Provided by: libbio-perl-perl_1.7.2-2_all
Bio::CodonUsage::IO - for reading and writing codon usage tables to file
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);
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.
Bio::Tools::CodonTable, Bio::WebAgent, Bio::CodonUsage::Table, Bio::CodonUsage::IO
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@example.com - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists Support Please direct usage questions or support issues to the mailing list: firstname.lastname@example.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://github.com/bioperl/bioperl-live/issues
Richard Adams, Richard.Adams@ed.ac.uk
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