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tableToHtml2.pl
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tableToHtml2.pl
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#!/usr/bin/env perl
use strict;
use warnings;
use File::Basename qw( basename dirname );
my $useFirstFieldColoring = 0;
my $alternateRowColoring = 1;
if (@ARGV > 0) {
if ($ARGV[0] eq "firstcol") {
$useFirstFieldColoring = 1;
} else {
$alternateRowColoring = int( $ARGV[0] );
}
}
my $showPNG = 1;
my $header1 = 0; # flag to change class of first row to "header"
if (@ARGV > 1) {
if ($ARGV[1] eq "linkonly") {
$showPNG = 0;
} elsif ($ARGV[1] eq "header") {
$header1 = 1;
}
}
#print "<html>\n";
#print "<body>\n";
my $message = <<'END_MESSAGE';
<html>
<head>
<title>FORGEdb</title>
<link rel="stylesheet" type="text/css" href="blog0.css" />
</head>
<body>
END_MESSAGE
print $message;
my $message2 = <<'END_MESSAGE';
</body> </html>
END_MESSAGE
print $message2;
print '<table class="center" border="1" cellspacing="0" cellpadding="2" style="font-family:Helvetica" style="text-align:center">' . "\n";
my $count = 0;
my $prevFirstCol = "";
while (<STDIN>) {
chomp;
#my $trclass= (++$count % 2 == 0) ? "row_even" : "row_odd";
my @things = split /\t/, $_;
my $trclass;
if ($useFirstFieldColoring) {
my $firstcol = $things[0];
if ($prevFirstCol ne $firstcol) {
++$count;
}
$trclass= ($count % 2 == 0) ? "row_even" : "row_odd";
$prevFirstCol = $firstcol;
} else {
$trclass= (int((++$count - 1)/$alternateRowColoring) % 2 == 0) ? "row_even" : "row_odd";
}
if ($header1 and ($count < 2)) {
$trclass = "header";
}
print "<tr class=$trclass>";
#my @things = split;
for (my $i = 0; $i < @things; ++$i) {
my $colspan= "";
my $align="style=\"text-align:center\"";
if (scalar(@things)<2){
$colspan= "colspan=10";
$align="style=\"text-align:left\"";
}
my $tdclass= "";
my $localpath = $things[$i]; # save this before fixpath changes it
$things[$i] = fixpath( $things[$i] );
if ($things[$i] =~ /^[0-9,\.Ee+-]+$/ or $things[$i] =~ /\>[0-9,\.Ee+-]+\</) {
$tdclass= "class=numeric";
if ($things[$i] =~ /\./) {
my $precision = 10000;
#$things[$i] = int( 0.5 + ($things[$i]*$precision) ) / $precision;
#TODO Preserve significant digits!
} elsif ($things[$i] =~ /^([\d]+)$/) {
$things[$i] = encomma($things[$i]);
}
} elsif (($things[$i] =~ /^http.*\/([^\/]+)$/) or ($things[$i] =~ /^\/\~.*\/([^\/]+)$/)) {
my $shortname = $1;
my $orig = $things[$i];
if ($showPNG and (($orig =~ /\.png$/i) or ($orig =~ /\.svg$/i))) {
my $filename = basename( $localpath );
my $localdirname = dirname( $localpath );
my $webdirname = dirname( $orig );
my $localthumbnail = "$localdirname/th_$filename";
if (-s $localthumbnail) {
# show thumbnail as a link to the image
my $webthumbnail = "$webdirname/th_$filename";
$things[$i] = "<a href=\"$orig\"><img src=\"$webthumbnail\"/></a>";
} else {
#warn "$localthumbnail not found\n";
# just show the image
$things[$i] = "<img src=\"$orig\"/>";
}
} else {
if ($shortname =~ /greatStart.php/) {
$shortname = "GREAT"; # used to be a very long name
}
$things[$i] = "<a href=\"$orig\">$shortname</a>";
}
}
print " <td $tdclass $colspan $align> " . $things[$i] . " </td>";
}
print "</tr>\n";
}
print "</table>\n";
#print "</body>\n";
#print "</html>\n";
sub fixpath {
my $orig = shift;
my $path = $orig;
if ($orig =~ /^\/home\/([^\/]+)\/public_html\/(.*)$/) {
my ($user,$relativePath) = ($1,$2);
$path = "/~$user/$relativePath";
} elsif ($orig =~ /.*\/([^\/]+)_enhancer\/(.*)$/) {
my ($user,$relativePath) = ($1,$2);
$path = "http://www.uwencode.org/proj/${user}_enhancer/$relativePath";
} elsif ($orig =~ /.net.lebowski.vol1.work.proj.(.*)$/) {
my $relativePath = $1;
$path = "http://www.uwencode.org/proj/$relativePath";
}
return $path;
}
#/net/lebowski/vol1/work/proj/ehaugen/2012oct17
#<a href="http://www.uwencode.org/proj/ehaugen_enhancer/2011Sep27/clusters.html">Clustered motifs.</a>
#<a href="http://www.uwencode.org/proj/ehaugen_enhancer/2011Sep27/summary.fvi_OnlyPromoters.factorscores2.html"> in promoters (Gencode V7 TSS +/- 2.5kb)</a>
sub encomma {
my $orig = shift;
my $remain = "$orig";
my $result = "";
while (length($remain) > 3) {
my $chunk = substr( $remain, length($remain) - 3 );
$remain = substr( $remain, 0, length($remain) - 3 );
if (length($result) > 0) {
$result = ",$result";
}
$result = "$chunk$result";
#warn "$remain | $result\n";
}
if ((length($result) > 0) and (length($remain)>0)) {
$result = ",$result";
}
$result = "$remain$result";
#warn "encomma($orig)=($result)\n";
return $result;
}