NAME

Bio::LiveSeq::Transcript - Transcript class for LiveSeq

SYNOPSIS

# documentation needed

DESCRIPTION

This stores informations about coding sequences (CDS). The implementation is that a Transcript object accesses a collection of Exon objects, inferring from them the nucleotide structure and sequence.

AUTHOR - Joseph A.L. Insana

Email: Insana@ebi.ac.uk, jinsana@gmx.net

Address:

EMBL Outstation, European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambs. CB10 1SD, United Kingdom 

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

Title   : new
Usage   : $transcript = Bio::LiveSeq::Transcript->new(-exons => \@obj_refs);

Function: generates a new Bio::LiveSeq::Transcript
Returns : reference to a new object of class Transcript
Errorcode -1
Args    : reference to an array of Exon object references

all_Exons

Title   : all_Exons
Usage   : $transcript_obj->all_Exons()
Function: returns references to all Exon objects the Transcript is composed of
Example : foreach $exon ($transcript->all_Exons()) { do_something }
Returns : array of object references
Args    : none

downstream_seq

Title   : downstream_seq
Usage   : $transcript_obj->downstream_seq()
        : $transcript_obj->downstream_seq(64)
Function: returns a string of nucleotides downstream of the end of the
          CDS. If there is some information of the real mRNA, from features in
          an attached Gene object, it will return up to those boundaries.
          Otherwise it will return 1000 nucleotides.
          If an argument is given it will override the default 1000 number
          and return instead /that/ requested number of nucleotides.
          But if a Gene object is attached, this argument will be ignored.
Returns : string
Args    : an optional integer number of nucleotides to be returned instead of
          the default if no gene attached

upstream_seq

Title   : upstream_seq
Usage   : $transcript_obj->upstream_seq()
        : $transcript_obj->upstream_seq(64)
Function: just like downstream_seq but returns nucleotides before the ATG
Note    : the default, if no Gene information present and no nucleotides
          number given, is to return up to 400 nucleotides.

get_Translation

Title   : valid
Usage   : $translation = $obj->get_Translation()
Function: retrieves the reference to the object of class Translation (if any)
          attached to a LiveSeq object
Returns : object reference
Args    : none

translation_table

Title   : translation_table
Usage   : $name = $obj->translation_table;
        : $name = $obj->translation_table(11);
Function: Returns or sets the translation_table used for translating the
          transcript.
          If it has never been set, it will return undef.
Returns : an integer

frame

Title   : frame
Usage   : $frame = $transcript->frame($label);
Function: Returns the frame of a particular nucleotide.
          Frame can be 0 1 or 2 and means the position in the codon triplet
          of the particulat nucleotide. 0 is the first codon_position.
          Codon_position (1 2 3) is simply frame+1.
          If the label asked for is not inside the Transcript, -1 will be
          returned.
Args    : a label
Returns : 0 1 or 2
Errorcode -1