NAME

Bio::Root::IO - BioPerl base IO handling class

SYNOPSIS

    # Use stream I/O in your module
    $self->{'io'} = Bio::Root::IO->new(-file => "myfile");
    $self->{'io'}->_print("some stuff");
    my $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.

AUTHOR Hilmar Lapp

new

 Title   : new
 Usage   : my $io = Bio::Root::IO->new( -file => 'data.txt' );
 Function: Create new class instance. It automatically calls C<_initialize_io>.
 Args    : Same named parameters as C<_initialize_io>.
 Returns : A Bio::Root::IO object

_initialize_io

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

_fh

 Title   : _fh
 Usage   : $io->_fh($newval);
 Function: Get or set the file handle for the stream encapsulated.
 Args    : Optional filehandle to use
 Returns : Filehandle for the stream

mode

 Title   : mode
 Usage   : $io->mode();
           $io->mode(-force => 1);
 Function: Determine if the object was opened for reading or writing
 Args    : -force: Boolean. Once mode() has been called, the mode is cached for
                   further calls to mode(). Use this argument to override this
                   behavior and re-check the object's mode.
 Returns : Mode of the object:
            'r'  for readable
            'w'  for writable
            'rw' for readable and writable
            '?'  if mode could not be determined (e.g. for a -url)

file

 Title   : file
 Usage   : $io->file('>'.$file);
           my $file = $io->file;
 Function: Get or set the name of the file to read or write.
 Args    : Optional file name (including its mode, e.g. '<' for reading or '>'
           for writing)
 Returns : A string representing the filename and its mode.

cleanfile

 Title   : cleanfile
 Usage   : my ($mode, $file) = $io->cleanfile;
 Function: Get the name of the file to read or write, stripped of its mode
           ('>', '<', '+>', '>>', etc).
 Args    : None
 Returns : In array context, an array of the mode and the clean filename.

format

 Title   : format
 Usage   : $io->format($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.
 Args    : None
 Returns : Format of the file or filehandle, e.g. fasta, fastq, genbank, embl.

variant

 Title   : format
 Usage   : $io->format($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. Also, 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.
 Args    : None
 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.

_print

 Title   : _print
 Usage   : $io->_print(@lines)
 Function: Print lines of text to the IO stream object.
 Args    : List of strings to print
 Returns : True on success, undef on failure

_insert

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

_readline

 Title   : _readline
 Usage   : local $Bio::Root::IO::HAS_EOL = 1;
           my $io = Bio::Root::IO->new(-file => 'data.txt');
           my $line = $io->_readline();
           $io->close;
 Function: Read a line of input and normalize all end of line characters.

           End of line characters are typically "\n" on Linux platforms, "\r\n"
           on Windows and "\r" on older Mac OS. By default, the _readline()
           method uses the value of $/, Perl's input record separator, to
           detect the end of each line. This means that you will not get the
           expected lines if your input has Mac-formatted end of line characters.
           Also, note that the current implementation does not handle pushed
           back input correctly unless the pushed back input ends with the
           value of $/. For each line parsed, its line ending, e.g. "\r\n" is
           converted to "\n", unless you provide the -raw argument.

           Altogether it is easier to let the PerlIO::eol module automatically
           detect the proper end of line character and normalize it to "\n". Do
           so by setting $Bio::Root::IO::HAS_EOL to 1.

 Args    : -raw : Avoid converting end of line characters to "\n" This option
                  has no effect when using $Bio::Root::IO::HAS_EOL = 1.
 Returns : Line of input, or undef when there is nothing to read anymore

_pushback

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

           Note that 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.

 Args    : newvalue
 Returns : True

close

 Title   : close
 Usage   : $io->close()
 Function: Closes the file handle associated with this IO instance,
           excepted if -noclose was specified.
 Args    : None
 Returns : True

flush

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

noclose

 Title   : noclose
 Usage   : $io->noclose($newval)
 Function: Get or set the NOCLOSE flag - setting this to true will prevent a
           filehandle from being closed when an object is cleaned up or
           explicitly closed.
 Args    : Optional new value (a scalar or undef)
 Returns : Value of noclose (a scalar)

_io_cleanup

exists_exe

 Title   : exists_exe
 Usage   : $exists = $io->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.
 Args    : Name of the executable
 Returns : 1 if the given program is callable as an executable, and 0 otherwise

tempfile

 Title   : tempfile
 Usage   : my ($handle,$tempfile) = $io->tempfile();
 Function: Create a temporary filename and a handle opened for reading and
           writing.
           Caveats: If you do not have File::Temp on your system you should
           avoid specifying TEMPLATE and SUFFIX.
 Args    : Named parameters compatible with File::Temp: DIR (defaults to
           $Bio::Root::IO::TEMPDIR), TEMPLATE, SUFFIX.
 Returns : A 2-element array, consisting of temporary handle and temporary
           file name.

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.

 Args    : args - ( key CLEANUP ) indicates whether or not to cleanup
           dir on object destruction, other keys as specified by File::Temp
 Returns : The name of a new temporary directory.

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.

 Args    : components of the pathname (directories and filename, NOT an
           extension)
 Returns : a string

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.

 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)
 Returns : number of files successfully deleted

_flush_on_write

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

save_tempfiles

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