Linux Certif

Toute la documentation sur la certification Linux LPI

Bio::LiveSeq::Transcript.3pm

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

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