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BioPerl-1.6.920
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Root::IO

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:

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
          -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)

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    : none

variant

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    : 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