Christopher Fields > BioPerl > Bio::LiveSeq::Transcript

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NAME ^

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

SYNOPSIS ^

  # documentation needed

DESCRIPTION ^

This stores information 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
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