Bio::CodonUsage::IO.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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