Ewan Birney

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.

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://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/

AUTHOR - Hilmar Lapp

Email hlapp@gmx.net

Describe contact details here

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.

           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)

file

 Title   : file
 Usage   : $obj->file($newval)
 Function:
 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
 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   : $io->close()
 Function: Closes the file handle associated with this IO instance.
 Example :
 Returns :
 Args    :

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)