#!/usr/local/bin/perl -w # # Read a palette definition, create HTML to display those colors # in a pattern so they can all be seen next to each other # to determine if any of them are so similar they meld together # # The input palette definition file has lines defined as such: #996600 1 # and yes, they do begin with the # character # That is the hex value 996600 for chrom 1 use strict; my $argc = @ARGV; # argument count if( $argc != 1 ) { print "usage: $0 \n"; exit( 255 ); } my $fName = $ARGV[0]; open(IN, "<$fName") or die "Can not open $fName"; # start the HTML page print "\n", "\n", "\n

UCSC Genome browser rearranged

\n", "Following pattern Blk Brn Red Org Ylo Grn Blu Vio Gray
\n", "Demonstrating each color next to all others\n\n"; my $totColors = 0; # to count the colors input my @palette; # will be the hex values for each my @names; # and corresponding name my $pIndex = 0; # index into the palette array while( my $line = ) { chomp($line); my @a = split(/\s/,$line); $palette[$totColors] = $a[0]; # hex value $names[$totColors] = $a[1]; # chrom name ++$totColors; } close(IN); for( my $k = 0; $k < 12; ++$k ) { print "

\n", '', "\n"; $pIndex = ($k * 2) + 1; my $fgColor = ""; print "\n"; for( my $i = 0; $i < 26; ++$i ) { if( $palette[$pIndex] eq "#000000" ) { $fgColor = ""; } else { $fgColor = ""; } print '"; $pIndex = ($pIndex + 1) % 26; } print "\n"; print "\n"; for( my $i = 0; $i < 26; ++$i ) { if( $palette[$pIndex] eq "#000000" ) { $fgColor = ""; } else { $fgColor = ""; } print '"; } print "\n"; print "\n"; $pIndex = (($k * 2) + 2) % 26; if( $pIndex > 24 ) { die "pIndex: $pIndex > 24 at k: $k"; } for( my $i = 0; $i < 26; ++$i ) { if( $palette[$pIndex] eq "#000000" ) { $fgColor = ""; } else { $fgColor = ""; } print '"; $pIndex = ($pIndex + 1) % 26; } print "\n"; print "

', "$names[$pIndex]

', "$names[$i]

', "$names[$pIndex]

\n\n"; } print "\n

\n"; open(IN0, "<$fName") or die "Can not open $fName"; print "\n"; while( my $line = ) { chomp $line; my @a = split(/\s/,$line); print '\n"; } close(IN0); print "

Hex Code	Chrom Name
', " $a[0]	$a[1]

\n", "\n", "\n";