Bio::Root IO
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Bio::Root::IO - module providing several methods often needed when dealing with file IO
Package variables
Privates (from "my" definitions)
$HAS_WIN32 = 0
Included modules
POSIX qw ( dup )
    # utilize stream I/O in your module
$self->{'io'} = Bio::Root::IO->new(-file => "myfile");
$self->{'io'}->_print("some stuff");
$line = $self->{'io'}->_readline();
# 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.
No description
Methods description
_fhcode    nextTop
 Title   : _fh
Usage : $obj->_fh($newval)
Function: Get/set the file handle for the stream encapsulated.
Example :
Returns : value of _filehandle
Args : newvalue (optional)
 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)
 Title   : initialize_io
Usage : $self->_initialize_io(@params);
Function: Initializes filehandle and other properties from the parameters.
Currently recognizes the following named parameters: -file name of file to open -input name of file, or GLOB, or IO::Handle object -fh file handle (mutually exclusive with -file) -flush boolean flag to autoflush after each write -noclose boolean flag, when set to true will not close a filehandle (must explictly call close($io->_fh) Returns : TRUE Args : named parameters
 Title   : _print
Usage : $obj->_print(@lines)
Example :
Returns : writes output
 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 :
Returns :
Args : newvalue
 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 :
 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)
 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
 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
 Title   : file
Usage : $obj->file($newval)
Function: Get/set the filename, if one has been designated.
Example :
Returns : value of file
Args : newvalue (optional)
 Title   : flush
Usage : $io->flush()
Function: Flushes the filehandle
Returns : none
Args : none
 Title   : mode
Usage : $obj->mode()
Example :
Returns : mode of filehandle:
'r' for readable
'w' for writeable
'?' 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
 Title   : new 
Usage :
Function: Overridden here to automatically call _initialize_io().
Example :
Returns : new instance of this class
Args : named parameters
 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)
 Title   : rmtree
Usage : Bio::Root::IO->rmtree($dirname );
Function: Remove a full directory tree
If File::Path exists on your system, this routine will merely delegate to it. Otherwise it runs a local version of that code. You should use this method to remove directories which contain files. You can call this method both as a class and an instance method. Returns : number of files successfully deleted Args : roots - rootdir to delete or reference to list of dirs verbose - a boolean value, which if TRUE will cause rmtree to print a message each time it
examines a file, giving the name of the file, and
indicating whether it's using rmdir or
unlink to remove it, or that it's skipping it.
(defaults to FALSE)
safe - a boolean value, which if TRUE will cause rmtree
to skip any files to which you do not have delete
access (if running under VMS) or write access (if
running under another OS). This will change in the
future when a criterion for 'delete permission'
under OSs other than VMS is settled. (defaults to
 Title   : tempdir
Usage : my ($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 $Bio::Root::IO::TEMPDIR for that. Calling this method will in fact create a new directory. Returns : The name of a new temporary directory. Args : args - ( key CLEANUP ) indicates whether or not to cleanup dir on object destruction, other keys as specified by File::Temp
 Title   : tempfile
Usage : my ($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.
Methods code
    $VERBOSE = 1;

    # try to load those modules that may cause trouble on some systems
eval { require File::Path; $FILEPATHLOADED = 1; }; if( $@ ) { print STDERR "Cannot load File::Path: $@" if( $VERBOSE > 0 ); # do nothing
} # If on Win32, attempt to find Win32 package
if($^O =~ /mswin/i) { eval { require Win32; $HAS_WIN32 = 1; }; } # Try to provide a path separator. Why doesn't File::Spec export this,
# or did I miss it?
if($^O =~ /mswin/i) { $PATHSEP = "\\"; } elsif($^O =~ /macos/i) { $PATHSEP = ":"; } else { # unix
$PATHSEP = "/"; } eval { require File::Spec; $FILESPECLOADED = 1; $TEMPDIR = File::Spec->tmpdir(); $ROOTDIR = File::Spec->rootdir(); require File::Temp; # tempfile creation
$FILETEMPLOADED = 1; }; if( $@ ) { if(! defined($TEMPDIR)) { # File::Spec failed
# determine tempdir
if (defined $ENV{'TEMPDIR'} && -d $ENV{'TEMPDIR'} ) { $TEMPDIR = $ENV{'TEMPDIR'}; } elsif( defined $ENV{'TMPDIR'} && -d $ENV{'TMPDIR'} ) { $TEMPDIR = $ENV{'TMPDIR'}; } if($^O =~ /mswin/i) { $TEMPDIR = 'C:\TEMP' unless $TEMPDIR; $ROOTDIR = 'C:'; } elsif($^O =~ /macos/i) { $TEMPDIR = "" unless $TEMPDIR; # what is a reasonable default on Macs?
$ROOTDIR = ""; # what is reasonable??
} else { # unix
$TEMPDIR = "/tmp" unless $TEMPDIR; $ROOTDIR = "/"; } if (!( -d $TEMPDIR && -w $TEMPDIR )) { $TEMPDIR = '.'; # last resort
} } # File::Temp failed (alone, or File::Spec already failed)
# determine open flags for tempfile creation -- we'll have to do this
# ourselves
use Fcntl; use Symbol; $OPENFLAGS = O_CREAT | O_EXCL | O_RDWR; for my $oflag (qw/FOLLOW BINARY LARGEFILE EXLOCK NOINHERIT TEMPORARY/){ my ($bit, $func) = (0, "Fcntl::O_" . $oflag); no strict 'refs'; $OPENFLAGS |= $bit if eval { $bit = &$func(); 1 }; }
sub _fh {
    my ($obj, $value) = @_;
    if ( defined $value) {
	$obj->{'_filehandle'} = $value;
    return $obj->{'_filehandle'};
sub _flush_on_write {
    my ($self,$value) = @_;
    if( defined $value) {
	$self->{'_flush_on_write'} = $value;
    return $self->{'_flush_on_write'};

sub _initialize_io {
    my($self, @args) = @_;


    my ($input, $noclose, $file, $fh, $flush) = $self->_rearrange([qw(INPUT 
							    FILE FH 
							    FLUSH)], @args);
    delete $self->{'_readbuffer'};
    delete $self->{'_filehandle'};
    $self->noclose( $noclose) if defined $noclose;
    # determine whether the input is a file(name) or a stream
if($input) { if(ref(\$input) eq "SCALAR") { # we assume that a scalar is a filename
if($file && ($file ne $input)) { $self->throw("input file given twice: $file and $input disagree"); } $file = $input; } elsif(ref($input) && ((ref($input) eq "GLOB") || $input->isa('IO::Handle'))) { # input is a stream
$fh = $input; } else { # let's be strict for now
$self->throw("unable to determine type of input $input: ". "not string and not GLOB"); } } if(defined($file) && defined($fh)) { $self->throw("Providing both a file and a filehandle for reading - only one please!"); } if(defined($file) && ($file ne '')) { $fh = Symbol::gensym(); open ($fh,$file) || $self->throw("Could not open $file: $!"); $self->file($file); } $self->_fh($fh) if $fh; # if not provided, defaults to STDIN and STDOUT
$self->_flush_on_write(defined $flush ? $flush : 1); return 1;
sub _io_cleanup {
    my ($self) = @_;

    my $v = $self->verbose;

    # we are planning to cleanup temp files no matter what    
if( exists($self->{'_rootio_tempfiles'}) && ref($self->{'_rootio_tempfiles'}) =~ /array/i) { if( $v > 0 ) { print STDERR "going to remove files ", join(",", @{$self->{'_rootio_tempfiles'}}), "\n"; } unlink (@{$self->{'_rootio_tempfiles'}} ); } # cleanup if we are not using File::Temp
if( $self->{'_cleanuptempdir'} && exists($self->{'_rootio_tempdirs'}) && ref($self->{'_rootio_tempdirs'}) =~ /array/i) { if( $v > 0 ) { print STDERR "going to remove dirs ", join(",", @{$self->{'_rootio_tempdirs'}}), "\n"; } $self->rmtree( $self->{'_rootio_tempdirs'}); }
sub _print {
    my $self = shift;
    my $fh = $self->_fh() ||\* STDOUT;
    print $fh @_;
sub _pushback {
    my ($obj, $value) = @_;

	$obj->{'_readbuffer'} ||= [];
	push @{$obj->{'_readbuffer'}}, $value;
sub _readline {
    my $self = shift;
    my %param =@_;
    my $fh = $self->_fh ||\* ARGV;
    my $line;

    # if the buffer been filled by _pushback then return the buffer
# contents, rather than read from the filehandle
$line = shift @{$self->{'_readbuffer'}} || <$fh>; #don't strip line endings if -raw is specified
$line =~ s/\r\n/\n/g if( (!$param{-raw}) && (defined $line) ); return $line;
sub catfile {
    my ($self, @args) = @_;

    return File::Spec->catfile(@args) if($FILESPECLOADED);
    # this is clumsy and not very appealing, but how do we specify the
# root directory?
if($args[0] eq '/') { $args[0] = $ROOTDIR; } return join($PATHSEP, @args);
sub close {
   my ($self) = @_;
   return if $self->noclose; # don't close if we explictly asked not to
if( defined $self->{'_filehandle'} ) { $self->flush; return if(\* STDOUT == $self->_fh ||\* STDERR == $self->_fh ||\* STDIN == $self->_fh ); # don't close STDOUT fh
if( ! ref($self->{'_filehandle'}) || ! $self->{'_filehandle'}->isa('IO::String') ) { close($self->{'_filehandle'}); } } $self->{'_filehandle'} = undef; delete $self->{'_readbuffer'};
sub exists_exe {
    my ($self, $exe) = @_;
    $exe = $self if(!(ref($self) || $exe));
    $exe .= '.exe' if(($^O =~ /mswin/i) && ($exe !~ /\.(exe|com|bat|cmd)$/i));
    return $exe if(-e $exe); # full path and exists
# Ewan's comment. I don't think we need this. People should not be
# asking for a program with a pathseparator starting it
# $exe =~ s/^$PATHSEP//;
# Not a full path, or does not exist. Let's see whether it's in the path.
if($FILESPECLOADED) { foreach my $dir (File::Spec->path()) { my $f = Bio::Root::IO->catfile($dir, $exe); return $f if(-e $f && -x $f ); } } return 0;
sub file {
    my ($obj, $value) = @_;
    if ( defined $value) {
	$obj->{'_file'} = $value;
    return $obj->{'_file'};
sub flush {
  my ($self) = shift;
  if( !defined $self->{'_filehandle'} ) {
    $self->throw("Attempting to call flush but no filehandle active");

  if( ref($self->{'_filehandle'}) =~ /GLOB/ ) {
    my $oldh = select($self->{'_filehandle'});
    $| = 1;
  } else {
sub mode {
    my ($obj, @arg) = @_;
	my %param = @arg;
    return $obj->{'_mode'} if defined $obj->{'_mode'} and !$param{-force};

    print STDERR "testing mode... " if $obj->verbose;

    # we need to dup() the original filehandle because
# doing fdopen() calls on an already open handle causes
# the handle to go stale. is this going to work for non-unix
# filehandles? -allen
my $fh = Symbol::gensym(); my $iotest = new IO::Handle; #test for a readable filehandle;
$iotest->fdopen( dup(fileno($obj->_fh)) , 'r' ); if($iotest->error == 0){ # note the hack here, we actually have to try to read the line
# and if we get something, pushback() it into the readbuffer.
# this is because solaris and windows xp (others?) don't set
# IO::Handle::error. for non-linux the r/w testing is done
# inside this read-test, instead of the write test below. ugh.
if($^O eq 'linux'){ $obj->{'_mode'} = 'r'; my $line = $iotest->getline; $obj->_pushback($line) if defined $line; $obj->{'_mode'} = defined $line ? 'r' : 'w'; return $obj->{'_mode'}; } else { my $line = $iotest->getline; $obj->_pushback($line) if defined $line; $obj->{'_mode'} = defined $line ? 'r' : 'w'; return $obj->{'_mode'}; } } $iotest->clearerr; #test for a writeable filehandle;
$iotest->fdopen( dup(fileno($obj->_fh)) , 'w' ); if($iotest->error == 0){ $obj->{'_mode'} = 'w'; # return $obj->{'_mode'};
} #wtf type of filehandle is this?
# $obj->{'_mode'} = '?';
return $obj->{'_mode'};
sub new {
    my ($caller, @args) = @_;
    my $self = $caller->SUPER::new(@args);

    return $self;
sub noclose {
    my $self = shift;

    return $self->{'_noclose'} = shift if @_;
    return $self->{'_noclose'};
sub rmtree {
    my($self,$roots, $verbose, $safe) = @_;
    if( $FILEPATHLOADED ) { 
	return File::Path::rmtree ($roots, $verbose, $safe); 
    my $force_writeable = ($^O eq 'os2' || $^O eq 'dos' || $^O eq 'MSWin32'
		       || $^O eq 'amigaos');
    my $Is_VMS = $^O eq 'VMS';

    my($count) = 0;
    $verbose ||= 0;
    $safe ||= 0;
    if ( defined($roots) && length($roots) ) {
	$roots = [$roots] unless ref $roots;
    } else {
	$self->warn("No root path(s) specified\n");
	return 0;

    foreach $root (@{$roots}) {
	$root =~ s#/\z##;
	(undef, undef, my $rp) = lstat $root or next;
	$rp &= 07777;	# don't forget setuid, setgid, sticky bits
if ( -d _ ) { # notabene: 0777 is for making readable in the first place,
# it's also intended to change it to writable in case we have
# to recurse in which case we are better than rm -rf for
# subtrees with strange permissions
chmod(0777, ($Is_VMS ? VMS::Filespec::fileify($root) : $root)) or $self->warn("Can't make directory $root read+writeable: $!") unless $safe; if (opendir(DIR, $root) ){ @files = readdir DIR; closedir(DIR); } else { $self->warn( "Can't read $root: $!"); @files = (); } # Deleting large numbers of files from VMS Files-11 filesystems
# is faster if done in reverse ASCIIbetical order
@files = reverse @files if $Is_VMS; ($root = VMS::Filespec::unixify($root)) =~ s#\.dir\z## if $Is_VMS; @files = map("$root/$_", grep $_!~/^\.{1,2}\z/s,@files); $count += $self->rmtree([@files],$verbose,$safe); if ($safe && ($Is_VMS ? !&VMS::Filespec::candelete($root) : !-w $root)) { print "skipped $root\n" if $verbose; next; } chmod 0777, $root or $self->warn( "Can't make directory $root writeable: $!") if $force_writeable; print "rmdir $root\n" if $verbose; if (rmdir $root) { ++$count; } else { $self->warn( "Can't remove directory $root: $!"); chmod($rp, ($Is_VMS ? VMS::Filespec::fileify($root) : $root)) or $self->warn("and can't restore permissions to " . sprintf("0%o",$rp) . "\n"); } } else { if ($safe && ($Is_VMS ? !&VMS::Filespec::candelete($root) : !(-l $root || -w $root))) { print "skipped $root\n" if $verbose; next; } chmod 0666, $root or $self->warn( "Can't make file $root writeable: $!") if $force_writeable; print "unlink $root\n" if $verbose; # delete all versions under VMS
for (;;) { unless (unlink $root) { $self->warn( "Can't unlink file $root: $!"); if ($force_writeable) { chmod $rp, $root or $self->warn("and can't restore permissions to " . sprintf("0%o",$rp) . "\n"); } last; } ++$count; last unless $Is_VMS && lstat $root; } } } $count;
sub tempdir {
    my ( $self, @args ) = @_;
    if($FILETEMPLOADED && File::Temp->can('tempdir') ) {
	return File::Temp::tempdir(@args);

    # we have to do this ourselves, not good
# we are planning to cleanup temp files no matter what
my %params = @args; $self->{'_cleanuptempdir'} = ( defined $params{CLEANUP} && $params{CLEANUP} == 1); my $tdir = $self->catfile($TEMPDIR, sprintf("dir_%s-%s-%s", $ENV{USER} || 'unknown', $$, $TEMPCOUNTER++)); mkdir($tdir, 0755); push @{$self->{'_rootio_tempdirs'}}, $tdir; return $tdir;
sub tempfile {
    my ($self, @args) = @_;
    my ($tfh, $file);
    my %params = @args;

    # map between naming with and without dash
foreach my $key (keys(%params)) { if( $key =~ /^-/ ) { my $v = $params{$key}; delete $params{$key}; $params{uc(substr($key,1))} = $v; } else { # this is to upper case
my $v = $params{$key}; delete $params{$key}; $params{uc($key)} = $v; } } $params{'DIR'} = $TEMPDIR if(! exists($params{'DIR'})); unless (exists $params{'UNLINK'} && defined $params{'UNLINK'} && ! $params{'UNLINK'} ) { $params{'UNLINK'} = 1; } else { $params{'UNLINK'} = 0 } if($FILETEMPLOADED) { if(exists($params{'TEMPLATE'})) { my $template = $params{'TEMPLATE'}; delete $params{'TEMPLATE'}; ($tfh, $file) = File::Temp::tempfile($template, %params); } else { ($tfh, $file) = File::Temp::tempfile(%params); } } else { my $dir = $params{'DIR'}; $file = $self->catfile($dir, (exists($params{'TEMPLATE'}) ? $params{'TEMPLATE'} : sprintf( "%s.%s.%s", $ENV{USER} || 'unknown', $$, $TEMPCOUNTER++))); # sneakiness for getting around long filenames on Win32?
if( $HAS_WIN32 ) { $file = Win32::GetShortPathName($file); } # taken from File::Temp
if ($] < 5.006) { $tfh = &Symbol::gensym; } # Try to make sure this will be marked close-on-exec
# XXX: Win32 doesn't respect this, nor the proper fcntl,
# but may have O_NOINHERIT. This may or may not be in Fcntl.
local $^F = 2; # Store callers umask
my $umask = umask(); # Set a known umaskr
umask(066); # Attempt to open the file
if ( sysopen($tfh, $file, $OPENFLAGS, 0600) ) { # Reset umask
umask($umask); } else { $self->throw("Could not open tempfile $file: $!\n"); } } if( $params{'UNLINK'} ) { push @{$self->{'_rootio_tempfiles'}}, $file; } return wantarray ? ($tfh,$file) : $tfh;
General documentation
Mailing ListsTop
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.                 - General discussion - About the mailing lists
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.
Bug reports can be submitted via email or the web:
AUTHOR - Hilmar LappTop
Describe contact details here
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _