Bio::EnsEMBL::IdMapping::TinyTranscript Class Reference

Inheritance diagram for Bio::EnsEMBL::IdMapping::TinyTranscript:

Public Member Functions
public Int	start ()
public Int	end ()
public Int	strand ()
public Int	length ()
public String	seq_md5_sum ()
public void	add_Translation ()
public Bio::EnsEMBL::IdMapping::TinyTranslation	translation ()
public void	add_Exon ()
public Arrayref	get_all_Exons ()
public String	biotype ()
public String	seq_region_name ()
Public Member Functions inherited from Bio::EnsEMBL::IdMapping::TinyFeature
public Bio::EnsEMBL::IdMapping::TinyFeature	new_fast ()
public Int	id ()
public String	stable_id ()
public Int	version ()
public String	created_date ()
public String	modified_date ()
public String	to_string ()

Detailed Description

Synopsis

# fetch a transcript from the db and create a lightweight
# transcript object from it
my $tr = $transcript_adaptor->fetch_by_stable_id('ENST000345437');
my $lightweight_tr =
  Bio::EnsEMBL::IdMapping::TinyTranscript->new_fast( [
    $tr->dbID,          $tr->stable_id,
    $tr->version,       $tr->created_date,
    $tr->modified_date, $tr->start,
    $tr->end,           $tr->strand,
    $tr->length,        md5_hex( $tr->spliced_seq ),
  ] );

Description

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

Definition at line 29 of file TinyTranscript.pm.

Member Function Documentation

add_Exon()

public void Bio::EnsEMBL::IdMapping::TinyTranscript::add_Exon

(

)

  Arg[1]      : Bio::EnsEMBL::IdMapping::TinyExon $exon - the exon to add
  Example     :

$tiny_transcript->add_Exon($tiny_exon);

  Description : Adds an exon to this transcript.
  Return type : none
  Exceptions  : thrown on wrong or missing argument
  Caller      : general
  Status      : At Risk
              : under development

Code:

add_Translation()

public void Bio::EnsEMBL::IdMapping::TinyTranscript::add_Translation

(

)

  Arg[1]      : Bio::EnsEMBL::IdMapping::TinyTranslation $tl - the translation
                to add
  Example     :

$tiny_transcript->add_Translation($tiny_translation);

  Description : Adds a translation to this transcript.
  Return type : none
  Exceptions  : thrown on wrong or missing argument
  Caller      : general
  Status      : At Risk
              : under development

Code:

biotype()

public String Bio::EnsEMBL::IdMapping::TinyTranscript::biotype

(

)

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

Code:

end()

public Int Bio::EnsEMBL::IdMapping::TinyTranscript::end

(

)

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

Code:

get_all_Exons()

public Arrayref Bio::EnsEMBL::IdMapping::TinyTranscript::get_all_Exons

(

)

  Example     :

 foreach my $exon (@{ $tiny_transcript->get_all_Exons }) {
@section autotoc_md17 do something with exon
                }

  Description : Returns all exons attached to that transcript.
  Return type : Arrayref of Bio::EnsEMBL::IdMapping::TinyExon objects
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

length()

public Int Bio::EnsEMBL::IdMapping::TinyTranscript::length

(

)

  Arg[1]      : (optional) Int - the transcript's length
  Description : Getter/setter for the transcript's length. Note that this is
                *not* the distance between start and end, but rather the sum of
                the lengths of all exons.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

seq_md5_sum()

public String Bio::EnsEMBL::IdMapping::TinyTranscript::seq_md5_sum

(

)

  Arg[1]      : (optional) String - the md5 digest of the transcript's sequence
  Description : Getter/setter for the md5 digest of the transcript's sequence.
                Note that when used as a setter, you are expected to pass a
                digest, not the raw sequence (i.e. the digest is not created for
                you).
  Return type : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

seq_region_name()

public String Bio::EnsEMBL::IdMapping::TinyTranscript::seq_region_name

(

)

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

Code:

start()

public Int Bio::EnsEMBL::IdMapping::TinyTranscript::start

(

)

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

Code:

strand()

public Int Bio::EnsEMBL::IdMapping::TinyTranscript::strand

(

)

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

Code:

translation()

public Bio::EnsEMBL::IdMapping::TinyTranslation Bio::EnsEMBL::IdMapping::TinyTranscript::translation

(

)

  Description : Getter for the transcript's translation.
  Return type : Bio::EnsEMBL::IdMapping::TinyTranslation
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

---

The documentation for this class was generated from the following file:

• ensembl/modules/Bio/EnsEMBL/IdMapping/TinyTranscript.pm