @array of arrayrefs structure or in the REST API that there would be an option to return for e.g. a JSON serialized data structure that can be unserialized into a native data structure for the language you are using. best, Leandro On Wed, Jul 14, 2010 at 3:21 PM, Syed Haider <[email protected]> wrote: > Hi Leandro, > > this is the only method that returns the results. What exactly are you after > ? > > Best > Syed > > On 14/07/2010 13:14, Leandro Hermida wrote: >> >> 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 >>>> >>>> >>> >
