Reference

Bio::CodonUsage::IO(3pm)

for reading and writing codon usage tables to file

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

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

[email protected]

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://github.com/bioperl/bioperl-live/issues

AUTHORS

Richard Adams, [email protected]

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

History