- SEE ALSO
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.
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.
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Please direct usage questions or support issues to the mailing list:
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.
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:
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 _
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
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
Title : write_data Usage : $io->write_data($cut); Purpose: To write a CUT to file Returns: void Args : a Bio::CodonUsage::Table object reference