Bio::Root::IO(3pm) | User Contributed Perl Documentation | Bio::Root::IO(3pm) |
# 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();
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.
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
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
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
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)
Title : file Usage : $io->file('>'.$file); my $file = $io->file; Function: Get or set the name of the file to read or write. Args : Optional file name (including its mode, e.g. '<' for reading or '>' for writing) Returns : A string representing the filename and its mode.
Title : cleanfile Usage : my ($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.
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.
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.
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
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
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
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
Title : close Usage : $io->close() Function: Closes the file handle associated with this IO instance, excepted if -noclose was specified. Args : None Returns : True
Title : flush Usage : $io->flush() Function: Flushes the filehandle Args : None Returns : True
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)
Title : exists_exe Usage : $exists = $io->exists_exe('clustalw'); $exists = Bio::Root::IO->exists_exe('clustalw') $exists = Bio::Root::IO::exists_exe('clustalw') Function: Determines whether the given executable exists either as file or within the path environment. The latter requires File::Spec to be installed. On Win32-based system, .exe is automatically appended to the program name unless the program name already ends in .exe. Args : Name of the executable Returns : 1 if the given program is callable as an executable, and 0 otherwise
Title : tempfile Usage : my ($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 $Bio::Root::IO::TEMPDIR), TEMPLATE, SUFFIX. Returns : A 2-element array, consisting of temporary handle and temporary file name.
Title : tempdir Usage : my ($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.
Title : catfile Usage : $path = Bio::Root::IO->catfile(@dirs, $filename); Function: Constructs a full pathname in a cross-platform safe way. If File::Spec exists on your system, this routine will merely delegate to it. Otherwise it tries to make a good guess. You should use this method whenever you construct a path name from directory and filename. Otherwise you risk cross-platform compatibility of your code. You can call this method both as a class and an instance method. Args : components of the pathname (directories and filename, NOT an extension) Returns : a string
Title : rmtree Usage : Bio::Root::IO->rmtree($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
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
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)
2018-10-27 | perl v5.26.2 |