NAME

Bio::CodonUsage::IO - for reading and writing codon usage tables to file

SYNOPSIS

use Bio::CodonUsage::IO;

## read in a codon usage file
my $io = Bio::CodonUsage::IO->new(-file => "in");
my $cut = $io->next_data();

## write it out again
my $out = Bio::CodonUsage::IO->new(-file => ">out");
$out->write_data($cut);

DESCRIPTION

This class provides standard IO methods for reading and writing text files of codon usage tables. These tables can initially be retrieved using Bio::DB::CUTG. At present only this format is supported for read/write.

Reading a CUTG will return a Bio::CodonUsage::Table object.

SEE ALSO

Bio::Tools::CodonTable, Bio::WebAgent, Bio::CodonUsage::Table, Bio::CodonUsage::IO

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

https://redmine.open-bio.org/projects/bioperl/

AUTHORS

Richard Adams, Richard.Adams@ed.ac.uk

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

Title  : new
Usage  : my $io = Bio::CodonUsage::IO->new(-file => "CUTfile");
Purpose: To  read/write a Bio:CodonUsage::Table object  
Returns: A  Bio:CodonUsage::IO object
Args   : a file or file handle 

next_data

Title  : next_data
Usage  : my $cut = $io->next_data();
Purpose: To  obtain a Bio:CodonUsage::Table object 
Returns: A  Bio:CodonUsage::Table object
Args   : none

write_data

Title  : write_data
Usage  : $io->write_data($cut);
Purpose: To  write a CUT to file
Returns: void
Args   : a Bio::CodonUsage::Table object reference