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.

cpanm Webservice::InterMine::Bio

perl -MCPAN -e shell
install Webservice::InterMine::Bio