Bio::LiveSeq::Transcript(3pm)				User Contributed Perl Documentation			     Bio::LiveSeq::Transcript(3pm)

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

perl v5.14.2							    2012-03-02					     Bio::LiveSeq::Transcript(3pm)