# HG changeset patch
# User romaingred
# Date 1511878082 18000
# Node ID 0cffda6c3d1a4b3e594ca9eeeb56d150145edc04
# Parent  241aa6141cac37f57be70500505857daae182cb3
Uploaded

diff -r 241aa6141cac -r 0cffda6c3d1a bin/html.pm
--- a/bin/html.pm	Tue Nov 28 08:54:52 2017 -0500
+++ b/bin/html.pm	Tue Nov 28 09:08:02 2017 -0500
@@ -66,10 +66,10 @@
   footer($h);
   close $h;
 
-  open  $h, '>',  $prefix.'-exons.html' || die "cannot create  $prefix-exons.html $!\n";
+  open  $h, '>',  $prefix.'-transcripts.html' || die "cannot create  $prefix-transcripts.html $!\n";
   header($h);
   navbar ( $h, $list_mainTabP, $current );
-  fut($h,'Exons',$Hex);
+  fut($h,'transcripts',$Hex);
   footer($h);
   close $h;
 }
@@ -187,21 +187,21 @@
         reads of size between $min and $max<br>with no mi, sn, t and r RNAs
         <p><a class=\"btn\" href=\"$name-bonafide_reads-genome.html\">Genome</a></p>
         <p><a class=\"btn\" href=\"$name-bonafide_reads-TEs.html\">TE</a></p>
-        <p><a class=\"btn\" href=\"$name-bonafide_reads-exons.html\">Exons</a></p>
+        <p><a class=\"btn\" href=\"$name-bonafide_reads-transcripts.html\">transcripts</a></p>
         <div class=\"row-fluid\">
           <div class=\"span6\">
             <h2>siRNAs</h2>
             bonafide reads of size between $simin and $simax
             <p><a class=\"btn\" href=\"$name-siRNAs-genome.html\">Genome</a></p>
             <p><a class=\"btn\" href=\"$name-siRNAs-TEs.html\">TE</a></p>
-            <p><a class=\"btn\" href=\"$name-siRNAs-exons.html\">Exons</a></p>
+            <p><a class=\"btn\" href=\"$name-siRNAs-transcripts.html\">transcripts</a></p>
           </div>
           <div class=\"span6\">
             <h2>piRNAs</h2>
             bonafide reads of size between $pimin and $pimax
             <p><a class=\"btn\" href=\"$name-piRNAs-genome.html\">Genome</a></p>
             <p><a class=\"btn\" href=\"$name-piRNAs-TEs.html\">TE</a></p>
-            <p><a class=\"btn\" href=\"$name-piRNAs-exons.html\">Exons</a></p>
+            <p><a class=\"btn\" href=\"$name-piRNAs-transcripts.html\">transcripts</a></p>
           </div>
         </div>
       </div>
@@ -209,7 +209,7 @@
        <h2>miRNAs</h2>
        <p><a class=\"btn\" href=\"$name-miRNAs-genome.html\">Genome</a></p>
        <p><a class=\"btn\" href=\"$name-miRNAs-TEs.html\">TE</a></p>
-       <p><a class=\"btn\" href=\"$name-miRNAs-exons.html\">Exons</a></p>
+       <p><a class=\"btn\" href=\"$name-miRNAs-transcripts.html\">transcripts</a></p>
     </div>
   </div>
 </div>
@@ -237,9 +237,9 @@
     elsif ( $f =~ /genome_minus\.bedgraph$/) { $HG{'bedgraph minus strand'} = $f; }
     elsif ( $f =~ /TEs_plus\.bedgraph$/) { $HTE{'bedgraph plus strand'} = $f; }
     elsif ( $f =~ /TEs_minus\.bedgraph$/) { $HTE{'bedgraph minus strand'} = $f; }
-    elsif ( $f =~ /exons_sorted\.bam$/) { $Hex{'exons mappers (sorted bam)'} = $f;}
-    elsif ( $f =~ /exons_unique_sorted\.bam$/) { $Hex{'exons unique mappers (sorted bam)'} = $f;}        
-    elsif ( $f =~ /exons_reads_counts\.txt$/) { $Hex{'read number per exon (txt)'} = $f;}
+    elsif ( $f =~ /transcripts_sorted\.bam$/) { $Hex{'transcripts mappers (sorted bam)'} = $f;}
+    elsif ( $f =~ /transcripts_unique_sorted\.bam$/) { $Hex{'transcripts unique mappers (sorted bam)'} = $f;}        
+    elsif ( $f =~ /transcripts_reads_counts\.txt$/) { $Hex{'read number per exon (txt)'} = $f;}
     elsif ( $f =~ /TEs_reads_counts\.txt$/) { $HTE{"read number per TE 0 to $misTE mismatches (txt)"} = $f; }
     elsif ( $f =~ /TEs_reads_counts_mismatches\.txt$/) { $HTE{"read number per TE with 1 to $misTE mismatches (txt)"} = $f; }
     elsif ( $f =~ /TEs_reads_counts_nomismatches\.txt$/) { $HTE{'read number per TE with no mismatch (txt)'} = $f; }
@@ -746,11 +746,11 @@
 {
   my ($dir, $name) = @_;
   my (@out,@group);
-  my $group = $dir.'/'.$name.'-subgroups-bonafide_reads-exons-*distribution-*.png';
+  my $group = $dir.'/'.$name.'-subgroups-bonafide_reads-transcripts-*distribution-*.png';
   @group = glob $group;
   foreach (my $g =0; $g <= $#group; $g++)
   {
-    if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-exons-.*distribution-.*\.png)/ )
+    if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-transcripts-.*distribution-.*\.png)/ )
     {
       my $tmp = $1;
       push @out, $1;