NAME
Webservice::InterMine::Bio::RegionQuery - Genomic Interval based queries.
SYNOPSIS
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);DESCRIPTION
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.
ATTRIBUTES
service (Service required)
A reference to an InterMine webservice.
organism (Str required)
The short name (eg: "D. melanogaster") for the organism these regions refer to.
feature_types (ArrayRef[Str] required)
A list of feature types to search the regions for. These should all be valid names for classes that inherit from SequenceFeature.
regions (ArrayRef[Str] required)
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.
extension (Int = 0)
A number of base-pairs to extend the regions on either side. Defaults to 0.
is_interbase (Bool = false)
Whether or not the regions should be interpreted as interbase co-ordinates. Defaults to false.
METHODS
get_list_request_parameters(List[Str => Str])
Returns the request parameters that this region query represents. This method is a required part of the Listable role.
list_upload_path (Str)
Returns the path to append to the base url to create a new list. This method is a required part of the Listable role.
list_append_path (Str)
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.
bed (Str)
Returns the sequence feature data as a string in BED format.
fasta (Str)
Returns the sequence feature data as a string in FASTA format.
gff3 (Str)
Returns the sequence feature data as a string in GFF3 format.