Bio::Root::IO(3) 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();
# 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.

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Please direct usage questions or support issues to the mailing list:

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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:

AUTHOR - Hilmar Lapp

Email [email protected]


Mark A. Jensen ( maj -at- fortinbras -dot- us )


The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


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


 Title   : initialize_io
 Usage   : $self->_initialize_io(@params);
 Function: Initializes filehandle and other properties from the parameters.
           Currently recognizes the following named parameters:
              -file     name of file to open
              -string   a string that is to be converted to a filehandle
              -url      name of URL to open
              -input    name of file, or GLOB, or IO::Handle object
              -fh       file handle (mutually exclusive with -file)
              -flush    boolean flag to autoflush after each write
              -noclose  boolean flag, when set to true will not close a
                        filehandle (must explicitly call close($io->_fh)
              -retries  number of times to try a web fetch before failure
              -ua_parms hashref of key => value parameters to pass 
                        to LWP::UserAgent->new()
                        (only meaningful with -url is set)
                        A useful value might be, for example,
                        { timeout => 60 } (ua default is 180 sec)
 Returns : TRUE
 Args    : named parameters


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


 Title   : mode
 Usage   : $obj->mode()
 Example :
 Returns : mode of filehandle:
           'r' for readable
           'w' for writable
           '?' 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


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


 Title   : _print
 Usage   : $obj->_print(@lines)
 Example :
 Returns : 1 on success, undef on failure


    Title   : _insert
    Usage   : $obj->_insert($string,1)
    Function: Insert some text in a file at the given line number (1-based).
    Returns : 1 on success
    Args    : string to write in file
              line number to insert the string at


 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 :


 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 : $obj->_pushback($newvalue)
 Returns : none
 Args    : newvalue
 Note    : This is only supported for pushing back data ending with the
           current, localized value of $/. Using this method to push modified
           data back onto the buffer stack is not supported; see bug 843.


 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


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


 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)


 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


 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.


 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


 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


 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 
           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


 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)


 Title   : save_tempfiles
 Usage   : $obj->save_tempfiles(1)
 Function: Boolean flag to indicate whether to retain tempfiles/tempdir
 Returns : Boolean value : 1 = save tempfiles/tempdirs, 0 = remove (default)
 Args    : Value evaluating to TRUE or FALSE