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lib/Bio/Graphics/Panel.pm  view on Meta::CPAN

=back

To use this method effectively, you will need a web server and an
image directory in the document tree that is writable by the web
server user.  For example, if your web server's document root is
located at /var/www/html, you might want to create a directory named
"tmpimages" for this purpose:

  mkdir /var/www/html/tmpimages
  chmod 1777 /var/www/html/tmpimages

The 1777 privilege will allow anyone to create files and
subdirectories in this directory, but only the owner of the file will
be able to delete it.

When you call image_and_map(), you must provide it with two vital
pieces of information: the URL of the image directory and the physical
location of the web server's document tree.  In our example, you would
call:

scripts/coverage_to_topoview.pl  view on Meta::CPAN

for my $kkey ( sort @all_keys ) {
    print "\t$kkey => " . $bdb_hash{$kkey} . "\n";
}

if ( $max_signal > 10000 ) {
    warn "WARNING: max_signal=$max_signal - TOO HIGH.  Consider log2?\n";
}

untie %bdb_hash;
chmod( 0666, $hashfile );     # ! sometimes very important

close COV;


sub is_bed4 {
    my $file = shift;
    my $cat  = $file =~ /gz$/ ? 'zcat' 
             : $file =~ /bz2/ ? 'bzcat'
             : 'cat';
    open WIG, "$cat $file |" or die "could not open $file: $!";

scripts/index_cov_files.pl  view on Meta::CPAN

	@SubsetNames= ();
	foreach my $file (sort @files) { 
		indexCoverageFile($file); # coverage files are in fact wiggle files.. 
		}
	$ResIndexHash{'subsets'}= join("\t",@SubsetNames); # record subsets, just in case..
	$ResIndexHash{'max_signal'}= $max_signal;
	my @all_keys= keys %ResIndexHash;
	foreach my $kkey ( sort @all_keys ) { print "\t$kkey => ".$ResIndexHash{$kkey}."\n"; }
	if( $max_signal>10000 ) { print "WARNING: max_signal=$max_signal - TOO HIGH!! Re-run with '-log' option\n"; } 
  untie %ResIndexHash;
	chmod(0666,$bdbfilename); # ! sometimes very important
	close(OUTDATF);

	return;
}
 
#*************************************************************************
#
#*************************************************************************

sub indexCoverageFile