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 listsSupport
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:
https://redmine.open-bio.org/projects/bioperl/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 : $self->_initialize_io(@params);
Function: Initializes filehandle and other properties from the parameters.
Currently recognizes the following named parameters:
-file name of file to open
-string a string that is to be converted to a filehandle
-url name of URL to open
-input name of file, or GLOB, or IO::Handle object
-fh file handle (mutually exclusive with -file)
-flush boolean flag to autoflush after each write
-noclose boolean flag, when set to true will not close a
filehandle (must explicitly call close($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_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 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
-forcefile
Title : file
Usage : $obj->file($newval)
Function: Get/set the filename, if one has been designated.
Example :
Returns : value of file
Args : newvalue (optional)format
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 : nonevariant
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._print
Title : _print
Usage : $obj->_print(@lines)
Function:
Example :
Returns : 1 on success, undef on failure_insert
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_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 : noneflush
Title : flush
Usage : $io->flush()
Function: Flushes the filehandle
Returns : none
Args : nonenoclose
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')
$exists = Bio::Root::IO::exists_exe('clustalw')
Function: Determines whether the given executable exists either as file
or within the path environment. The latter requires File::Spec
to be installed.
On Win32-based system, .exe is automatically appended to the program
name unless the program name already ends in .exe.
Example :
Returns : 1 if the given program is callable as an executable, and 0 otherwise
Args : the name of the executabletempfile
Title : tempfile
Usage : my ($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::Tempcatfile
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