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Bio-EnsEMBL-112.0_52
River stage zero No dependents
/ Bio::EnsEMBL::Upstream

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
  developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.

  Questions may also be sent to the Ensembl help desk at
  <http://www.ensembl.org/Help/Contact>.

NAME

Bio::EnsEMBL::Upstream - Object that defines an upstream region

SYNOPSIS

  use Bio::EnsEMBL::Upstream;

  my $upstream = Bio::EnsEMBL::Upstream->new(
    -transcript => $transcript,
    -length     => 2000           # bp
  );

  # Retrieve coordinates of upstream region
  my $upstream_region_start = $upstream->upstart;
  my $upstream_region_end   = $upstream->upend;

  # Retrieve coordinates in 'downstream' first intron
  my $intron_region_start = $upstream->downstart;
  my $intron_region_end   = $upstream->downend;

  # Coordinates are returned in the same scheme as the input transcript.
  # However, the coordinates of an upstream region can be transformed to
  # any other scheme using a slice

  $upstream->transform($slice);

  # Coordinates can be retrieved in scheme in the same manner as the
  # above.

DESCRIPTION

An object that determines the upstream region of a transcript. Such a region is non-coding and ensures that other genes or transcripts are not present. Ultimately, these objects can be used to looking for promoter elements. To this end, it is also possible to derive a region downstream of the first exon, within the first intron and where promoter elements sometimes are found.

METHODS

new

  Arg [transcript] : (optional) Bio::EnsEMBL::Transcript
  Arg [length]     : (optional) int $length
  Example    : $upstream = Bio::EnsEMBL::Upstream->new(-transcript => $transcript, 
                                                       -length => 2000);
  Description: Creates a new upstream object
  Returntype : Bio::EnsEMBL::Upstream
  Exceptions : none
  Caller     : Bio::EnsEMBL::Transcript, general
  Status     : Stable

transcript

  Arg        : (optional) Bio::EnsEMBL::Transcript
  Example    : $self->transcript($transcript);
  Description: Getter/setter for transcript object
  Returntype : Bio::EnsEMBL::Transcript
  Exceptions : Throws if argument is not undefined 
               or a Bio::EnsEMBL::Transcript
  Caller     : $self->new, $self->_derive_coords, 
               $self->_first_coding_Exon
  Status     : Stable

length

  Arg        : (optional) int $length
  Example    : $self->length(2000); # bp
  Description: Getter/setter for upstream region length.
  Returntype : int
  Exceptions : Throws if length is requested before it has been set.
  Caller     : $self->new, $self->_derive_coords
  Status     : Stable

_flush_cache

  Arg        : none
  Example    : $self->_flush_cache;
  Description: Empties cached coordinates (called when 
               coordinate scheme or region length has changed).
  Returntype : none
  Exceptions : none
  Caller     : $self->length, $self->transform
  Status     : Stable

upstart

  Arg        : none
  Example    : $self->upstart;
  Description: Returns the start coordinate of the region 
               upstream of the transcript.  This coordinate 
               is always the furthest from the translation 
               initiation codon, whereas upend always abutts 
               the translation initiation codon.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

upend

  Arg        : none
  Example    : $self->upend;
  Description: Returns the end coordinate of the region 
               upstream of the transcript.  This coordinate 
               always always abutts the translation 
               initiation codon, whereas upstart always 
               returns the coorindate furthest from the 
               translation initiation codon.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

downstart

  Arg        : none
  Example    : $self->downstart;
  Description: Returns the start coordinate of the region 
               in the first intron of the transcript.  This 
               coordinate is always closest to the first 
               exon (irregardless of strand).
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

downend

  Arg        : none
  Example    : $self->downend;
  Description: Returns the end coordinate of the region 
               in the first intron of the transcript.  This 
               coordinate is always furthest from the first 
               exon (irregardless of strand).
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

transform

  Arg        : 
  Example    : 
  Description: Not yet implemented
  Returntype : 
  Exceptions : 
  Caller     : 
  Status     : At Risk

derive_upstream_coords

  Arg        : none
  Example    : my ($upstart, $upend) 
                       = $self->derive_upstream_coords;
  Description: Derives upstream coordinates (for 
               compatability with older scripts).
  Returntype : arrayref
  Exceptions : none
  Caller     : general
  Status     : Stable

derive_downstream_coords

  Arg        : none
  Example    : my ($downstart, $downend) 
                       = $self->derive_downstream_coords;
  Description: Derives downstream coordinates (for 
               compatability with older scripts).
  Returntype : arrayref
  Exceptions : none
  Caller     : general
  Status     : Stable

_derive_coords

  Arg        : string $direction (either 'up' or 'down').
  Example    : $self->_derive_coords('up');
  Description: Determines the coordinates of either upstream 
               or downstream region.
  Returntype : none
  Exceptions : Throws if argument is not either 'up' or 'down'
  Caller     : $self->upstart, $self->upend, $self->downstart, 
               $self->downend
  Status     : Stable

_bases_to_trim

  Arg        : string $end_to_trim (either 'right_end' or 
               'left_end').
  Arg        : Bio::EnsEMBL::Slice
  Example    : $self->_derive_coords('right_end', $slice);
  Description: Finds exons from other genes/transcripts that
               invade our upstream/downstream slice and 
               returns the number of bases that should be 
               truncated from the appropriate end of the 
               upstream/downstream region.
  Returntype : in
  Exceptions : Throws if argument is not either 'right_end' 
               or 'left_end'
  Caller     : $self->_derive_coords
  Status     : Stable

_first_coding_Exon

  Arg        : none
  Example    : $self->_first_coding_Exon;
  Description: Finds the first exon of our transcript that 
               contains coding bases.
  Returntype : Bio::EnsEMBL::Exon
  Exceptions : none
  Caller     : $self->_derive_coords, $self->_bases_to_trim
  Status     : Stable