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