Author image Zhenguo Zhang
and 1 contributors


Bio::CUA::Seq - a module processing sequence object


        use Bio::CUA::Seq;

        my $obj = Bio::CUA::Seq->new(
                -seq  => 'AGGTGCCG...',
                -id   => 'test_id',
                -desc => 'sequence description'

        # available methods
        $obj->length; # get sequence length
        $obj->id; # get sequence id
        $obj->desc; # get sequence description
        $obj->seq; # get sequence string


This module is called by Bio::CUA::SeqIO to create sequence object which has some basic methods required by the modules in the distribution The purpose of this module is to increase the portability of the distribution.



 Title   : new
 Usage   : my $obj = Bio::CUA::Seq->new(%params);
 Function: create sequence object
 Returns : an object of this class
 Args    : arguments are specified in a hash and acceptable keys as follows:

the sequence string for the object, which can only be characters in the range A-Z and a-z. Other characters are eliminated by the method.


the sequence name


extra description of this sequence


 Title   : length
 Usage   : my $len = $self->length;
 Function: get the length of the sequence
 Returns : an integer
 Args    : None


 Title   : id
 Usage   : my $id = $self->id;
 Function: get sequence name/id
 Returns : a string
 Args    : None


 Title   : desc
 Usage   : my $desc = $self->desc
 Function: get sequence description
 Returns : a string or undef if not exist
 Args    : None


 Title   : seq
 Usage   : my $seq = $self->seq
 Function: get sequence string of the object
 Returns : a string
 Args    : None


Zhenguo Zhang, <zhangz.sci at>


Please report any bugs or feature requests to bug-bio-cua at, or through the web interface at I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.


You can find documentation for this module with the perldoc command.

    perldoc Bio::CUA::Seq

You can also look for information at:



Copyright 2015 Zhenguo Zhang.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see