Author image Zhenguo Zhang
and 1 contributors

NAME

Bio::CUA::SeqIO - a package to parse sequence file if module Bio::SeqIO is unavailable in the system.

SYNOPSIS

        use Bio::CUA::SeqIO;

        # create an IO to a sequence file in FASTA format
        my $io = Bio::CUA::SeqIO->new("seq_file.fa")

        # read each sequence as a Bio::CUA::Seq object from this io
        while(my $seq = $io->next_seq)
        {
                printf("%s: %d\n", $seq->id, $seq->length);
        }

DESCRIPTION

This is an auxiliary module to process sequences in case the module Bio::SeqIO is not installed in the system. At present, this module can only process fasta-formatted sequence file.

METHODS

new

 Title   : new
 Usage   : $io = Bio::CUA::SeqIO->new(-file => "seq_file.fa")
 Function: create an IO to read sequences from a file
 Returns : an object of this class
 Args    : a hash in the format of
 -file => "seq_file.fa"

next_seq

 Title   : next_seq
 Usage   : my $seq = $self->next_seq;
 Function: read next sequence in the IO stream
 Returns : an object of L<Bio::CUA::Seq> or undef if no more
 sequence
 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::SeqIO

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/.