Location: /modules/EnsEMBL/Web/Object/DAS/enhanced_transcript.pm
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  • Features (EnsEMBL::Web::Object::DAS::transcript)


  • Types (EnsEMBL::Web::Object::DAS::transcript)


  • EntryPoints (EnsEMBL::Web::Object::DAS)
  • FeatureIDs (EnsEMBL::Web::Object::DAS)
  • FeatureTypes (EnsEMBL::Web::Object::DAS)
  • GroupIDs (EnsEMBL::Web::Object::DAS)
  • Locations (EnsEMBL::Web::Object::DAS)
  • Stylesheet (EnsEMBL::Web::Object::DAS::transcript)
  • Stylesheet (EnsEMBL::Web::Object::DAS)
  • Types (EnsEMBL::Web::Object::DAS)
  • _Stylesheet (EnsEMBL::Web::Object::DAS)
  • _group_info
  • _group_info (EnsEMBL::Web::Object::DAS::transcript)
  • base_features (EnsEMBL::Web::Object::DAS)
  • get_projections (EnsEMBL::Web::Object::DAS)
  • loc (EnsEMBL::Web::Object::DAS)
  • new (EnsEMBL::Web::Object::DAS)
  • ori (EnsEMBL::Web::Object::DAS)
  • project_onto_coord_system (EnsEMBL::Web::Object::DAS::transcript)
  • real_species (EnsEMBL::Web::Object::DAS)
  • slice_cache (EnsEMBL::Web::Object::DAS)
Documentation coverage: 10 %


    debugging - return chromosomal coordinates as well as clone coordinates when requested DO NOT use when live. Also print some warnings Return das features... structure returned is an arrayref of hashrefs, each array element refers to a different segment, the hashrefs contain segment info (seg type, seg name, seg start, seg end) and an array of feature hashes

    For transcripts the format is:

    > {species}.ASSEMBLY[-{coordinate_system}]/[enhanced_]transcript[-{database}[-{logicname}]*]

    If database is missing assumes core, if logicname is missing assumes all transcript features

    coordinate_system defines the coord system on whihc to return the features E.g..

    * /das/Homo_sapiens.NCBI36-toplevel.transcript-core-ensembl

    * /das/Homo_sapiens.NCBI36-clone.transcript-vega

    Part 4 Fetch features on the segments requested... The approach is to map all requested slices onto the top level in the Factory, irrespective of their actual coord system. By retrieving features on this top level coord_system partially overlapping features can be retrieved. When features are requested to be *returned* on a different coordinate system such as clone, then this change in coordinates is done at the very end, using information in the %projection_mappings hash.
    Part 6 Grab and return features Now we do all the nasty stuff of retrieving features and creating DAS objects for them...
    Part 7 Return the reference to an array of the slice specific hashes.
    _ Part 1 initialize data structures...
    _ Part 2 parse the DSN to work out what we want to display Relevant part of DSN is stored in $ENV{'ENSEMBL_DAS_SUBTYPE'}
    _ Part 3 parse CGI parameters to get out feature types, group ids and feature ids * FeatureTypes - Currently ignored... * Group IDs - filter in this case transcripts * Feature IDs - filter in ths case exons
    _ Part 5 Fetch features based on group_id and filter_id - filter_id currently only works for exons and group_id only for transcripts

    Inherited from EnsEMBL::Web::Object::DAS::transcript
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    Returns a list of types served by this das source....
    Inherited from EnsEMBL::Web::Object::DAS::transcript
    View source