Bio::LiveSeq::TranscriUser)Contributed Perl DocumenBio::LiveSeq::Transcript(3)NAMEBio::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
perl v5.14.1 2011-07-22 Bio::LiveSeq::Transcript(3)
