Added framework for methylseq analysis.

[htsworkflow.git] / htswanalysis / scripts / SummarizeProject2.pm
diff --git a/htswanalysis/scripts/SummarizeProject2.pm b/htswanalysis/scripts/SummarizeProject2.pm

index b509ac32480c326114883337b0d2ad5b501907d5..25ffa0273497b5a05919370da182e92c564c87a3 100755 (executable)
--- a/htswanalysis/scripts/SummarizeProject2.pm
+++ b/htswanalysis/scripts/SummarizeProject2.pm
@@ -74,6 +74,32 @@ for my $i (0..scalar(@{$xml->{qPCR}})-1) {
  $qPCR_Summary .= "</TABLE>\n";
  }
  
+my $methylseq_summary = "";
+if(exists($xml->{Methylseq})) {
+  $methylseq_sumary "<TABLE BORDER=1>\n";
+  $methylseq_summary .= "<TR>\n";
+  $methylseq_summary .= "<TD><EM>msp1</EM></TD>\n";
+  $methylseq_summary .= "<TD><EM>hpa2</EM></TD>\n";
+  $methylseq_summary .= "<TD><EM>Assayed</EM></TD>\n";
+  $methylseq_summary .= "<TD><EM>Methylated</EM></TD>\n";
+  $methylseq_summary .= "<TD><EM>Errors</EM></TD>\n";
+  $methylseq_summary .= "<TD><EM>Data</EM></TD></TR>\n";
+
+  for my $i (0..scalar(@{$xml->{Methylseq}})-1) {
+    my $task = $xml->{Methylseq}->[$i]->{TaskId};
+    my $genome = $xml->{Methylseq}->[$i]->{Genome};
+    my $name = $xml->{Methylseq}->[$i]->{Name};
+
+    my $msp1   = $xml->{Methylseq}->[$i]->{Msp1}->{Library};
+    my $hpa2   = $xml->{Methylseq}->[$i]->{Hpa2}->{Library};
+
+    $methylseq_summary .= `$root_dir/scripts/SummarizeMethylseq.pm $name $task $msp1 $hpa2 $genome`;
+
+  }
+  $methylseq_summary .= "</TABLE>\n";
+}
+
+
  my $profile_summary = "";
  if(exists($xml->{ProfileReads})) {
    $profile_summary = "<BR><H2>Read Profiles (<A HREF=http://genome.ucsc.edu/cgi-bin/hgGateway>Genome Browser</A>)</H2>\n";
@@ -180,6 +206,7 @@ print "<HTML><HEAD><TITLE>$project_name Analysis Summary</TITLE></HEAD><BODY>\n"
  print "<H1><CENTER>$project_name Analysis Summary</CENTER></H1>\n";
  print SummarizeLibrary($library_info);
  print $profile_summary;
+print $methylseq_summary;
  print $library_comparisons;
  print $peak_call_comparisons;
  print $motif_finding;