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 to 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 not be available on all platforms. At present, File::Spec and File::Temp are attempted. This module defines $PATHSEP, $TEMPDIR, and $ROOTDIR, which will always be set, and $OPENFLAGS, which will be set if either of File::Spec or File::Temp fails. The -noclose boolean (accessed via the noclose method) prevents a filehandle from being closed when the IO object is cleaned up. This is special behavior when a object like a parser might share a filehandle with an object like an indexer where it is not proper to close the filehandle as it will continue to be reused until the end of the stream is reached. In general you won't want to play with this flag.

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://bugzilla.bioperl.org/ 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 : $self->_initialize_io(@params); Function: Initializes filehandle and other properties from the parameters. Currently recognizes the following named parameters: -file name of file to open -input name of file, or GLOB, or IO::Handle object -fh file handle (mutually exclusive with -file) -flush boolean flag to autoflush after each write -noclose boolean flag, when set to true will not close a filehandle (must explictly call close($io->_fh) Returns : TRUE Args : named parameters

_fh
Title : _fh Usage : $obj->_fh($newval) Function: Get/set the file handle for the stream encapsulated. Example : Returns : value of _filehandle Args : newvalue (optional)

mode
Title : mode Usage : $obj->mode() Function: Example : Returns : mode of filehandle: 'r' for readable 'w' for writeable '?' if mode could not be determined Args : -force (optional), see notes. Notes : once mode() has been called, the filehandle's mode is cached for further calls to mode(). to override this behavior so that mode() re-checks the filehandle's mode, call with arg -force

file
Title : file Usage : $obj->file($newval) Function: Get/set the filename, if one has been designated. Example : Returns : value of file Args : newvalue (optional)

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

_readline
Title : _readline Usage : $obj->_readline(%args) 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 : Args : Accepts a hash of arguments, currently only -raw is recognized passing (-raw => 1) prevents \r\n sequences from being changed to \n. The default value of -raw is undef, allowing \r\n to be converted to \n. Returns :

_pushback
Title : _pushback Usage : $obj->_pushback($newvalue) Function: puts a line previously read with _readline back into a buffer. buffer can hold as many lines as system memory permits. Example : Returns : Args : newvalue

close
Title : close Usage : $io->close() Function: Closes the file handle associated with this IO instance. Will not close the FH if -noclose is specified Returns : none Args : none

flush
Title : flush Usage : $io->flush() Function: Flushes the filehandle Returns : none Args : none

noclose
Title : noclose Usage : $obj->noclose($newval) Function: Get/Set the NOCLOSE flag - setting this to true will prevent a filehandle from being closed when an object is cleaned up or explicitly closed This is a bit of hack Returns : value of noclose (a scalar) Args : on set, new value (a scalar or undef, optional)

exists_exe
Title : exists_exe Usage : $exists = $obj->exists_exe('clustalw'); $exists = Bio::Root::IO->exists_exe('clustalw') $exists = Bio::Root::IO::exists_exe('clustalw') Function: Determines whether the given executable exists either as file or within the path environment. The latter requires File::Spec to be installed. On Win32-based system, .exe is automatically appended to the program name unless the program name already ends in .exe. Example : Returns : 1 if the given program is callable as an executable, and 0 otherwise Args : the name of the executable

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)

rmtree
Title : rmtree Usage : Bio::Root::IO->rmtree($dirname ); Function: Remove a full directory tree If File::Path exists on your system, this routine will merely delegate to it. Otherwise it runs a local version of that code. You should use this method to remove directories which contain files. You can call this method both as a class and an instance method. Returns : number of files successfully deleted Args : roots - rootdir to delete or reference to list of dirs verbose - a boolean value, which if TRUE will cause C<rmtree> to print a message each time it examines a file, giving the name of the file, and indicating whether it's using C<rmdir> or C<unlink> to remove it, or that it's skipping it. (defaults to FALSE) safe - a boolean value, which if TRUE will cause C<rmtree> to skip any files to which you do not have delete access (if running under VMS) or write access (if running under another OS). This will change in the future when a criterion for 'delete permission' under OSs other than VMS is settled. (defaults to FALSE)

_flush_on_write
Title : _flush_on_write Usage : $obj->_flush_on_write($newval) Function: Boolean flag to indicate whether to flush the filehandle on writing when the end of a component is finished (Sequences,Alignments,etc) Returns : value of _flush_on_write Args : newvalue (optional)