Webservice::InterMine::Bio::RegionQuery - Genomic Interval based queries.
my $service = Webservice::InterMine->get_service('flymine', 'API-KEY'); my $region_query = Webservice::InterMine::Bio::RegionQuery->new( service => $service, organism => "D. melanogaster", regions => ["2L:14614843..14619614", "Foo",], # Foo will be ignored. feature_types => ["Exon", "Transcript"], ); print "Sequence data...", "\n"; print $region_query->bed; print $region_query->fasta; print $region_query->gff3; print "Making a list... (requires an API-KEY)", "\n"; my $list = $service->new_list(content => $region_query);
An abstraction of the API methods offered by biological mines for performing genomic region based queries. These queries search for features of given types overlapping a specified set of regions in a given organism. The features may be either retrieved in biological formats, or stored as a list of features on the originating server. Creating lists will require the use of an API-Key.
A reference to an InterMine webservice.
The short name (eg: "D. melanogaster") for the organism these regions refer to.
A list of feature types to search the regions for. These should all be valid names for classes that inherit from SequenceFeature.
A list of regions to search for features within. These should all be valid regions in either BED format, or dotted notation (eg: "2L:14614843..14619614" or "2R\t5866034\t5868996"). Invalid regions will be ignored.
A number of base-pairs to extend the regions on either side. Defaults to 0.
Whether or not the regions should be interpreted as interbase co-ordinates. Defaults to false.
Returns the request parameters that this region query represents. This method is a required part of the Listable role.
Returns the path to append to the base url to create a new list. This method is a required part of the Listable role.
Returns the path to append to the base url to append elements to an existing list. At present this is not implemented. This method is a required part of the Listable role.
Returns the sequence feature data as a string in BED format.
Returns the sequence feature data as a string in FASTA format.
Returns the sequence feature data as a string in GFF3 format.