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Bio::Root::IO.3pm

NAME

Bio::Root::IO - module providing several methods often needed when dealing with file IO

SYNOPSIS

     # 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();
 
 

DESCRIPTION

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.

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:

   http://bugzilla.open-bio.org/
 
 

AUTHOR - Hilmar Lapp

Email hlapp@gmx.net

CONTRIBUTORS

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

APPENDIX

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
               -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 explictly 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
 
 

_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 : 1 on success, undef on failure
 
 

_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 : $obj->_pushback($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.
 
 

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)
 
 

save_tempfiles

  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