Bio::CUA::SeqIO - a package to parse sequence file if module Bio::SeqIO is unavailable in the system.
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); }
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.
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"
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
Zhenguo Zhang, <zhangz.sci at gmail.com>
<zhangz.sci at gmail.com>
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.
bug-bio-cua at rt.cpan.org
You can find documentation for this module with the perldoc command.
perldoc Bio::CUA::SeqIO
You can also look for information at:
RT: CPAN's request tracker (report bugs here)
http://rt.cpan.org/NoAuth/Bugs.html?Dist=Bio-CUA
AnnoCPAN: Annotated CPAN documentation
http://annocpan.org/dist/Bio-CUA
CPAN Ratings
http://cpanratings.perl.org/d/Bio-CUA
Search CPAN
http://search.cpan.org/dist/Bio-CUA/
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/.
To install Bio::CUA, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::CUA
CPAN shell
perl -MCPAN -e shell install Bio::CUA
For more information on module installation, please visit the detailed CPAN module installation guide.