Moving QC functionalty into repository so we can run outside of the pipeline.

[htsworkflow.git] / htswanalysis / scripts / WriteQCSummary.pm

diff --git a/htswanalysis/scripts/WriteQCSummary.pm b/htswanalysis/scripts/WriteQCSummary.pm
index aef28d97cba5f191a17dcf50b94ec93804dbf60e..9593c8940ba4e984fe08c7ca3fc33225fc543a03 100755 (executable)
--- a/htswanalysis/scripts/WriteQCSummary.pm
+++ b/htswanalysis/scripts/WriteQCSummary.pm
@@ -35,8 +35,8 @@ while(<QPCR>) {
   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);
+  $lane =~ /^(\d\d\d\d\d\d)_(.+?)_s(\d+)_(.+?)\.align_\d+\.(.+?)\.txt\.qPCR$/;
+  my($date,$fc,$lanes,$name,$genome) = ($1,$2,$3,$4,$5,$6);
 
   $qpcr_sum{$lanes}{'best'} = $factor;
   $qpcr_sum{$lanes}{'enrich'} = $enrich;
@@ -71,7 +71,7 @@ for my $i (0..scalar(@{$xml->{Library}})-1) {
 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`;
+my @files = `ls -1 *.align_??.*.txt.profile.png`;
 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);
@@ -83,7 +83,7 @@ for my $file (@files) {
   printf "<TD BGCOLOR=#%s>%0.2fM</TD>\n",$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 "<TD><IMG SRC=\"",$date,"_",$fc,"_s",$lanes,"_",$libname,"_",$lib,".percent_base.png\" WIDTH=\"300\" HEIGHT=\"300\"></TD>";
   print "</TR>\n";
 }
 print "</TABLE>\n";