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 streammode
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 : Trueclose
Title : close
Usage : $io->close()
Function: Closes the file handle associated with this IO instance,
excepted if -noclose was specified.
Args : None
Returns : Trueflush
Title : flush
Usage : $io->flush()
Function: Flushes the filehandle
Args : None
Returns : Truenoclose
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')
$exists = Bio::Root::IO::exists_exe('clustalw')
Function: Determines whether the given executable exists either as file
or within the path environment. The latter requires File::Spec
to be installed.
On Win32-based system, .exe is automatically appended to the program
name unless the program name already ends in .exe.
Args : Name of the executable
Returns : 1 if the given program is callable as an executable, and 0 otherwisetempfile
Title : tempfile
Usage : my ($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, $filename);
Function: Constructs a full pathname in a cross-platform safe way.
If File::Spec exists on your system, this routine will merely
delegate to it. Otherwise it tries to make a good guess.
You should use this method whenever you construct a path name
from directory and filename. Otherwise you risk cross-platform
compatibility of your code.
You can call this method both as a class and an instance method.
Args : components of the pathname (directories and filename, NOT an
extension)
Returns : a stringrmtree
Title : rmtree
Usage : Bio::Root::IO->rmtree($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_writesave_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)