Mercurial > repos > brasset_jensen > srnapipe

diff bin/html.pm @ 60:9645d995fb3c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Fix for spaces in datasets names.
author pierre.pouchin
date Wed, 24 Oct 2018 07:40:20 -0400
parents 263819fdda14
children 9185ca0a7b43
line wrap: on
line diff
--- a/bin/html.pm	Tue Oct 23 11:02:17 2018 -0400
+++ b/bin/html.pm	Wed Oct 24 07:40:20 2018 -0400
@@ -10,25 +10,25 @@
 
 sub main_page
 {
-	my ( $dir, $file, $list_mainTabP, $current, $ma, $ma_uni, $dir_root ) = @_;
-	my ( $futHashP, $uniqueTabP, $randTabP, $pngTabP ) = get_genome ( $dir, $dir_root );
+  my ( $dir, $file, $list_mainTabP, $current, $ma, $ma_uni, $dir_root ) = @_;
+  my ( $futHashP, $uniqueTabP, $randTabP, $pngTabP ) = get_genome ( $dir, $dir_root );
 
-	open my $h, '>', $file || die "cannot create $file $!\n";
-	header ( $h );
-	navbar ( $h, $list_mainTabP, $current );
-	print $h "<div class=\"container\"><p><a class=\"btn\" href=\"$current-sub.html\">View details &raquo;</a></p></div>\n";
-	futurette( $h, $current, $pngTabP, $futHashP );
-	print  $h "<div class=\"container\"><h2>mappers #: $ma</h2><h2>unique mappers #: $ma_uni</h2> </div>\n";
-	carousel2( $h, $uniqueTabP, $randTabP, $dir_root );
-	footer($h);
-	close $h;
+  open my $h, '>', $file || die "cannot create $file $!\n";
+  header ( $h );
+  navbar ( $h, $list_mainTabP, $current );
+  print $h "<div class=\"container\"><p><a class=\"btn\" href=\"$current-sub.html\">View details &raquo;</a></p></div>\n";
+  futurette( $h, $current, $pngTabP, $futHashP );
+  print  $h "<div class=\"container\"><h2>mappers #: $ma</h2><h2>unique mappers #: $ma_uni</h2> </div>\n";
+  carousel2( $h, $uniqueTabP, $randTabP, $dir_root );
+  footer($h);
+  close $h;
 }
 
 sub menu_page
 {
-	my ( $dir, $file, $list_mainTabP, $current, $min, $max, $simin, $simax, $pimin, $pimax, $dir_root ) = @_;
+  my ( $dir, $file, $list_mainTabP, $current, $min, $max, $simin, $simax, $pimin, $pimax, $dir_root ) = @_;
   my $html_ref = $1 if $dir =~ /$dir_root(.*)/;
-	open my $h, '>', $file || die "cannot create $file $!\n";
+  open my $h, '>', $file || die "cannot create $file $!\n";
   header($h);
   navbar ( $h, $list_mainTabP, $current );
   span( $h, $current, $min, $max, $simin, $simax, $pimin, $pimax );
@@ -40,7 +40,7 @@
 
 sub details_pages
 {
-	my ( $dir_details, $prefix, $list_mainTabP, $current, $misTE, $dir_root, $ppp ) = @_;
+  my ( $dir_details, $prefix, $list_mainTabP, $current, $misTE, $dir_root, $ppp ) = @_;
   my ($Hex, $HTE, $HG, $NonUniTE, $NonUniG, $UniG ) = get_subgroups( $dir_details, $current, $misTE, $dir_root );
 
   my $html_ref = $1.'-PPP.html' if $prefix =~ /$dir_root(.*)/;
@@ -49,9 +49,9 @@
   navbar ( $h, $list_mainTabP, $current );
   if ( $prefix =~ /piRNAs$/ && $ppp eq 'true' )
   {
-  	print $h " <div class=\"container\">";
-  	print $h " <p><a class=\"btn\" href=\"$html_ref\">Ping Pong Partners</a></p>\n";
-  	print $h "</div>";
+    print $h " <div class=\"container\">";
+    print $h " <p><a class=\"btn\" href=\"$html_ref\">Ping Pong Partners</a></p>\n";
+    print $h "</div>";
   }
   fut($h,'Transposable elements',$HTE);
   carousel($h,$NonUniTE,$dir_root);
@@ -76,14 +76,14 @@
 
 sub ppp_page
 {
-	my ( $dir, $file, $list_mainTabP, $current, $ppp, $dir_root ) = @_;
+  my ( $dir, $file, $list_mainTabP, $current, $ppp, $dir_root ) = @_;
 
-	my $ppp_file = $ppp.'ppp.txt';
-	open my $h, '>', $file || die "cannot create $file $!\n";
-	header($h);
- 	navbar ( $h, $list_mainTabP, $current );
- 	print $h '<div class="container"> <table class="wb-tables table table-striped table-hover">'."\n";
- 	print $h '<thead>
+  my $ppp_file = $ppp.'ppp.txt';
+  open my $h, '>', $file || die "cannot create $file $!\n";
+  header($h);
+  navbar ( $h, $list_mainTabP, $current );
+  print $h '<div class="container"> <table class="wb-tables table table-striped table-hover">'."\n";
+  print $h '<thead>
   <tr>
     <th data-sortable="true">ID</th>
     <th data-sortable="true">overlap sum</th>
@@ -96,22 +96,22 @@
   </thead>
   <tbody>';
 
- 	open my $f, '<', $ppp_file || die "cannot open $ppp_file  $!\n";
- 	while ( <$f> )
- 	{
- 		chomp;
- 		print $h '<tr>';
- 		my ( $id, $sum, $ten, $mean, $sd, $zscore, $prob) = split /\t/, $_;
- 		if( -d "$ppp/$id" ) 
- 		{
- 			my $sub_html = $ppp.$id.'.html';
+  open my $f, '<', $ppp_file || die "cannot open $ppp_file  $!\n";
+  while ( <$f> )
+  {
+    chomp;
+    print $h '<tr>';
+    my ( $id, $sum, $ten, $mean, $sd, $zscore, $prob) = split /\t/, $_;
+    if( -d "$ppp/$id" )
+    {
+      my $sub_html = $ppp.$id.'.html';
       my $sub_html_ref = $1.$id if $ppp =~ /$dir_root(.*)/;
- 			print $h "<td> <a href=\"$sub_html_ref.html\">$id</a> </td>";
+      print $h "<td> <a href=\"$sub_html_ref.html\">$id</a> </td>";
 
- 			open my $sub, '>', $sub_html || die "cannot create $sub_html\n";
- 			{
- 				header($sub);
- 				print $sub "
+      open my $sub, '>', $sub_html || die "cannot create $sub_html\n";
+      {
+        header($sub);
+        print $sub "
 					<div align=\"center\">
 					<h2>$id</h2>
 					<p> <img class=\"featurette-image\" src=\"$id/histogram.png\"/></p>
@@ -121,20 +121,19 @@
 					<p><a href=\"$id/sens.txt\">sense reads without PPP</a></p>
 					<p><a href=\"$id/antisens.txt\">reverse reads without PPP</a></p>
 					</div>";
- 				footer($sub);
- 			}
- 			close $sub;
+        footer($sub);
+      }
+      close $sub;
+    }
+    else { print $h "<td> $id </td>\n"; }
+    print $h "<td> $sum </td><td> $ten </td><td> $mean </td><td> $sd </td><td> $zscore </td><td> $prob </td>\n";
 
- 		}
- 		else { print $h "<td> $id </td>\n"; }
- 		print $h "<td> $sum </td><td> $ten </td><td> $mean </td><td> $sd </td><td> $zscore </td><td> $prob </td>\n";
-
- 		print $h '</tr>';
- 	}
- 	close $f;
- 	print $h "</tbody></table></div>";
- 	footer($h);
- 	close $h;
+    print $h '</tr>';
+  }
+  close $f;
+  print $h "</tbody></table></div>";
+  footer($h);
+  close $h;
 }
 
 sub get_genome
@@ -142,37 +141,37 @@
   my ( $dir, $dir_root ) = @_;
   my ( %hash, @group,  @Unique, @NonUnique, @png );
 
-  my $fut = $dir.'/*';
+  my $fut = "'$dir'".'/*';
   my @fut = glob $fut;
 
 
-	foreach my $fr ( @fut )
-	{
+  foreach my $fr ( @fut )
+  {
     my $f = $1 if $fr =~ /$dir_root(.*)/;
-		if ( $fr =~ /.*Gviz/ )
-		{
-			my $nu = $fr.'/rand/*';
-			@NonUnique =  glob $nu;
-			my $u = $fr.'/unique/*';
-			@Unique =  glob $u;
-		}
-		elsif ( $f =~ /.*distribution\.txt$/ ) { $hash{'mappers size distribution (txt)'} = $f; }
-		elsif ( $f =~ /.*distribution\.png$/ ) { push @png, $f; } 
-		elsif ( $f =~ /.*unique\.fastq$/ ) { $hash{'unique mappers (fastq.gz)'} = $f.'.gz'; `gzip $fr`; }
-		elsif ( $f =~ /.*rejected\.fastq$/ ) { $hash{'unmapped (fastq.gz)'} = $f.'.gz'; `gzip $fr`; }
-		elsif ( $f =~ /.*all\.fastq$/ ) { $hash{'mappers (fastq.gz)'} = $f.'.gz'; `gzip $fr`; }
-		elsif ( $f =~ /.*dup_unique\.txt$/ ) { $hash{'unique mappers (txt)'} = $f; }
-		elsif ( $f =~ /.*dup_mapnum\.txt$/ ) { $hash{'mappers (txt)'} = $f; }
-		elsif ( $f =~ /.*dup_nonmapp\.txt$/ ) { $hash{'unmapped (txt)'} = $f; }
-		elsif ( $f =~ /.*_unique_sorted\.bam$/ ) { $hash{'unique alignment (bam)'} = $f; }
-		elsif ( $f =~ /.*_sorted\.bam$/ ) { $hash{'alignment (bam)'} = $f; }
-		elsif ( $f =~ /.*unique_plus.bedgraph/) { $hash{'bedgraph unique plus strand'} = $f; }
+    if ( $fr =~ /.*Gviz/ )
+    {
+      my $nu = "'$fr'".'/rand/*';
+      @NonUnique =  glob $nu;
+      my $u = "'$fr'".'/unique/*';
+      @Unique =  glob $u;
+    }
+    elsif ( $f =~ /.*distribution\.txt$/ ) { $hash{'mappers size distribution (txt)'} = $f; }
+    elsif ( $f =~ /.*distribution\.png$/ ) { push @png, $f; }
+    elsif ( $f =~ /.*unique\.fastq$/ ) { $hash{'unique mappers (fastq.gz)'} = $f.'.gz'; `gzip '$fr'`; }
+    elsif ( $f =~ /.*rejected\.fastq$/ ) { $hash{'unmapped (fastq.gz)'} = $f.'.gz'; `gzip '$fr'`; }
+    elsif ( $f =~ /.*all\.fastq$/ ) { $hash{'mappers (fastq.gz)'} = $f.'.gz'; `gzip '$fr'`; }
+    elsif ( $f =~ /.*dup_unique\.txt$/ ) { $hash{'unique mappers (txt)'} = $f; }
+    elsif ( $f =~ /.*dup_mapnum\.txt$/ ) { $hash{'mappers (txt)'} = $f; }
+    elsif ( $f =~ /.*dup_nonmapp\.txt$/ ) { $hash{'unmapped (txt)'} = $f; }
+    elsif ( $f =~ /.*_unique_sorted\.bam$/ ) { $hash{'unique alignment (bam)'} = $f; }
+    elsif ( $f =~ /.*_sorted\.bam$/ ) { $hash{'alignment (bam)'} = $f; }
+    elsif ( $f =~ /.*unique_plus.bedgraph/) { $hash{'bedgraph unique plus strand'} = $f; }
     elsif ( $f =~ /.*unique_minus.bedgraph/) { $hash{'bedgraph unique minus strand'} = $f; }
     elsif ( $f =~ /.*plus.bedgraph/) { $hash{'bedgraph plus strand'} = $f; }
     elsif ( $f =~ /.*minus.bedgraph/) { $hash{'bedgraph minus strand'} = $f; }
     else { unlink $fr; }
-	}
-	return (\%hash, \@Unique, \@NonUnique, \@png);
+  }
+  return (\%hash, \@Unique, \@NonUnique, \@png);
 }
 
 sub span
@@ -221,11 +220,11 @@
   my ( $dir, $name, $misTE, $dir_root ) = @_;
   my (%Hex, %HTE, %HG, @group, @png, @pngTE,  @NonUniTE, @UniG, @NonUniG );
 
-  my $fut = $dir.'/*';
+  my $fut = "'$dir'".'/*';
   my @fut = glob $fut;
   my $f ='';
-	foreach my $fr ( @fut )
-	{
+  foreach my $fr ( @fut )
+  {
     $f = $1 if $fr =~  /$dir_root(.*)/;
 
     if ( $f =~ /genome_unique_sorted\.bam$/ ) { $HG{'genome unique mappers (sorted bam)'} =  $f; }
@@ -238,25 +237,25 @@
     elsif ( $f =~ /TEs_plus\.bedgraph$/) { $HTE{'bedgraph plus strand'} = $f; }
     elsif ( $f =~ /TEs_minus\.bedgraph$/) { $HTE{'bedgraph minus strand'} = $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 ( $f =~ /transcripts_unique_sorted\.bam$/) { $Hex{'transcripts unique mappers (sorted bam)'} = $f;}
     elsif ( $f =~ /transcripts_reads_counts\.txt$/) { $Hex{'read number per transcript (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; }
     elsif ( $f =~ /TEs_unique_sorted\.bam$/) { $HTE{'TEs unique mappers (sorted bam)'} = $f; }
     elsif ( $f =~ /TEs_sorted\.bam$/) { $HTE{'TEs mappers (sorted bam)'} = $f; }
-		elsif ( $fr =~ /.*Gviz_TEs/ )
-		{
-			my $nu = $fr.'/*';
-			@NonUniTE =  glob $nu;
-		}
-		elsif ( $fr =~ /.*Gviz_genome/ )
-		{
-			my $nu = $fr.'/rand/*';
-			@NonUniG =  glob $nu;
-			my $u = $fr.'/unique/*';
-			@UniG =  glob $u;
-		}
+    elsif ( $fr =~ /.*Gviz_TEs/ )
+    {
+      my $nu = "'$fr'".'/*';
+      @NonUniTE =  glob $nu;
+    }
+    elsif ( $fr =~ /.*Gviz_genome/ )
+    {
+      my $nu = "'$fr'".'/rand/*';
+      @NonUniG =  glob $nu;
+      my $u = "'$fr'".'/unique/*';
+      @UniG =  glob $u;
+    }
     else { unlink $fr; }
   }
   return (\%Hex, \%HTE, \%HG, \@NonUniTE,  \@NonUniG, \@UniG);
@@ -480,7 +479,7 @@
 sub navbar
 {
   my ( $file, $fastq, $actif ) = @_;
-  
+
   print $file "
   <div class=\"navbar navbar-inverse navbar-fixed-top\">
   <div class=\"navbar-inner\">
@@ -526,7 +525,7 @@
   <script type=\"text/javascript\" src=\"js/jquery.js\"></script>
   <script type=\"text/javascript\" src=\"js/jquery-1.3.2.js\"></script>
   <script type=\"text/javascript\" src=\"js/jquery.galleriffic.js\"></script>
-  <script type=\"text/javascript\" src=\"js/jquery.opacityrollover.js\"></script>  
+  <script type=\"text/javascript\" src=\"js/jquery.opacityrollover.js\"></script>
   <script type=\"text/javascript\" src=\"js/bootstrap-table.js\"></script>
   <script type=\"text/javascript\" src=\"js/bootstrap.min.js\"></script>
   <script type=\"text/javascript\">
@@ -613,7 +612,7 @@
   ";
   foreach my $u (@{$non_unique})
   {
-  	my $name = basename($u,'.png');
+    my $name = basename($u,'.png');
     $u = $1 if $u =~ /$dir_root(.*)/;
     print $file "
     <li>
@@ -652,7 +651,7 @@
 
   foreach my $u (@{$unique})
   {
-  	my $name = basename($u,'.png');
+    my $name = basename($u,'.png');
     $u = $1 if $u =~ /$dir_root(.*)/;
     print $file "
     <li>
@@ -682,7 +681,7 @@
 
   foreach my $nu (@{$non_unique})
   {
-  	my $name = basename($nu,'.png');
+    my $name = basename($nu,'.png');
     $nu = $1 if $nu =~ /$dir_root(.*)/;
     print $file "
         <li>
@@ -750,7 +749,7 @@
 {
   my ($dir, $name) = @_;
   my (@out,@group);
-  my $group = $dir.'/'.$name.'-subgroups-bonafide_reads-transcripts-*distribution-*.png';
+  my $group = "'$dir'".'/'."'$name'".'-subgroups-bonafide_reads-transcripts-*distribution-*.png';
   @group = glob $group;
   foreach (my $g =0; $g <= $#group; $g++)
   {
@@ -767,7 +766,7 @@
 {
   my ($dir, $name) = @_;
   my (@out,@group);
-  my $group = $dir.'/'.$name.'-subgroups-bonafide_reads-TE-*distribution-*.png';
+  my $group = "'$dir'".'/'."'$name'".'-subgroups-bonafide_reads-TE-*distribution-*.png';
   @group = glob $group;
   foreach (my $g =0; $g <= $#group; $g++)
   {
@@ -784,9 +783,9 @@
 {
   my ($dir,$name) = @_;
   my (%distri,@group);
-  my $group = $dir.'/'.$name.'-subgroups-bonafide_reads-TE-PPPartners-*';
+  my $group = "'$dir'".'/'."'$name'".'-subgroups-bonafide_reads-TE-PPPartners-*';
   @group = glob $group;
-  
+
   foreach (my $g =0; $g <= $#group; $g++)
   {
     if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-TE-PPPartners-.*)/ )
@@ -831,7 +830,7 @@
 {
   my ($h, $hash) = @_;
   my $cmp = 0;
-  
+
   print $h "<div class=\"container\">\n";
   print $h "<div class=\"row text-center\">";
   while ( my ($k,$v) = each %{$hash} )
@@ -851,7 +850,7 @@
     ";
     $cmp++;
   }
-  
+
   print $h "</div></div>";
 }
 
@@ -880,7 +879,7 @@
     ";
     $cmp++;
   }
-  
+
   print $h "</div></div>";
 }