+#!/usr/bin/perl -w
+
+use strict;
+use warnings;
+
+use XML::Simple;
+
+my $library_info = shift;
+my $xml = XMLin($library_info, ForceArray => 1);
+
+my %num_align;
+
+my $qpcr_filename = shift;
+open(QPCR,$qpcr_filename);
+
+my %qpcr_sum;
+
+while(<QPCR>) {
+ chomp;
+ my($lane,$factor,$enrich) = split(/ /,$_);
+ my $line2 = <QPCR>; chomp $line2;
+ my($lane2,$factor2,$enrich2) = split(/ /,$line2);
+
+ next if(!defined($enrich));
+
+ my @a = split(/\//,$factor);
+ $factor = $a[scalar(@a)-1];
+ @a = split(/\//,$factor2);
+ $factor2 = $a[scalar(@a)-1];
+
+ my $bgcolor;
+ if($enrich < 2) { $bgcolor = "FF6600"; }
+ elsif($enrich< 5) { $bgcolor = "FFCC33"; }
+ elsif($enrich< 10) { $bgcolor = "00CCFF"; }
+ elsif($enrich eq "nan") { $bgcolor = "FFFFFF"; }
+ else { $bgcolor = "66FF66"; }
+
+ $lane =~ /^(.+?)\/(\d\d\d\d\d\d)_(.+?)_s(\d+)_(.+?)\.align_\d+\.(.+?)\.txt\.qPCR$/;
+ my($fc,$date,$fc2,$lanes,$name,$genome) = ($1,$2,$3,$4,$5,$6);
+
+ $qpcr_sum{$lanes}{'best'} = $factor;
+ $qpcr_sum{$lanes}{'enrich'} = $enrich;
+ $qpcr_sum{$lanes}{'bgcolor'} = $bgcolor;
+
+ $qpcr_sum{$lanes}{'best2'} = $factor2;
+ $qpcr_sum{$lanes}{'enrich2'} = $enrich2;
+ $qpcr_sum{$lanes}{'bgcolor2'} = $bgcolor;
+}
+
+for my $i (0..scalar(@{$xml->{Library}})-1) {
+ my $lib = $xml->{Library}->[$i]->{Name};
+ for my $t (0..scalar(@{$xml->{Library}->[$i]->{Track}})-1) {
+ my $N = scalar(@{$xml->{Library}->[$i]->{Track}});
+ my($date,$fc,$lane,$desc);
+ my $filename = $xml->{Library}->[$i]->{Track}->[$t]->{Filename};
+ $filename =~ /^(\d+)_(.+?)_s(\d+)_(.+?)_$lib.align/;
+ ($date,$fc,$lane,$desc) = ($1,$2,$3,$4);
+ my $num_reads = $xml->{Library}->[$i]->{Track}->[$t]->{Count};
+
+ my $bgcolor;
+ if($num_reads < 3000000) { $bgcolor = "FF3300"; }
+ elsif($num_reads < 5000000) { $bgcolor = "FFCC33"; }
+ elsif($num_reads < 10000000) { $bgcolor = "00CCFF"; }
+ else { $bgcolor = "66FF66"; }
+
+ $num_align{$lane}{'num'} = $num_reads;
+ $num_align{$lane}{'bgcolor'} = $bgcolor;
+ }
+}
+
+print "<TABLE BORDER=1>";
+print "<TR><TD><EM>Lane\(s\)</EM></TD><TD><EM>Lib</EM></TD><TD><EM>Library Name</EM></TD><TD><EM>Aligned Reads</EM></TD><TD><EM>qPCR Factor</EM></TD><TD><EM>Fold enr.</EM></TD><TD><EM>Profile at TSS</EM></TD><TD>IVC Calls</TD></TR>\n";
+
+my @files = `ls -1 QC/*.align_??.*.txt.profile.gif`;
+for my $file (@files) {
+ $file =~ /(\d\d\d\d\d\d)_(.+?)_s(\d+)_(.+?)_([Ss][Ll]\d+)/;
+ my($date,$fc,$lanes,$libname,$lib) = ($1,$2,$3,$4,$5);
+ my $lane = substr($lanes,0,1);
+ print "<TR>\n";
+ print "<TD>$lanes</TD>";
+ print "<TD>$lib</TD>\n";
+ print "<TD>$libname</TD>\n";
+ printf "<TD BGCOLOR=#%s>%0.2fM</TD>\n",$num_align{$lanes}{'bgcolor'},$num_align{$lanes}{'num'}/1000000.0;
+ printf "<TD BGCOLOR=#%s>%s</TD><TD BGCOLOR=#%s>%0.2f<BR>%0.2f</TD>\n",$qpcr_sum{$lanes}{'bgcolor'},$qpcr_sum{$lanes}{'best'}."<BR>".$qpcr_sum{$lanes}{'best2'},$qpcr_sum{$lanes}{'bgcolor'},$qpcr_sum{$lanes}{'enrich'},$qpcr_sum{$lanes}{'enrich2'};
+ print "<TD><OBJECT DATA=\"",`basename $file`,"\" WIDTH=\"300\" HEIGHT=\"300\"></OBJECT></TD>";
+ print "<TD><IMG SRC=\"s_",$lane,"_percent_base.png\" WIDTH=\"300\" HEIGHT=\"300\"></TD>";
+ print "</TR>\n";
+}
+print "</TABLE>\n";
+
+print "</BODY></HTML>\n";