Mercurial > repos > brasset_jensen > srnapipe

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

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Fix for spaces in datasets names.
author pierre.pouchin
date Wed, 24 Oct 2018 07:40:20 -0400
parents 263819fdda14
children 9185ca0a7b43
comparison
equal deleted inserted replaced
59:eeb89c3331ad 60:9645d995fb3c
8 our @ISA = qw( Exporter ); 8 our @ISA = qw( Exporter );
9 our @EXPORT_OK = qw( &main_page &details_pages &menu_page &ppp_page ); 9 our @EXPORT_OK = qw( &main_page &details_pages &menu_page &ppp_page );
10 10
11 sub main_page 11 sub main_page
12 { 12 {
13 my ( $dir, $file, $list_mainTabP, $current, $ma, $ma_uni, $dir_root ) = @_; 13 my ( $dir, $file, $list_mainTabP, $current, $ma, $ma_uni, $dir_root ) = @_;
14 my ( $futHashP, $uniqueTabP, $randTabP, $pngTabP ) = get_genome ( $dir, $dir_root ); 14 my ( $futHashP, $uniqueTabP, $randTabP, $pngTabP ) = get_genome ( $dir, $dir_root );
15 15
16 open my $h, '>', $file || die "cannot create $file $!\n"; 16 open my $h, '>', $file || die "cannot create $file $!\n";
17 header ( $h ); 17 header ( $h );
18 navbar ( $h, $list_mainTabP, $current ); 18 navbar ( $h, $list_mainTabP, $current );
19 print $h "<div class=\"container\"><p><a class=\"btn\" href=\"$current-sub.html\">View details &raquo;</a></p></div>\n"; 19 print $h "<div class=\"container\"><p><a class=\"btn\" href=\"$current-sub.html\">View details &raquo;</a></p></div>\n";
20 futurette( $h, $current, $pngTabP, $futHashP ); 20 futurette( $h, $current, $pngTabP, $futHashP );
21 print $h "<div class=\"container\"><h2>mappers #: $ma</h2><h2>unique mappers #: $ma_uni</h2> </div>\n"; 21 print $h "<div class=\"container\"><h2>mappers #: $ma</h2><h2>unique mappers #: $ma_uni</h2> </div>\n";
22 carousel2( $h, $uniqueTabP, $randTabP, $dir_root ); 22 carousel2( $h, $uniqueTabP, $randTabP, $dir_root );
23 footer($h); 23 footer($h);
24 close $h; 24 close $h;
25 } 25 }
26 26
27 sub menu_page 27 sub menu_page
28 { 28 {
29 my ( $dir, $file, $list_mainTabP, $current, $min, $max, $simin, $simax, $pimin, $pimax, $dir_root ) = @_; 29 my ( $dir, $file, $list_mainTabP, $current, $min, $max, $simin, $simax, $pimin, $pimax, $dir_root ) = @_;
30 my $html_ref = $1 if $dir =~ /$dir_root(.*)/; 30 my $html_ref = $1 if $dir =~ /$dir_root(.*)/;
31 open my $h, '>', $file || die "cannot create $file $!\n"; 31 open my $h, '>', $file || die "cannot create $file $!\n";
32 header($h); 32 header($h);
33 navbar ( $h, $list_mainTabP, $current ); 33 navbar ( $h, $list_mainTabP, $current );
34 span( $h, $current, $min, $max, $simin, $simax, $pimin, $pimax ); 34 span( $h, $current, $min, $max, $simin, $simax, $pimin, $pimax );
35 print $h " <div class=\"container\"> <div class=\"row text-center\"> <img src=\"$html_ref/pie_chart.png\"/><br />\n"; 35 print $h " <div class=\"container\"> <div class=\"row text-center\"> <img src=\"$html_ref/pie_chart.png\"/><br />\n";
36 print $h " <A HREF=\"$html_ref/repartition.txt\">text file</A><br/>\n </div></div>"; 36 print $h " <A HREF=\"$html_ref/repartition.txt\">text file</A><br/>\n </div></div>";
38 close $h; 38 close $h;
39 } 39 }
40 40
41 sub details_pages 41 sub details_pages
42 { 42 {
43 my ( $dir_details, $prefix, $list_mainTabP, $current, $misTE, $dir_root, $ppp ) = @_; 43 my ( $dir_details, $prefix, $list_mainTabP, $current, $misTE, $dir_root, $ppp ) = @_;
44 my ($Hex, $HTE, $HG, $NonUniTE, $NonUniG, $UniG ) = get_subgroups( $dir_details, $current, $misTE, $dir_root ); 44 my ($Hex, $HTE, $HG, $NonUniTE, $NonUniG, $UniG ) = get_subgroups( $dir_details, $current, $misTE, $dir_root );
45 45
46 my $html_ref = $1.'-PPP.html' if $prefix =~ /$dir_root(.*)/; 46 my $html_ref = $1.'-PPP.html' if $prefix =~ /$dir_root(.*)/;
47 open my $h, '>', $prefix.'-TEs.html' || die "cannot create $prefix-TEs.html $!\n"; 47 open my $h, '>', $prefix.'-TEs.html' || die "cannot create $prefix-TEs.html $!\n";
48 header($h); 48 header($h);
49 navbar ( $h, $list_mainTabP, $current ); 49 navbar ( $h, $list_mainTabP, $current );
50 if ( $prefix =~ /piRNAs$/ && $ppp eq 'true' ) 50 if ( $prefix =~ /piRNAs$/ && $ppp eq 'true' )
51 { 51 {
52 print $h " <div class=\"container\">"; 52 print $h " <div class=\"container\">";
53 print $h " <p><a class=\"btn\" href=\"$html_ref\">Ping Pong Partners</a></p>\n"; 53 print $h " <p><a class=\"btn\" href=\"$html_ref\">Ping Pong Partners</a></p>\n";
54 print $h "</div>"; 54 print $h "</div>";
55 } 55 }
56 fut($h,'Transposable elements',$HTE); 56 fut($h,'Transposable elements',$HTE);
57 carousel($h,$NonUniTE,$dir_root); 57 carousel($h,$NonUniTE,$dir_root);
58 footer($h); 58 footer($h);
59 close $h; 59 close $h;
74 close $h; 74 close $h;
75 } 75 }
76 76
77 sub ppp_page 77 sub ppp_page
78 { 78 {
79 my ( $dir, $file, $list_mainTabP, $current, $ppp, $dir_root ) = @_; 79 my ( $dir, $file, $list_mainTabP, $current, $ppp, $dir_root ) = @_;
80 80
81 my $ppp_file = $ppp.'ppp.txt'; 81 my $ppp_file = $ppp.'ppp.txt';
82 open my $h, '>', $file || die "cannot create $file $!\n"; 82 open my $h, '>', $file || die "cannot create $file $!\n";
83 header($h); 83 header($h);
84 navbar ( $h, $list_mainTabP, $current ); 84 navbar ( $h, $list_mainTabP, $current );
85 print $h '<div class="container"> <table class="wb-tables table table-striped table-hover">'."\n"; 85 print $h '<div class="container"> <table class="wb-tables table table-striped table-hover">'."\n";
86 print $h '<thead> 86 print $h '<thead>
87 <tr> 87 <tr>
88 <th data-sortable="true">ID</th> 88 <th data-sortable="true">ID</th>
89 <th data-sortable="true">overlap sum</th> 89 <th data-sortable="true">overlap sum</th>
90 <th data-sortable="true">ten overlap sum</th> 90 <th data-sortable="true">ten overlap sum</th>
91 <th data-sortable="true">mean</th> 91 <th data-sortable="true">mean</th>
94 <th data-sortable="true">p-value</th> 94 <th data-sortable="true">p-value</th>
95 </tr> 95 </tr>
96 </thead> 96 </thead>
97 <tbody>'; 97 <tbody>';
98 98
99 open my $f, '<', $ppp_file || die "cannot open $ppp_file $!\n"; 99 open my $f, '<', $ppp_file || die "cannot open $ppp_file $!\n";
100 while ( <$f> ) 100 while ( <$f> )
101 { 101 {
102 chomp; 102 chomp;
103 print $h '<tr>'; 103 print $h '<tr>';
104 my ( $id, $sum, $ten, $mean, $sd, $zscore, $prob) = split /\t/, $_; 104 my ( $id, $sum, $ten, $mean, $sd, $zscore, $prob) = split /\t/, $_;
105 if( -d "$ppp/$id" ) 105 if( -d "$ppp/$id" )
106 { 106 {
107 my $sub_html = $ppp.$id.'.html'; 107 my $sub_html = $ppp.$id.'.html';
108 my $sub_html_ref = $1.$id if $ppp =~ /$dir_root(.*)/; 108 my $sub_html_ref = $1.$id if $ppp =~ /$dir_root(.*)/;
109 print $h "<td> <a href=\"$sub_html_ref.html\">$id</a> </td>"; 109 print $h "<td> <a href=\"$sub_html_ref.html\">$id</a> </td>";
110 110
111 open my $sub, '>', $sub_html || die "cannot create $sub_html\n"; 111 open my $sub, '>', $sub_html || die "cannot create $sub_html\n";
112 { 112 {
113 header($sub); 113 header($sub);
114 print $sub " 114 print $sub "
115 <div align=\"center\"> 115 <div align=\"center\">
116 <h2>$id</h2> 116 <h2>$id</h2>
117 <p> <img class=\"featurette-image\" src=\"$id/histogram.png\"/></p> 117 <p> <img class=\"featurette-image\" src=\"$id/histogram.png\"/></p>
118 <p><a href=\"$id/overlap_size.txt\">ping pong signature</a></p> 118 <p><a href=\"$id/overlap_size.txt\">ping pong signature</a></p>
119 <p><a href=\"$id/sensPPP.txt\">sense reads with PPP</a></p> 119 <p><a href=\"$id/sensPPP.txt\">sense reads with PPP</a></p>
120 <p><a href=\"$id/antisensPPP.txt\">reverse reads with PPP</a></p> 120 <p><a href=\"$id/antisensPPP.txt\">reverse reads with PPP</a></p>
121 <p><a href=\"$id/sens.txt\">sense reads without PPP</a></p> 121 <p><a href=\"$id/sens.txt\">sense reads without PPP</a></p>
122 <p><a href=\"$id/antisens.txt\">reverse reads without PPP</a></p> 122 <p><a href=\"$id/antisens.txt\">reverse reads without PPP</a></p>
123 </div>"; 123 </div>";
124 footer($sub); 124 footer($sub);
125 } 125 }
126 close $sub; 126 close $sub;
127 127 }
128 } 128 else { print $h "<td> $id </td>\n"; }
129 else { print $h "<td> $id </td>\n"; } 129 print $h "<td> $sum </td><td> $ten </td><td> $mean </td><td> $sd </td><td> $zscore </td><td> $prob </td>\n";
130 print $h "<td> $sum </td><td> $ten </td><td> $mean </td><td> $sd </td><td> $zscore </td><td> $prob </td>\n"; 130
131 131 print $h '</tr>';
132 print $h '</tr>'; 132 }
133 } 133 close $f;
134 close $f; 134 print $h "</tbody></table></div>";
135 print $h "</tbody></table></div>"; 135 footer($h);
136 footer($h); 136 close $h;
137 close $h;
138 } 137 }
139 138
140 sub get_genome 139 sub get_genome
141 { 140 {
142 my ( $dir, $dir_root ) = @_; 141 my ( $dir, $dir_root ) = @_;
143 my ( %hash, @group, @Unique, @NonUnique, @png ); 142 my ( %hash, @group, @Unique, @NonUnique, @png );
144 143
145 my $fut = $dir.'/*'; 144 my $fut = "'$dir'".'/*';
146 my @fut = glob $fut; 145 my @fut = glob $fut;
147 146
148 147
149 foreach my $fr ( @fut ) 148 foreach my $fr ( @fut )
150 { 149 {
151 my $f = $1 if $fr =~ /$dir_root(.*)/; 150 my $f = $1 if $fr =~ /$dir_root(.*)/;
152 if ( $fr =~ /.*Gviz/ ) 151 if ( $fr =~ /.*Gviz/ )
153 { 152 {
154 my $nu = $fr.'/rand/*'; 153 my $nu = "'$fr'".'/rand/*';
155 @NonUnique = glob $nu; 154 @NonUnique = glob $nu;
156 my $u = $fr.'/unique/*'; 155 my $u = "'$fr'".'/unique/*';
157 @Unique = glob $u; 156 @Unique = glob $u;
158 } 157 }
159 elsif ( $f =~ /.*distribution\.txt$/ ) { $hash{'mappers size distribution (txt)'} = $f; } 158 elsif ( $f =~ /.*distribution\.txt$/ ) { $hash{'mappers size distribution (txt)'} = $f; }
160 elsif ( $f =~ /.*distribution\.png$/ ) { push @png, $f; } 159 elsif ( $f =~ /.*distribution\.png$/ ) { push @png, $f; }
161 elsif ( $f =~ /.*unique\.fastq$/ ) { $hash{'unique mappers (fastq.gz)'} = $f.'.gz'; `gzip $fr`; } 160 elsif ( $f =~ /.*unique\.fastq$/ ) { $hash{'unique mappers (fastq.gz)'} = $f.'.gz'; `gzip '$fr'`; }
162 elsif ( $f =~ /.*rejected\.fastq$/ ) { $hash{'unmapped (fastq.gz)'} = $f.'.gz'; `gzip $fr`; } 161 elsif ( $f =~ /.*rejected\.fastq$/ ) { $hash{'unmapped (fastq.gz)'} = $f.'.gz'; `gzip '$fr'`; }
163 elsif ( $f =~ /.*all\.fastq$/ ) { $hash{'mappers (fastq.gz)'} = $f.'.gz'; `gzip $fr`; } 162 elsif ( $f =~ /.*all\.fastq$/ ) { $hash{'mappers (fastq.gz)'} = $f.'.gz'; `gzip '$fr'`; }
164 elsif ( $f =~ /.*dup_unique\.txt$/ ) { $hash{'unique mappers (txt)'} = $f; } 163 elsif ( $f =~ /.*dup_unique\.txt$/ ) { $hash{'unique mappers (txt)'} = $f; }
165 elsif ( $f =~ /.*dup_mapnum\.txt$/ ) { $hash{'mappers (txt)'} = $f; } 164 elsif ( $f =~ /.*dup_mapnum\.txt$/ ) { $hash{'mappers (txt)'} = $f; }
166 elsif ( $f =~ /.*dup_nonmapp\.txt$/ ) { $hash{'unmapped (txt)'} = $f; } 165 elsif ( $f =~ /.*dup_nonmapp\.txt$/ ) { $hash{'unmapped (txt)'} = $f; }
167 elsif ( $f =~ /.*_unique_sorted\.bam$/ ) { $hash{'unique alignment (bam)'} = $f; } 166 elsif ( $f =~ /.*_unique_sorted\.bam$/ ) { $hash{'unique alignment (bam)'} = $f; }
168 elsif ( $f =~ /.*_sorted\.bam$/ ) { $hash{'alignment (bam)'} = $f; } 167 elsif ( $f =~ /.*_sorted\.bam$/ ) { $hash{'alignment (bam)'} = $f; }
169 elsif ( $f =~ /.*unique_plus.bedgraph/) { $hash{'bedgraph unique plus strand'} = $f; } 168 elsif ( $f =~ /.*unique_plus.bedgraph/) { $hash{'bedgraph unique plus strand'} = $f; }
170 elsif ( $f =~ /.*unique_minus.bedgraph/) { $hash{'bedgraph unique minus strand'} = $f; } 169 elsif ( $f =~ /.*unique_minus.bedgraph/) { $hash{'bedgraph unique minus strand'} = $f; }
171 elsif ( $f =~ /.*plus.bedgraph/) { $hash{'bedgraph plus strand'} = $f; } 170 elsif ( $f =~ /.*plus.bedgraph/) { $hash{'bedgraph plus strand'} = $f; }
172 elsif ( $f =~ /.*minus.bedgraph/) { $hash{'bedgraph minus strand'} = $f; } 171 elsif ( $f =~ /.*minus.bedgraph/) { $hash{'bedgraph minus strand'} = $f; }
173 else { unlink $fr; } 172 else { unlink $fr; }
174 } 173 }
175 return (\%hash, \@Unique, \@NonUnique, \@png); 174 return (\%hash, \@Unique, \@NonUnique, \@png);
176 } 175 }
177 176
178 sub span 177 sub span
179 { 178 {
180 my ( $file, $name, $min, $max, $simin, $simax, $pimin, $pimax ) = @_; 179 my ( $file, $name, $min, $max, $simin, $simax, $pimin, $pimax ) = @_;
219 sub get_subgroups 218 sub get_subgroups
220 { 219 {
221 my ( $dir, $name, $misTE, $dir_root ) = @_; 220 my ( $dir, $name, $misTE, $dir_root ) = @_;
222 my (%Hex, %HTE, %HG, @group, @png, @pngTE, @NonUniTE, @UniG, @NonUniG ); 221 my (%Hex, %HTE, %HG, @group, @png, @pngTE, @NonUniTE, @UniG, @NonUniG );
223 222
224 my $fut = $dir.'/*'; 223 my $fut = "'$dir'".'/*';
225 my @fut = glob $fut; 224 my @fut = glob $fut;
226 my $f =''; 225 my $f ='';
227 foreach my $fr ( @fut ) 226 foreach my $fr ( @fut )
228 { 227 {
229 $f = $1 if $fr =~ /$dir_root(.*)/; 228 $f = $1 if $fr =~ /$dir_root(.*)/;
230 229
231 if ( $f =~ /genome_unique_sorted\.bam$/ ) { $HG{'genome unique mappers (sorted bam)'} = $f; } 230 if ( $f =~ /genome_unique_sorted\.bam$/ ) { $HG{'genome unique mappers (sorted bam)'} = $f; }
232 elsif ( $f =~ /genome_sorted\.bam$/ ) { $HG{'genome mappers (sorted bam)'} = $f; } 231 elsif ( $f =~ /genome_sorted\.bam$/ ) { $HG{'genome mappers (sorted bam)'} = $f; }
233 elsif ( $f =~ /miRNAs_reads_counts\.txt$/ ) { $HG{'miRNAs per type (txt)'} = $f; } 232 elsif ( $f =~ /miRNAs_reads_counts\.txt$/ ) { $HG{'miRNAs per type (txt)'} = $f; }
236 elsif ( $f =~ /genome_plus\.bedgraph$/) { $HG{'bedgraph plus strand'} = $f; } 235 elsif ( $f =~ /genome_plus\.bedgraph$/) { $HG{'bedgraph plus strand'} = $f; }
237 elsif ( $f =~ /genome_minus\.bedgraph$/) { $HG{'bedgraph minus strand'} = $f; } 236 elsif ( $f =~ /genome_minus\.bedgraph$/) { $HG{'bedgraph minus strand'} = $f; }
238 elsif ( $f =~ /TEs_plus\.bedgraph$/) { $HTE{'bedgraph plus strand'} = $f; } 237 elsif ( $f =~ /TEs_plus\.bedgraph$/) { $HTE{'bedgraph plus strand'} = $f; }
239 elsif ( $f =~ /TEs_minus\.bedgraph$/) { $HTE{'bedgraph minus strand'} = $f; } 238 elsif ( $f =~ /TEs_minus\.bedgraph$/) { $HTE{'bedgraph minus strand'} = $f; }
240 elsif ( $f =~ /transcripts_sorted\.bam$/) { $Hex{'transcripts mappers (sorted bam)'} = $f;} 239 elsif ( $f =~ /transcripts_sorted\.bam$/) { $Hex{'transcripts mappers (sorted bam)'} = $f;}
241 elsif ( $f =~ /transcripts_unique_sorted\.bam$/) { $Hex{'transcripts unique mappers (sorted bam)'} = $f;} 240 elsif ( $f =~ /transcripts_unique_sorted\.bam$/) { $Hex{'transcripts unique mappers (sorted bam)'} = $f;}
242 elsif ( $f =~ /transcripts_reads_counts\.txt$/) { $Hex{'read number per transcript (txt)'} = $f;} 241 elsif ( $f =~ /transcripts_reads_counts\.txt$/) { $Hex{'read number per transcript (txt)'} = $f;}
243 elsif ( $f =~ /TEs_reads_counts\.txt$/) { $HTE{"read number per TE 0 to $misTE mismatches (txt)"} = $f; } 242 elsif ( $f =~ /TEs_reads_counts\.txt$/) { $HTE{"read number per TE 0 to $misTE mismatches (txt)"} = $f; }
244 elsif ( $f =~ /TEs_reads_counts_mismatches\.txt$/) { $HTE{"read number per TE with 1 to $misTE mismatches (txt)"} = $f; } 243 elsif ( $f =~ /TEs_reads_counts_mismatches\.txt$/) { $HTE{"read number per TE with 1 to $misTE mismatches (txt)"} = $f; }
245 elsif ( $f =~ /TEs_reads_counts_nomismatches\.txt$/) { $HTE{'read number per TE with no mismatch (txt)'} = $f; } 244 elsif ( $f =~ /TEs_reads_counts_nomismatches\.txt$/) { $HTE{'read number per TE with no mismatch (txt)'} = $f; }
246 elsif ( $f =~ /TEs_unique_sorted\.bam$/) { $HTE{'TEs unique mappers (sorted bam)'} = $f; } 245 elsif ( $f =~ /TEs_unique_sorted\.bam$/) { $HTE{'TEs unique mappers (sorted bam)'} = $f; }
247 elsif ( $f =~ /TEs_sorted\.bam$/) { $HTE{'TEs mappers (sorted bam)'} = $f; } 246 elsif ( $f =~ /TEs_sorted\.bam$/) { $HTE{'TEs mappers (sorted bam)'} = $f; }
248 elsif ( $fr =~ /.*Gviz_TEs/ ) 247 elsif ( $fr =~ /.*Gviz_TEs/ )
249 { 248 {
250 my $nu = $fr.'/*'; 249 my $nu = "'$fr'".'/*';
251 @NonUniTE = glob $nu; 250 @NonUniTE = glob $nu;
252 } 251 }
253 elsif ( $fr =~ /.*Gviz_genome/ ) 252 elsif ( $fr =~ /.*Gviz_genome/ )
254 { 253 {
255 my $nu = $fr.'/rand/*'; 254 my $nu = "'$fr'".'/rand/*';
256 @NonUniG = glob $nu; 255 @NonUniG = glob $nu;
257 my $u = $fr.'/unique/*'; 256 my $u = "'$fr'".'/unique/*';
258 @UniG = glob $u; 257 @UniG = glob $u;
259 } 258 }
260 else { unlink $fr; } 259 else { unlink $fr; }
261 } 260 }
262 return (\%Hex, \%HTE, \%HG, \@NonUniTE, \@NonUniG, \@UniG); 261 return (\%Hex, \%HTE, \%HG, \@NonUniTE, \@NonUniG, \@UniG);
263 } 262 }
264 263
478 } 477 }
479 478
480 sub navbar 479 sub navbar
481 { 480 {
482 my ( $file, $fastq, $actif ) = @_; 481 my ( $file, $fastq, $actif ) = @_;
483 482
484 print $file " 483 print $file "
485 <div class=\"navbar navbar-inverse navbar-fixed-top\"> 484 <div class=\"navbar navbar-inverse navbar-fixed-top\">
486 <div class=\"navbar-inner\"> 485 <div class=\"navbar-inner\">
487 <div class=\"container\"> 486 <div class=\"container\">
488 <button type=\"button\" class=\"btn btn-navbar\" data-toggle=\"collapse\" data-target=\".nav-collapse\"> 487 <button type=\"button\" class=\"btn btn-navbar\" data-toggle=\"collapse\" data-target=\".nav-collapse\">
524 <!-- Placed at the end of the document so the pages load faster --> 523 <!-- Placed at the end of the document so the pages load faster -->
525 <script type=\"text/javascript\" src=\"js/filter.js\"></script> 524 <script type=\"text/javascript\" src=\"js/filter.js\"></script>
526 <script type=\"text/javascript\" src=\"js/jquery.js\"></script> 525 <script type=\"text/javascript\" src=\"js/jquery.js\"></script>
527 <script type=\"text/javascript\" src=\"js/jquery-1.3.2.js\"></script> 526 <script type=\"text/javascript\" src=\"js/jquery-1.3.2.js\"></script>
528 <script type=\"text/javascript\" src=\"js/jquery.galleriffic.js\"></script> 527 <script type=\"text/javascript\" src=\"js/jquery.galleriffic.js\"></script>
529 <script type=\"text/javascript\" src=\"js/jquery.opacityrollover.js\"></script> 528 <script type=\"text/javascript\" src=\"js/jquery.opacityrollover.js\"></script>
530 <script type=\"text/javascript\" src=\"js/bootstrap-table.js\"></script> 529 <script type=\"text/javascript\" src=\"js/bootstrap-table.js\"></script>
531 <script type=\"text/javascript\" src=\"js/bootstrap.min.js\"></script> 530 <script type=\"text/javascript\" src=\"js/bootstrap.min.js\"></script>
532 <script type=\"text/javascript\"> 531 <script type=\"text/javascript\">
533 jQuery(document).ready(function(\$) { 532 jQuery(document).ready(function(\$) {
534 // We only want these styles applied when javascript is enabled 533 // We only want these styles applied when javascript is enabled
611 <input type=\"text\" id=\"myInput0\" onkeyup=\"search(this)\" placeholder=\"Search for names...\"> 610 <input type=\"text\" id=\"myInput0\" onkeyup=\"search(this)\" placeholder=\"Search for names...\">
612 <ul class=\"thumbs noscript\"> 611 <ul class=\"thumbs noscript\">
613 "; 612 ";
614 foreach my $u (@{$non_unique}) 613 foreach my $u (@{$non_unique})
615 { 614 {
616 my $name = basename($u,'.png'); 615 my $name = basename($u,'.png');
617 $u = $1 if $u =~ /$dir_root(.*)/; 616 $u = $1 if $u =~ /$dir_root(.*)/;
618 print $file " 617 print $file "
619 <li> 618 <li>
620 <a class=\"thumb\" href=\"$u\" title=\"$name\">$name</a> 619 <a class=\"thumb\" href=\"$u\" title=\"$name\">$name</a>
621 </li> 620 </li>
650 <ul class=\"thumbs noscript\"> 649 <ul class=\"thumbs noscript\">
651 "; 650 ";
652 651
653 foreach my $u (@{$unique}) 652 foreach my $u (@{$unique})
654 { 653 {
655 my $name = basename($u,'.png'); 654 my $name = basename($u,'.png');
656 $u = $1 if $u =~ /$dir_root(.*)/; 655 $u = $1 if $u =~ /$dir_root(.*)/;
657 print $file " 656 print $file "
658 <li> 657 <li>
659 <a class=\"thumb\" href=\"$u\" title=\"$name\">$name</a> 658 <a class=\"thumb\" href=\"$u\" title=\"$name\">$name</a>
660 </li> 659 </li>
680 <ul class=\"thumbs noscript\"> 679 <ul class=\"thumbs noscript\">
681 "; 680 ";
682 681
683 foreach my $nu (@{$non_unique}) 682 foreach my $nu (@{$non_unique})
684 { 683 {
685 my $name = basename($nu,'.png'); 684 my $name = basename($nu,'.png');
686 $nu = $1 if $nu =~ /$dir_root(.*)/; 685 $nu = $1 if $nu =~ /$dir_root(.*)/;
687 print $file " 686 print $file "
688 <li> 687 <li>
689 <a class=\"thumb\" href=\"$nu\" title=\"$name\">$name</a> 688 <a class=\"thumb\" href=\"$nu\" title=\"$name\">$name</a>
690 </li> 689 </li>
748 747
749 sub get_distri_exon 748 sub get_distri_exon
750 { 749 {
751 my ($dir, $name) = @_; 750 my ($dir, $name) = @_;
752 my (@out,@group); 751 my (@out,@group);
753 my $group = $dir.'/'.$name.'-subgroups-bonafide_reads-transcripts-*distribution-*.png'; 752 my $group = "'$dir'".'/'."'$name'".'-subgroups-bonafide_reads-transcripts-*distribution-*.png';
754 @group = glob $group; 753 @group = glob $group;
755 foreach (my $g =0; $g <= $#group; $g++) 754 foreach (my $g =0; $g <= $#group; $g++)
756 { 755 {
757 if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-transcripts-.*distribution-.*\.png)/ ) 756 if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-transcripts-.*distribution-.*\.png)/ )
758 { 757 {
765 764
766 sub get_distri_TE 765 sub get_distri_TE
767 { 766 {
768 my ($dir, $name) = @_; 767 my ($dir, $name) = @_;
769 my (@out,@group); 768 my (@out,@group);
770 my $group = $dir.'/'.$name.'-subgroups-bonafide_reads-TE-*distribution-*.png'; 769 my $group = "'$dir'".'/'."'$name'".'-subgroups-bonafide_reads-TE-*distribution-*.png';
771 @group = glob $group; 770 @group = glob $group;
772 foreach (my $g =0; $g <= $#group; $g++) 771 foreach (my $g =0; $g <= $#group; $g++)
773 { 772 {
774 if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-TE-.*distribution-.*\.png)/ ) 773 if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-TE-.*distribution-.*\.png)/ )
775 { 774 {
782 781
783 sub get_PPP 782 sub get_PPP
784 { 783 {
785 my ($dir,$name) = @_; 784 my ($dir,$name) = @_;
786 my (%distri,@group); 785 my (%distri,@group);
787 my $group = $dir.'/'.$name.'-subgroups-bonafide_reads-TE-PPPartners-*'; 786 my $group = "'$dir'".'/'."'$name'".'-subgroups-bonafide_reads-TE-PPPartners-*';
788 @group = glob $group; 787 @group = glob $group;
789 788
790 foreach (my $g =0; $g <= $#group; $g++) 789 foreach (my $g =0; $g <= $#group; $g++)
791 { 790 {
792 if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-TE-PPPartners-.*)/ ) 791 if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-TE-PPPartners-.*)/ )
793 { 792 {
794 my $tmp = $1; 793 my $tmp = $1;
829 828
830 sub PPPrint 829 sub PPPrint
831 { 830 {
832 my ($h, $hash) = @_; 831 my ($h, $hash) = @_;
833 my $cmp = 0; 832 my $cmp = 0;
834 833
835 print $h "<div class=\"container\">\n"; 834 print $h "<div class=\"container\">\n";
836 print $h "<div class=\"row text-center\">"; 835 print $h "<div class=\"row text-center\">";
837 while ( my ($k,$v) = each %{$hash} ) 836 while ( my ($k,$v) = each %{$hash} )
838 { 837 {
839 print $h "</div><div class=\"row text-center\">" if $cmp != 0 && $cmp % 2 == 0; 838 print $h "</div><div class=\"row text-center\">" if $cmp != 0 && $cmp % 2 == 0;
849 <p class=\"featurette-p\"><a href=\"$v->[1]\">reverse reads without PPP</a></p> 848 <p class=\"featurette-p\"><a href=\"$v->[1]\">reverse reads without PPP</a></p>
850 </div> 849 </div>
851 "; 850 ";
852 $cmp++; 851 $cmp++;
853 } 852 }
854 853
855 print $h "</div></div>"; 854 print $h "</div></div>";
856 } 855 }
857 856
858 sub printDistri 857 sub printDistri
859 { 858 {
878 <p class=\"featurette-p\"><a href=\"$txt\">text file</a></p> 877 <p class=\"featurette-p\"><a href=\"$txt\">text file</a></p>
879 </div> 878 </div>
880 "; 879 ";
881 $cmp++; 880 $cmp++;
882 } 881 }
883 882
884 print $h "</div></div>"; 883 print $h "</div></div>";
885 } 884 }
886 885
887 sub mapnum 886 sub mapnum
888 { 887 {