LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

CONTACT

  Please email comments or questions to the public Ensembl
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  Questions may also be sent to the Ensembl help desk at
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NAME

Bio::EnsEMBL::IdMapping::TinyExon - lightweight exon object

SYNOPSIS

  # fetch an exon from the db and create a lightweight exon object
  # from it
  my $exon = $exon_adaptor->fetch_by_stable_id('ENSE000345437');
  my $lightweight_exon = Bio::EnsEMBL::IdMapping::TinyExon->new_fast( [
      $exon->dbID,
      $exon->stable_id,
      $exon->version,
      $exon->created_date,
      $exon->modified_date,
      $exon->start,
      $exon->end,
      $exon->strand,
      $exon->slice->seq_region_name,
      $exon->slice->coord_system_name,
      $exon->slice->coord_system->version,
      $exon->slice->subseq( $exon->start, $exon->end, $exon->strand ),
      $exon->phase,
      $need_project,
  ] );

DESCRIPTION

This is a lightweight exon object for the stable Id mapping. See the documentation in TinyFeature for general considerations about its design.

METHODS

  start
  end
  strand
  seq_region_name
  coord_system_name
  coord_system_version
  seq
  phase
  need_project
  common_start
  common_end
  common_strand
  common_sr_name
  length

start

  Arg[1]      : (optional) Int - the exon's start coordinate
  Description : Getter/setter for the exon's start coordinate.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

end

  Arg[1]      : (optional) Int - the exon's end coordinate
  Description : Getter/setter for the exon's end coordinate.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

strand

  Arg[1]      : (optional) Int - the exon's strand
  Description : Getter/setter for the exon's strand.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

seq_region_name

  Arg[1]      : (optional) String - seq_region name
  Description : Getter/setter for the seq_region name of the slice the exon is
                on.
  Return type : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

coord_system_name

  Arg[1]      : (optional) String - coord_system name
  Description : Getter/setter for the coord_system name of the slice the exon is
                on.
  Return type : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

coord_system_version

  Arg[1]      : (optional) String - coord_system version
  Description : Getter/setter for the coord_system version of the slice the
                exon is on.
  Return type : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

seq

  Arg[1]      : (optional) String - the exon's sequence
  Description : Getter/setter for the exon's sequence.
  Return type : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

phase

  Arg[1]      : (optional) Int - the exon's phase
  Description : Getter/setter for the exon's phase.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

need_project

  Arg[1]      : (optional) Boolean - attribute to set
  Description : Getter/setter for the attribute determining whether an exon
                needs to be projected onto a common coord_system. You don't need
                to do so if the native coord_system is common to the source and
                target assemblies, or if no common coord_system is found (the
                Cache object has methods to determine this).
  Return type : Boolean
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

common_start

  Arg[1]      : (optional) Int - the exon's start in common coord_system
                coordinates
  Description : Getter/setter for the exon's start in common coord_system
                coordinates. Will return $self->start if no projection to a
                common coord_system is required.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

common_end

  Arg[1]      : (optional) Int - the exon's end in common coord_system
                coordinates
  Description : Getter/setter for the exon's end in common coord_system
                coordinates. Will return $self->end if no projection to a
                common coord_system is required.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

common_strand

  Arg[1]      : (optional) Int - the exon's strand in common coord_system
                coordinates
  Description : Getter/setter for the exon's strand in common coord_system
                coordinates. Will return $self->strand if no projection to a
                common coord_system is required.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

common_sr_name

  Arg[1]      : (optional) String - seq_region name of the exon's slice on the
                common coord_system
  Description : Getter/setter for the seq_region name of the exon's slice on the
                common coord_system coordinates. Will return
                $self->seq_region_name if no projection to a common coord_system
                is required.
  Return type : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

length

  Description : Returns the exon length (distance between start and end).
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

cpanm Bio::EnsEMBL

perl -MCPAN -e shell
install Bio::EnsEMBL