Bio::Root::IO - module providing several methods often needed when dealing with file IO # utilize stream I/O in your module $self->{'io'} = Bio::Root::IO->new(-file => "myfile"); $self->{'io'}->_print("some stuff"); $line = $self->{'io'}->_readline(); $self->{'io'}->_pushback($line); $self->{'io'}->close(); # obtain platform-compatible filenames $path = Bio::Root::IO->catfile($dir, $subdir, $filename); # obtain a temporary file (created in $TEMPDIR) ($handle) = $io->tempfile(); This module provides methods that will usually be needed for any sort of file- or stream-related input/output, e.g., keeping track of a file handle, transient printing and reading from the file handle, a close method, automatically closing the handle on garbage collection, etc. To use this for your own code you will either want to inherit from this module, or instantiate an object for every file or stream you are dealing with. In the first case this module will most likely not be the first class off which your class inherits; therefore you need to call _initialize_io() with the named parameters in order set file handle, open file, etc automatically. Most methods start with an underscore, indicating they are private. In OO speak, they are not private but protected, that is, use them in your module code, but a client code of your module will usually not want to call them (except those not starting with an underscore). In addition this module contains a couple of convenience methods for cross-platform safe tempfile creation and similar tasks. There are some CPAN modules related that may be not be available on all platforms. At present, File::Spec and File::Temp are attempted. This module exports $TEMPFILE and $ROOTDIR, which will always be set, $PATHSEP, which will be set if File::Spec fails, and $OPENFLAGS, which will be set if either of File::Spec or File::Temp fails.

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://bio.perl.org/MailList.html - About the mailing lists

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 email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ Email hlapp@gmx.net Describe contact details here The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : Function: Overridden here to automatically call _initialize_io(). Example : Returns : new instance of this class Args : named parameters

_initialize_io
Title : initialize_io Usage : $self->_initialize_io(@params); Function: Initializes filehandle and other properties. Currently recognized the following named parameters: -file, -fh Example : Returns : TRUE Args : named parameters

_fh
Title : _fh Usage : $obj->_fh($newval) Function: Example : Returns : value of _filehandle Args : newvalue (optional)

_print
Title : _print Usage : $obj->_print(@lines) Function: Example : Returns : writes output

_readline
Title : _readline Usage : $obj->_readline Function: Reads a line of input. Note that this method implicitely uses the value of $/ that is in effect when called. Note also that the current implementation does not handle pushed back input correctly unless the pushed back input ends with the value of $/. Example : Returns :

_pushback
Title : _pushback Usage : $obj->_pushback($newvalue) Function: puts a line previously read with _readline back into a buffer Example : Returns : Args : newvalue

close
Title : close Usage : $seqio->close() Function: Closes the file handle associated with this seqio system Example : Returns : Args :

tempfile
Title : tempfile Usage : my ($handle,$tempfile) = $io->tempfile(); Function: Returns a temporary filename and a handle opened for writing and and reading. Caveats : If you do not have File::Temp on your system you should avoid specifying TEMPLATE and SUFFIX. (We don't want to recode everything, okay?) Returns : a 2-element array, consisting of temporary handle and temporary file name Args : named parameters compatible with File::Temp: DIR (defaults to $Bio::Root::IO::TEMPDIR), TEMPLATE, SUFFIX.

tempdir
Title : tempdir Usage : my ($tempdir) = $io->tempdir(CLEANUP=>1); Function: Creates and returns the name of a new temporary directory. Note that you should not use this function for obtaining "the" temp directory. Use $Bio::Root::IO::TEMPDIR for that. Calling this method will in fact create a new directory. Returns : The name of a new temporary directory. Args : args - ( key CLEANUP ) indicates whether or not to cleanup dir on object destruction, other keys as specified by File::Temp

catfile
Title : catfile Usage : $path = Bio::Root::IO->catfile(@dirs,$filename); Function: Constructs a full pathname in a cross-platform safe way. If File::Spec exists on your system, this routine will merely delegate to it. Otherwise it tries to make a good guess. You should use this method whenever you construct a path name from directory and filename. Otherwise you risk cross-platform compatibility of your code. You can call this method both as a class and an instance method. Returns : a string Args : components of the pathname (directories and filename, NOT an extension)