Author image Zhenguo Zhang
and 1 contributors

NAME

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

SYNOPSIS

        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

DESCRIPTION

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

METHODS

new

 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:
-seq

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.

-id

the sequence name

-desc

extra description of this sequence

length

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

id

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

desc

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

seq

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

AUTHOR

Zhenguo Zhang, <zhangz.sci at gmail.com>

BUGS

Please report any bugs or feature requests to bug-bio-cua at rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-CUA. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.

SUPPORT

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

    perldoc Bio::CUA::Seq

You can also look for information at:

ACKNOWLEDGEMENTS

LICENSE AND COPYRIGHT

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 http://www.gnu.org/licenses/.