Provided by: libbio-perl-perl_1.6.923-1_all bug


       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();

           # 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

       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.


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AUTHOR - Hilmar Lapp



       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   : format
        Usage   : $self->format($newval)
        Function: Get the format of a Bio::Root::IO sequence file or filehandle. Every
                  object inheriting Bio::Root::IO is guaranteed to have a format.
        Returns : format of the file or filehandle, e.g. fasta, fastq, genbank, embl.
        Args    : none

        Title   : format
        Usage   : $self->format($newval)
        Function: Get the variant of a Bio::Root::IO sequence file or filehandle.
                  The format variant depends on the specific format used. Note that not
                  all formats have variants
        Returns : variant of the file or filehandle, e.g. sanger, solexa or illumina for
                  the fastq format, or undef for formats that do not have variants.
        Args    : none
        Note    : The Bio::Root::IO-implementing modules that require access to variants
                  need to define a global hash that has the allowed variants as its keys.

        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