srnapipe: bin/html.pm annotate

author	pierre.pouchin
date	Wed, 16 Jan 2019 08:18:13 -0500
parents	9645d995fb3c
children

rev	line source
61 9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	1 package html;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	2
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	3 use strict;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	4 use warnings;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	5 use File::Basename;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	6
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	7 use Exporter;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	8 our @ISA = qw( Exporter );
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	9 our @EXPORT_OK = qw( &main_page &details_pages &menu_page &ppp_page );
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	10
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	11 sub main_page
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	12 {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	13 my ( $dir, $file, $list_mainTabP, $current, $ma, $ma_uni, $dir_root ) = @_;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	14 my ( $futHashP, $uniqueTabP, $randTabP, $pngTabP ) = get_genome ( $dir, $dir_root );
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	15
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	16 open my $h, '>', $file \|\| die "cannot create $file $!\n";
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	17 header ( $h );
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	18 navbar ( $h, $list_mainTabP, $current );
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	19 print $h "<div class=\"container\"><p><a class=\"btn\" href=\"$current-sub.html\">View details »</a></p></div>\n";
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	20 futurette( $h, $current, $pngTabP, $futHashP );
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	21 print $h "<div class=\"container\"><h2>mappers #: $ma</h2><h2>unique mappers #: $ma_uni</h2> </div>\n";
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	22 carousel2( $h, $uniqueTabP, $randTabP, $dir_root );
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	23 footer($h);
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	24 close $h;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	25 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	26
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	27 sub menu_page
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	28 {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	29 my ( $dir, $file, $list_mainTabP, $current, $min, $max, $simin, $simax, $pimin, $pimax, $dir_root ) = @_;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	30 my $html_ref = $1 if $dir =~ /$dir_root(.*)/;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	31 open my $h, '>', $file \|\| die "cannot create $file $!\n";
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	32 header($h);
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	33 navbar ( $h, $list_mainTabP, $current );
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	34 span( $h, $current, $min, $max, $simin, $simax, $pimin, $pimax );
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	35 print $h " <div class=\"container\"> <div class=\"row text-center\"> <img src=\"$html_ref/pie_chart.png\"/><br />\n";
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	36 print $h " <A HREF=\"$html_ref/repartition.txt\">text file</A><br/>\n </div></div>";
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	37 footer($h);
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	38 close $h;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	39 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	40
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	41 sub details_pages
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	42 {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	43 my ( $dir_details, $prefix, $list_mainTabP, $current, $misTE, $dir_root, $ppp ) = @_;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	44 my ($Hex, $HTE, $HG, $NonUniTE, $NonUniG, $UniG ) = get_subgroups( $dir_details, $current, $misTE, $dir_root );
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	45
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	46 my $html_ref = $1.'-PPP.html' if $prefix =~ /$dir_root(.*)/;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	47 open my $h, '>', $prefix.'-TEs.html' \|\| die "cannot create $prefix-TEs.html $!\n";
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	48 header($h);
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	49 navbar ( $h, $list_mainTabP, $current );
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	50 if ( $prefix =~ /piRNAs$/ && $ppp eq 'true' )
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	51 {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	52 print $h " <div class=\"container\">";
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	53 print $h " <p><a class=\"btn\" href=\"$html_ref\">Ping Pong Partners</a></p>\n";
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	54 print $h "</div>";
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	55 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	56 fut($h,'Transposable elements',$HTE);
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	57 carousel($h,$NonUniTE,$dir_root);
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	58 footer($h);
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	59 close $h;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	60
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	61 open $h, '>', $prefix.'-genome.html' \|\| die "cannot create $prefix-genome.html $!\n";
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	62 header($h);
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	63 navbar ( $h, $list_mainTabP, $current );
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	64 fut($h,'Genome',$HG);
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	65 carousel2($h,$UniG, $NonUniG,$dir_root);
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	66 footer($h);
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	67 close $h;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	68
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	69 open $h, '>', $prefix.'-transcripts.html' \|\| die "cannot create $prefix-transcripts.html $!\n";
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	70 header($h);
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	71 navbar ( $h, $list_mainTabP, $current );
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	72 fut($h,'transcripts',$Hex);
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	73 footer($h);
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	74 close $h;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	75 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	76
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	77 sub ppp_page
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	78 {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	79 my ( $dir, $file, $list_mainTabP, $current, $ppp, $dir_root ) = @_;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	80
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	81 my $ppp_file = $ppp.'ppp.txt';
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	82 open my $h, '>', $file \|\| die "cannot create $file $!\n";
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	83 header($h);
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	84 navbar ( $h, $list_mainTabP, $current );
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	85 print $h '<div class="container"> <table class="wb-tables table table-striped table-hover">'."\n";
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	86 print $h '<thead>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	87 <tr>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	88 <th data-sortable="true">ID</th>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	89 <th data-sortable="true">overlap sum</th>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	90 <th data-sortable="true">ten overlap sum</th>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	91 <th data-sortable="true">mean</th>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	92 <th data-sortable="true">standard deviation</th>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	93 <th data-sortable="true">z-score</th>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	94 <th data-sortable="true">p-value</th>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	95 </tr>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	96 </thead>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	97 <tbody>';
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	98
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	99 open my $f, '<', $ppp_file \|\| die "cannot open $ppp_file $!\n";
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	100 while ( <$f> )
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	101 {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	102 chomp;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	103 print $h '<tr>';
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	104 my ( $id, $sum, $ten, $mean, $sd, $zscore, $prob) = split /\t/, $_;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	105 if( -d "$ppp/$id" )
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	106 {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	107 my $sub_html = $ppp.$id.'.html';
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	108 my $sub_html_ref = $1.$id if $ppp =~ /$dir_root(.*)/;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	109 print $h "<td> <a href=\"$sub_html_ref.html\">$id</a> </td>";
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	110
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	111 open my $sub, '>', $sub_html \|\| die "cannot create $sub_html\n";
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	112 {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	113 header($sub);
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	114 print $sub "
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	115 <div align=\"center\">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	116 <h2>$id</h2>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	117 <p> <img class=\"featurette-image\" src=\"$id/histogram.png\"/></p>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	118 <p><a href=\"$id/overlap_size.txt\">ping pong signature</a></p>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	119 <p><a href=\"$id/sensPPP.txt\">sense reads with PPP</a></p>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	120 <p><a href=\"$id/antisensPPP.txt\">reverse reads with PPP</a></p>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	121 <p><a href=\"$id/sens.txt\">sense reads without PPP</a></p>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	122 <p><a href=\"$id/antisens.txt\">reverse reads without PPP</a></p>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	123 </div>";
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	124 footer($sub);
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	125 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	126 close $sub;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	127 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	128 else { print $h "<td> $id </td>\n"; }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	129 print $h "<td> $sum </td><td> $ten </td><td> $mean </td><td> $sd </td><td> $zscore </td><td> $prob </td>\n";
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	130
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	131 print $h '</tr>';
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	132 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	133 close $f;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	134 print $h "</tbody></table></div>";
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	135 footer($h);
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	136 close $h;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	137 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	138
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	139 sub get_genome
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	140 {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	141 my ( $dir, $dir_root ) = @_;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	142 my ( %hash, @group, @Unique, @NonUnique, @png );
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	143
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	144 my $fut = "'$dir'".'/*';
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	145 my @fut = glob $fut;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	146
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	147
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	148 foreach my $fr ( @fut )
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	149 {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	150 my $f = $1 if $fr =~ /$dir_root(.*)/;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	151 if ( $fr =~ /.*Gviz/ )
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	152 {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	153 my $nu = "'$fr'".'/rand/*';
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	154 @NonUnique = glob $nu;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	155 my $u = "'$fr'".'/unique/*';
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	156 @Unique = glob $u;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	157 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	158 elsif ( $f =~ /.*distribution\.txt$/ ) { $hash{'mappers size distribution (txt)'} = $f; }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	159 elsif ( $f =~ /.*distribution\.png$/ ) { push @png, $f; }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	160 elsif ( $f =~ /.*unique\.fastq$/ ) { $hash{'unique mappers (fastq.gz)'} = $f.'.gz'; `gzip '$fr'`; }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	161 elsif ( $f =~ /.*rejected\.fastq$/ ) { $hash{'unmapped (fastq.gz)'} = $f.'.gz'; `gzip '$fr'`; }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	162 elsif ( $f =~ /.*all\.fastq$/ ) { $hash{'mappers (fastq.gz)'} = $f.'.gz'; `gzip '$fr'`; }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	163 elsif ( $f =~ /.*dup_unique\.txt$/ ) { $hash{'unique mappers (txt)'} = $f; }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	164 elsif ( $f =~ /.*dup_mapnum\.txt$/ ) { $hash{'mappers (txt)'} = $f; }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	165 elsif ( $f =~ /.*dup_nonmapp\.txt$/ ) { $hash{'unmapped (txt)'} = $f; }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	166 elsif ( $f =~ /.*_unique_sorted\.bam$/ ) { $hash{'unique alignment (bam)'} = $f; }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	167 elsif ( $f =~ /.*_sorted\.bam$/ ) { $hash{'alignment (bam)'} = $f; }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	168 elsif ( $f =~ /.*unique_plus.bedgraph/) { $hash{'bedgraph unique plus strand'} = $f; }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	169 elsif ( $f =~ /.*unique_minus.bedgraph/) { $hash{'bedgraph unique minus strand'} = $f; }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	170 elsif ( $f =~ /.*plus.bedgraph/) { $hash{'bedgraph plus strand'} = $f; }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	171 elsif ( $f =~ /.*minus.bedgraph/) { $hash{'bedgraph minus strand'} = $f; }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	172 else { unlink $fr; }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	173 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	174 return (\%hash, \@Unique, \@NonUnique, \@png);
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	175 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	176
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	177 sub span
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	178 {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	179 my ( $file, $name, $min, $max, $simin, $simax, $pimin, $pimax ) = @_;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	180
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	181 print $file "
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	182 <div class=\"container text-center\">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	183 <div class=\"row-fluid\">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	184 <div class=\"span6\">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	185 <h2>Bonafide</h2>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	186 reads of size between $min and $max<br>with no mi, sn, t and r RNAs
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	187 <p><a class=\"btn\" href=\"$name-bonafide_reads-genome.html\">Genome</a></p>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	188 <p><a class=\"btn\" href=\"$name-bonafide_reads-TEs.html\">TE</a></p>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	189 <p><a class=\"btn\" href=\"$name-bonafide_reads-transcripts.html\">Transcripts</a></p>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	190 <div class=\"row-fluid\">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	191 <div class=\"span6\">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	192 <h2>siRNAs</h2>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	193 bonafide reads of size between $simin and $simax
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	194 <p><a class=\"btn\" href=\"$name-siRNAs-genome.html\">Genome</a></p>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	195 <p><a class=\"btn\" href=\"$name-siRNAs-TEs.html\">TE</a></p>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	196 <p><a class=\"btn\" href=\"$name-siRNAs-transcripts.html\">Transcripts</a></p>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	197 </div>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	198 <div class=\"span6\">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	199 <h2>piRNAs</h2>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	200 bonafide reads of size between $pimin and $pimax
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	201 <p><a class=\"btn\" href=\"$name-piRNAs-genome.html\">Genome</a></p>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	202 <p><a class=\"btn\" href=\"$name-piRNAs-TEs.html\">TE</a></p>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	203 <p><a class=\"btn\" href=\"$name-piRNAs-transcripts.html\">Transcripts</a></p>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	204 </div>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	205 </div>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	206 </div>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	207 <div class=\"span6\">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	208 <h2>miRNAs</h2>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	209 <p><a class=\"btn\" href=\"$name-miRNAs-genome.html\">Genome</a></p>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	210 <p><a class=\"btn\" href=\"$name-miRNAs-TEs.html\">TE</a></p>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	211 <p><a class=\"btn\" href=\"$name-miRNAs-transcripts.html\">Transcripts</a></p>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	212 </div>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	213 </div>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	214 </div>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	215 ";
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	216 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	217
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	218 sub get_subgroups
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	219 {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	220 my ( $dir, $name, $misTE, $dir_root ) = @_;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	221 my (%Hex, %HTE, %HG, @group, @png, @pngTE, @NonUniTE, @UniG, @NonUniG );
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	222
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	223 my $fut = "'$dir'".'/*';
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	224 my @fut = glob $fut;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	225 my $f ='';
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	226 foreach my $fr ( @fut )
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	227 {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	228 $f = $1 if $fr =~ /$dir_root(.*)/;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	229
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	230 if ( $f =~ /genome_unique_sorted\.bam$/ ) { $HG{'genome unique mappers (sorted bam)'} = $f; }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	231 elsif ( $f =~ /genome_sorted\.bam$/ ) { $HG{'genome mappers (sorted bam)'} = $f; }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	232 elsif ( $f =~ /miRNAs_reads_counts\.txt$/ ) { $HG{'miRNAs per type (txt)'} = $f; }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	233 elsif ( $f =~ /genome_unique_plus\.bedgraph$/) { $HG{'bedgraph unique plus strand'} = $f; }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	234 elsif ( $f =~ /genome_unique_minus\.bedgraph$/) { $HG{'bedgraph unique minus strand'} = $f; }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	235 elsif ( $f =~ /genome_plus\.bedgraph$/) { $HG{'bedgraph plus strand'} = $f; }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	236 elsif ( $f =~ /genome_minus\.bedgraph$/) { $HG{'bedgraph minus strand'} = $f; }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	237 elsif ( $f =~ /TEs_plus\.bedgraph$/) { $HTE{'bedgraph plus strand'} = $f; }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	238 elsif ( $f =~ /TEs_minus\.bedgraph$/) { $HTE{'bedgraph minus strand'} = $f; }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	239 elsif ( $f =~ /transcripts_sorted\.bam$/) { $Hex{'transcripts mappers (sorted bam)'} = $f;}
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	240 elsif ( $f =~ /transcripts_unique_sorted\.bam$/) { $Hex{'transcripts unique mappers (sorted bam)'} = $f;}
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	241 elsif ( $f =~ /transcripts_reads_counts\.txt$/) { $Hex{'read number per transcript (txt)'} = $f;}
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	242 elsif ( $f =~ /TEs_reads_counts\.txt$/) { $HTE{"read number per TE 0 to $misTE mismatches (txt)"} = $f; }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	243 elsif ( $f =~ /TEs_reads_counts_mismatches\.txt$/) { $HTE{"read number per TE with 1 to $misTE mismatches (txt)"} = $f; }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	244 elsif ( $f =~ /TEs_reads_counts_nomismatches\.txt$/) { $HTE{'read number per TE with no mismatch (txt)'} = $f; }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	245 elsif ( $f =~ /TEs_unique_sorted\.bam$/) { $HTE{'TEs unique mappers (sorted bam)'} = $f; }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	246 elsif ( $f =~ /TEs_sorted\.bam$/) { $HTE{'TEs mappers (sorted bam)'} = $f; }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	247 elsif ( $fr =~ /.*Gviz_TEs/ )
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	248 {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	249 my $nu = "'$fr'".'/*';
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	250 @NonUniTE = glob $nu;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	251 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	252 elsif ( $fr =~ /.*Gviz_genome/ )
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	253 {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	254 my $nu = "'$fr'".'/rand/*';
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	255 @NonUniG = glob $nu;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	256 my $u = "'$fr'".'/unique/*';
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	257 @UniG = glob $u;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	258 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	259 else { unlink $fr; }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	260 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	261 return (\%Hex, \%HTE, \%HG, \@NonUniTE, \@NonUniG, \@UniG);
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	262 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	263
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	264 sub header
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	265 {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	266 my $file = shift;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	267 print $file "
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	268 <!DOCTYPE html>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	269 <html lang=\"en\">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	270 <head>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	271 <meta charset=\"utf-8\">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	272 <title>pipeline</title>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	273 <meta name=\"viewport\" content=\"width=device-width, initial-scale=1.0\">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	274 <meta name=\"description\" content=\"\">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	275 <meta name=\"author\" content=\"\">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	276 <!-- Le styles -->
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	277 <link href=\"css/bootstrap.css\" rel=\"stylesheet\">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	278 <link href=\"css/bootstrap-table.css\" rel=\"stylesheet\">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	279 <style type=\"text/css\">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	280 body {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	281 padding-top: 60px;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	282 padding-bottom: 40px;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	283 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	284 div#page {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	285 width: 940px;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	286 background-color: #fff;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	287 margin: 0 auto;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	288 text-align: left;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	289 border-color: #fff;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	290 border-style: none solid solid;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	291 border-width: medium 1px 1px;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	292 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	293
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	294 div.content {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	295 display: none;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	296 float: right;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	297 width: 550px;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	298 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	299 div.content a, div.navigation a {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	300 text-decoration: none;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	301 color: #777;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	302 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	303 div.content a:focus, div.content a:hover, div.content a:active {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	304 text-decoration: underline;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	305 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	306
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	307 div.controls {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	308 margin-top: 5px;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	309 height: 23px;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	310 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	311
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	312 div.controls a {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	313 padding: 5px;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	314 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	315 div.ss-controls {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	316 float: left;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	317 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	318 div.nav-controls {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	319 float: right;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	320 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	321 div.slideshow-container {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	322 position: relative;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	323 clear: both;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	324 height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	325 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	326 div.loader {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	327 position: absolute;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	328 top: 0;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	329 left: 0;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	330 background-image: url('loader.gif');
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	331 background-repeat: no-repeat;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	332 background-position: center;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	333 width: 550px;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	334 height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	335 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	336 div.slideshow {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	337
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	338 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	339
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	340 div.slideshow span.image-wrapper {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	341 display: block;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	342 position: absolute;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	343 top: 0;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	344 left: 0;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	345 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	346 div.slideshow a.advance-link {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	347 display: block;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	348 width: 550px;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	349 height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	350 line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	351 text-align: center;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	352 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	353 div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	354 text-decoration: none;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	355 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	356 div.slideshow img {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	357 vertical-align: middle;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	358 border: 1px solid #ccc;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	359 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	360
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	361 div.image-title {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	362 font-weight: bold;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	363 font-size: 1.4em;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	364 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	365
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	366 div.image-desc {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	367 line-height: 1.3em;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	368 padding-top: 12px;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	369 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	370 div.navigation {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	371
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	372 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	373 ul.thumbs {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	374 clear: both;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	375 margin: 0;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	376 padding: 0;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	377 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	378 ul.thumbs li {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	379 float: none;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	380 padding: 0;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	381 margin: 0;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	382 list-style: none;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	383 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	384 a.thumb {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	385 padding: 0;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	386 display: inline;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	387 border: none;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	388 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	389 ul.thumbs li.selected a.thumb {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	390 color: #000;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	391 font-weight: bold;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	392 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	393 a.thumb:focus {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	394 outline: none;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	395 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	396 ul.thumbs img {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	397 border: none;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	398 display: block;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	399 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	400 div.pagination {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	401 clear: both;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	402 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	403 div.navigation div.top {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	404 margin-bottom: 12px;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	405 height: 11px;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	406 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	407 div.navigation div.bottom {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	408 margin-top: 12px;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	409 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	410 div.pagination a, div.pagination span.current, div.pagination span.ellipsis {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	411 display: block;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	412 float: left;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	413 margin-right: 2px;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	414 padding: 4px 7px 2px 7px;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	415 border: 1px solid #ccc;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	416 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	417 div.pagination a:hover {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	418 background-color: #eee;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	419 text-decoration: none;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	420 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	421 div.pagination span.current {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	422 font-weight: bold;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	423 background-color: #000;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	424 border-color: #000;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	425 color: #fff;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	426 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	427 div.pagination span.ellipsis {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	428 border: none;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	429 padding: 5px 0 3px 2px;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	430 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	431
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	432 div.download {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	433 float: right;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	434 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	435
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	436 div.caption-container {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	437 position: relative;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	438 clear: left;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	439 height: 75px;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	440 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	441 span.image-caption {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	442 display: block;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	443 position: absolute;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	444 width: 550px;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	445 top: 0;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	446 left: 0;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	447 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	448 div.caption {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	449 padding: 12px;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	450 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	451
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	452 /* Featurettes
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	453 ------------------------- */
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	454
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	455 .featurette {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	456 padding-top: 20px; /* Vertically center images part 1: add padding above and below text. */
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	457 overflow: hidden; /* Vertically center images part 2: clear their floats. */
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	458 text-align: center;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	459 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	460
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	461 .featurette-p
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	462 {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	463 text-align: left;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	464 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	465
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	466 .featurette-image {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	467 margin-top: 10px; /* Vertically center images part 3: negative margin up the image the same amount of the padding to center it. */
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	468 width: 450px;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	469 height: auto;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	470 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	471
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	472 </style>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	473 <link href=\"css/bootstrap-responsive.css\" rel=\"stylesheet\">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	474 </head>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	475 <body>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	476 ";
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	477 }
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	478
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	479 sub navbar
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	480 {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	481 my ( $file, $fastq, $actif ) = @_;
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	482
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	483 print $file "
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	484 <div class=\"navbar navbar-inverse navbar-fixed-top\">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	485 <div class=\"navbar-inner\">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	486 <div class=\"container\">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	487 <button type=\"button\" class=\"btn btn-navbar\" data-toggle=\"collapse\" data-target=\".nav-collapse\">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	488 <span class=\"icon-bar\"></span>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	489 <span class=\"icon-bar\"></span>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	490 <span class=\"icon-bar\"></span>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	491 </button>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	492 <a class=\"brand\" href=\"report.txt\">Report</a>
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	493 <div class=\"nav-collapse collapse\">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	494 <ul class=\"nav\">
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	495 ";
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	496 for (my $i = 0 ; $i <= $#{$fastq}; $i++)
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	497 {
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	498 # my $fa = basename($fastq->[$i],'.dat');
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	499 my $fa = $fastq->[$i];
9185ca0a7b43 Updated package according to recommendations. pierre.pouchin parents: 60 diff changeset	500 if ($actif eq $fa){ print $file "<li class=\"active\"><a href=\"$fastq->[$i].html\">$fa</a></li>";}

61

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

1 package html;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

2

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

3 use strict;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

4 use warnings;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

5 use File::Basename;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

6

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

7 use Exporter;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

8 our @ISA = qw( Exporter );

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

9 our @EXPORT_OK = qw( &main_page &details_pages &menu_page &ppp_page );

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

10

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

11 sub main_page

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

12 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

13 my ( $dir, $file, $list_mainTabP, $current, $ma, $ma_uni, $dir_root ) = @_;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

14 my ( $futHashP, $uniqueTabP, $randTabP, $pngTabP ) = get_genome ( $dir, $dir_root );

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

15

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

16 open my $h, '>', $file || die "cannot create $file $!\n";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

17 header ( $h );

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

18 navbar ( $h, $list_mainTabP, $current );

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

19 print $h "<div class=\"container\"><p><a class=\"btn\" href=\"$current-sub.html\">View details »</a></p></div>\n";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

20 futurette( $h, $current, $pngTabP, $futHashP );

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

21 print $h "<div class=\"container\"><h2>mappers #: $ma</h2><h2>unique mappers #: $ma_uni</h2> </div>\n";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

22 carousel2( $h, $uniqueTabP, $randTabP, $dir_root );

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

23 footer($h);

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

24 close $h;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

25 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

26

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

27 sub menu_page

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

28 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

29 my ( $dir, $file, $list_mainTabP, $current, $min, $max, $simin, $simax, $pimin, $pimax, $dir_root ) = @_;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

30 my $html_ref = $1 if $dir =~ /$dir_root(.*)/;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

31 open my $h, '>', $file || die "cannot create $file $!\n";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

32 header($h);

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

33 navbar ( $h, $list_mainTabP, $current );

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

34 span( $h, $current, $min, $max, $simin, $simax, $pimin, $pimax );

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

35 print $h " <div class=\"container\"> <div class=\"row text-center\"> <img src=\"$html_ref/pie_chart.png\"/><br />\n";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

36 print $h " <A HREF=\"$html_ref/repartition.txt\">text file</A><br/>\n </div></div>";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

37 footer($h);

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

38 close $h;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

39 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

40

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

41 sub details_pages

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

42 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

43 my ( $dir_details, $prefix, $list_mainTabP, $current, $misTE, $dir_root, $ppp ) = @_;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

44 my ($Hex, $HTE, $HG, $NonUniTE, $NonUniG, $UniG ) = get_subgroups( $dir_details, $current, $misTE, $dir_root );

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

45

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

46 my $html_ref = $1.'-PPP.html' if $prefix =~ /$dir_root(.*)/;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

47 open my $h, '>', $prefix.'-TEs.html' || die "cannot create $prefix-TEs.html $!\n";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

48 header($h);

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

49 navbar ( $h, $list_mainTabP, $current );

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

50 if ( $prefix =~ /piRNAs$/ && $ppp eq 'true' )

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

51 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

52 print $h " <div class=\"container\">";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

53 print $h " <p><a class=\"btn\" href=\"$html_ref\">Ping Pong Partners</a></p>\n";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

54 print $h "</div>";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

55 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

56 fut($h,'Transposable elements',$HTE);

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

57 carousel($h,$NonUniTE,$dir_root);

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

58 footer($h);

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

59 close $h;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

60

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

61 open $h, '>', $prefix.'-genome.html' || die "cannot create $prefix-genome.html $!\n";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

62 header($h);

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

63 navbar ( $h, $list_mainTabP, $current );

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

64 fut($h,'Genome',$HG);

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

65 carousel2($h,$UniG, $NonUniG,$dir_root);

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

66 footer($h);

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

67 close $h;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

68

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

69 open $h, '>', $prefix.'-transcripts.html' || die "cannot create $prefix-transcripts.html $!\n";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

70 header($h);

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

71 navbar ( $h, $list_mainTabP, $current );

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

72 fut($h,'transcripts',$Hex);

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

73 footer($h);

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

74 close $h;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

75 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

76

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

77 sub ppp_page

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

78 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

79 my ( $dir, $file, $list_mainTabP, $current, $ppp, $dir_root ) = @_;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

80

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

81 my $ppp_file = $ppp.'ppp.txt';

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

82 open my $h, '>', $file || die "cannot create $file $!\n";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

83 header($h);

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

84 navbar ( $h, $list_mainTabP, $current );

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

85 print $h '<div class="container"> <table class="wb-tables table table-striped table-hover">'."\n";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

86 print $h '<thead>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

87 <tr>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

88 <th data-sortable="true">ID</th>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

89 <th data-sortable="true">overlap sum</th>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

90 <th data-sortable="true">ten overlap sum</th>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

91 <th data-sortable="true">mean</th>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

92 <th data-sortable="true">standard deviation</th>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

93 <th data-sortable="true">z-score</th>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

94 <th data-sortable="true">p-value</th>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

95 </tr>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

96 </thead>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

97 <tbody>';

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

98

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

99 open my $f, '<', $ppp_file || die "cannot open $ppp_file $!\n";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

100 while ( <$f> )

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

101 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

102 chomp;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

103 print $h '<tr>';

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

104 my ( $id, $sum, $ten, $mean, $sd, $zscore, $prob) = split /\t/, $_;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

105 if( -d "$ppp/$id" )

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

106 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

107 my $sub_html = $ppp.$id.'.html';

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

108 my $sub_html_ref = $1.$id if $ppp =~ /$dir_root(.*)/;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

109 print $h "<td> <a href=\"$sub_html_ref.html\">$id</a> </td>";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

110

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

111 open my $sub, '>', $sub_html || die "cannot create $sub_html\n";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

112 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

113 header($sub);

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

114 print $sub "

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

115 <div align=\"center\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

116 <h2>$id</h2>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

117 <p> <img class=\"featurette-image\" src=\"$id/histogram.png\"/></p>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

118 <p><a href=\"$id/overlap_size.txt\">ping pong signature</a></p>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

119 <p><a href=\"$id/sensPPP.txt\">sense reads with PPP</a></p>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

120 <p><a href=\"$id/antisensPPP.txt\">reverse reads with PPP</a></p>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

121 <p><a href=\"$id/sens.txt\">sense reads without PPP</a></p>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

122 <p><a href=\"$id/antisens.txt\">reverse reads without PPP</a></p>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

123 </div>";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

124 footer($sub);

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

125 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

126 close $sub;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

127 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

128 else { print $h "<td> $id </td>\n"; }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

129 print $h "<td> $sum </td><td> $ten </td><td> $mean </td><td> $sd </td><td> $zscore </td><td> $prob </td>\n";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

130

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

131 print $h '</tr>';

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

132 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

133 close $f;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

134 print $h "</tbody></table></div>";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

135 footer($h);

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

136 close $h;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

137 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

138

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

139 sub get_genome

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

140 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

141 my ( $dir, $dir_root ) = @_;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

142 my ( %hash, @group, @Unique, @NonUnique, @png );

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

143

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

144 my $fut = "'$dir'".'/*';

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

145 my @fut = glob $fut;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

146

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

147

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

148 foreach my $fr ( @fut )

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

149 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

150 my $f = $1 if $fr =~ /$dir_root(.*)/;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

151 if ( $fr =~ /.*Gviz/ )

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

152 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

153 my $nu = "'$fr'".'/rand/*';

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

154 @NonUnique = glob $nu;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

155 my $u = "'$fr'".'/unique/*';

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

156 @Unique = glob $u;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

157 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

158 elsif ( $f =~ /.*distribution\.txt$/ ) { $hash{'mappers size distribution (txt)'} = $f; }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

159 elsif ( $f =~ /.*distribution\.png$/ ) { push @png, $f; }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

160 elsif ( $f =~ /.*unique\.fastq$/ ) { $hash{'unique mappers (fastq.gz)'} = $f.'.gz'; `gzip '$fr'`; }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

161 elsif ( $f =~ /.*rejected\.fastq$/ ) { $hash{'unmapped (fastq.gz)'} = $f.'.gz'; `gzip '$fr'`; }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

162 elsif ( $f =~ /.*all\.fastq$/ ) { $hash{'mappers (fastq.gz)'} = $f.'.gz'; `gzip '$fr'`; }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

163 elsif ( $f =~ /.*dup_unique\.txt$/ ) { $hash{'unique mappers (txt)'} = $f; }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

164 elsif ( $f =~ /.*dup_mapnum\.txt$/ ) { $hash{'mappers (txt)'} = $f; }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

165 elsif ( $f =~ /.*dup_nonmapp\.txt$/ ) { $hash{'unmapped (txt)'} = $f; }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

166 elsif ( $f =~ /.*_unique_sorted\.bam$/ ) { $hash{'unique alignment (bam)'} = $f; }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

167 elsif ( $f =~ /.*_sorted\.bam$/ ) { $hash{'alignment (bam)'} = $f; }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

168 elsif ( $f =~ /.*unique_plus.bedgraph/) { $hash{'bedgraph unique plus strand'} = $f; }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

169 elsif ( $f =~ /.*unique_minus.bedgraph/) { $hash{'bedgraph unique minus strand'} = $f; }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

170 elsif ( $f =~ /.*plus.bedgraph/) { $hash{'bedgraph plus strand'} = $f; }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

171 elsif ( $f =~ /.*minus.bedgraph/) { $hash{'bedgraph minus strand'} = $f; }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

172 else { unlink $fr; }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

173 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

174 return (\%hash, \@Unique, \@NonUnique, \@png);

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

175 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

176

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

177 sub span

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

178 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

179 my ( $file, $name, $min, $max, $simin, $simax, $pimin, $pimax ) = @_;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

180

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

181 print $file "

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

182 <div class=\"container text-center\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

183 <div class=\"row-fluid\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

184 <div class=\"span6\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

185 <h2>Bonafide</h2>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

186 reads of size between $min and $max<br>with no mi, sn, t and r RNAs

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

187 <p><a class=\"btn\" href=\"$name-bonafide_reads-genome.html\">Genome</a></p>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

188 <p><a class=\"btn\" href=\"$name-bonafide_reads-TEs.html\">TE</a></p>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

189 <p><a class=\"btn\" href=\"$name-bonafide_reads-transcripts.html\">Transcripts</a></p>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

190 <div class=\"row-fluid\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

191 <div class=\"span6\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

192 <h2>siRNAs</h2>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

193 bonafide reads of size between $simin and $simax

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

194 <p><a class=\"btn\" href=\"$name-siRNAs-genome.html\">Genome</a></p>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

195 <p><a class=\"btn\" href=\"$name-siRNAs-TEs.html\">TE</a></p>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

196 <p><a class=\"btn\" href=\"$name-siRNAs-transcripts.html\">Transcripts</a></p>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

197 </div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

198 <div class=\"span6\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

199 <h2>piRNAs</h2>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

200 bonafide reads of size between $pimin and $pimax

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

201 <p><a class=\"btn\" href=\"$name-piRNAs-genome.html\">Genome</a></p>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

202 <p><a class=\"btn\" href=\"$name-piRNAs-TEs.html\">TE</a></p>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

203 <p><a class=\"btn\" href=\"$name-piRNAs-transcripts.html\">Transcripts</a></p>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

204 </div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

205 </div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

206 </div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

207 <div class=\"span6\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

208 <h2>miRNAs</h2>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

209 <p><a class=\"btn\" href=\"$name-miRNAs-genome.html\">Genome</a></p>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

210 <p><a class=\"btn\" href=\"$name-miRNAs-TEs.html\">TE</a></p>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

211 <p><a class=\"btn\" href=\"$name-miRNAs-transcripts.html\">Transcripts</a></p>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

212 </div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

213 </div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

214 </div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

215 ";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

216 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

217

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

218 sub get_subgroups

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

219 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

220 my ( $dir, $name, $misTE, $dir_root ) = @_;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

221 my (%Hex, %HTE, %HG, @group, @png, @pngTE, @NonUniTE, @UniG, @NonUniG );

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

222

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

223 my $fut = "'$dir'".'/*';

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

224 my @fut = glob $fut;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

225 my $f ='';

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

226 foreach my $fr ( @fut )

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

227 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

228 $f = $1 if $fr =~ /$dir_root(.*)/;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

229

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

230 if ( $f =~ /genome_unique_sorted\.bam$/ ) { $HG{'genome unique mappers (sorted bam)'} = $f; }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

231 elsif ( $f =~ /genome_sorted\.bam$/ ) { $HG{'genome mappers (sorted bam)'} = $f; }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

232 elsif ( $f =~ /miRNAs_reads_counts\.txt$/ ) { $HG{'miRNAs per type (txt)'} = $f; }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

233 elsif ( $f =~ /genome_unique_plus\.bedgraph$/) { $HG{'bedgraph unique plus strand'} = $f; }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

234 elsif ( $f =~ /genome_unique_minus\.bedgraph$/) { $HG{'bedgraph unique minus strand'} = $f; }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

235 elsif ( $f =~ /genome_plus\.bedgraph$/) { $HG{'bedgraph plus strand'} = $f; }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

236 elsif ( $f =~ /genome_minus\.bedgraph$/) { $HG{'bedgraph minus strand'} = $f; }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

237 elsif ( $f =~ /TEs_plus\.bedgraph$/) { $HTE{'bedgraph plus strand'} = $f; }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

238 elsif ( $f =~ /TEs_minus\.bedgraph$/) { $HTE{'bedgraph minus strand'} = $f; }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

239 elsif ( $f =~ /transcripts_sorted\.bam$/) { $Hex{'transcripts mappers (sorted bam)'} = $f;}

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

240 elsif ( $f =~ /transcripts_unique_sorted\.bam$/) { $Hex{'transcripts unique mappers (sorted bam)'} = $f;}

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

241 elsif ( $f =~ /transcripts_reads_counts\.txt$/) { $Hex{'read number per transcript (txt)'} = $f;}

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

242 elsif ( $f =~ /TEs_reads_counts\.txt$/) { $HTE{"read number per TE 0 to $misTE mismatches (txt)"} = $f; }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

243 elsif ( $f =~ /TEs_reads_counts_mismatches\.txt$/) { $HTE{"read number per TE with 1 to $misTE mismatches (txt)"} = $f; }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

244 elsif ( $f =~ /TEs_reads_counts_nomismatches\.txt$/) { $HTE{'read number per TE with no mismatch (txt)'} = $f; }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

245 elsif ( $f =~ /TEs_unique_sorted\.bam$/) { $HTE{'TEs unique mappers (sorted bam)'} = $f; }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

246 elsif ( $f =~ /TEs_sorted\.bam$/) { $HTE{'TEs mappers (sorted bam)'} = $f; }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

247 elsif ( $fr =~ /.*Gviz_TEs/ )

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

248 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

249 my $nu = "'$fr'".'/*';

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

250 @NonUniTE = glob $nu;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

251 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

252 elsif ( $fr =~ /.*Gviz_genome/ )

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

253 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

254 my $nu = "'$fr'".'/rand/*';

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

255 @NonUniG = glob $nu;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

256 my $u = "'$fr'".'/unique/*';

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

257 @UniG = glob $u;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

258 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

259 else { unlink $fr; }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

260 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

261 return (\%Hex, \%HTE, \%HG, \@NonUniTE, \@NonUniG, \@UniG);

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

262 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

263

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

264 sub header

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

265 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

266 my $file = shift;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

267 print $file "

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

268 <!DOCTYPE html>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

269 <html lang=\"en\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

270 <head>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

271 <meta charset=\"utf-8\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

272 <title>pipeline</title>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

273 <meta name=\"viewport\" content=\"width=device-width, initial-scale=1.0\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

274 <meta name=\"description\" content=\"\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

275 <meta name=\"author\" content=\"\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

276

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

277 <link href=\"css/bootstrap.css\" rel=\"stylesheet\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

278 <link href=\"css/bootstrap-table.css\" rel=\"stylesheet\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

279 <style type=\"text/css\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

280 body {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

281 padding-top: 60px;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

282 padding-bottom: 40px;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

283 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

284 div#page {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

285 width: 940px;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

286 background-color: #fff;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

287 margin: 0 auto;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

288 text-align: left;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

289 border-color: #fff;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

290 border-style: none solid solid;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

291 border-width: medium 1px 1px;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

292 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

293

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

294 div.content {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

295 display: none;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

296 float: right;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

297 width: 550px;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

298 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

299 div.content a, div.navigation a {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

300 text-decoration: none;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

301 color: #777;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

302 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

303 div.content a:focus, div.content a:hover, div.content a:active {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

304 text-decoration: underline;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

305 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

306

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

307 div.controls {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

308 margin-top: 5px;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

309 height: 23px;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

310 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

311

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

312 div.controls a {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

313 padding: 5px;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

314 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

315 div.ss-controls {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

316 float: left;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

317 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

318 div.nav-controls {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

319 float: right;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

320 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

321 div.slideshow-container {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

322 position: relative;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

323 clear: both;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

324 height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

325 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

326 div.loader {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

327 position: absolute;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

328 top: 0;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

329 left: 0;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

330 background-image: url('loader.gif');

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

331 background-repeat: no-repeat;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

332 background-position: center;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

333 width: 550px;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

334 height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

335 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

336 div.slideshow {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

337

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

338 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

339

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

340 div.slideshow span.image-wrapper {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

341 display: block;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

342 position: absolute;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

343 top: 0;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

344 left: 0;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

345 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

346 div.slideshow a.advance-link {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

347 display: block;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

348 width: 550px;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

349 height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

350 line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

351 text-align: center;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

352 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

353 div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

354 text-decoration: none;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

355 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

356 div.slideshow img {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

357 vertical-align: middle;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

358 border: 1px solid #ccc;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

359 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

360

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

361 div.image-title {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

362 font-weight: bold;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

363 font-size: 1.4em;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

364 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

365

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

366 div.image-desc {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

367 line-height: 1.3em;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

368 padding-top: 12px;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

369 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

370 div.navigation {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

371

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

372 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

373 ul.thumbs {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

374 clear: both;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

375 margin: 0;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

376 padding: 0;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

377 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

378 ul.thumbs li {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

379 float: none;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

380 padding: 0;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

381 margin: 0;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

382 list-style: none;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

383 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

384 a.thumb {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

385 padding: 0;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

386 display: inline;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

387 border: none;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

388 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

389 ul.thumbs li.selected a.thumb {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

390 color: #000;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

391 font-weight: bold;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

392 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

393 a.thumb:focus {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

394 outline: none;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

395 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

396 ul.thumbs img {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

397 border: none;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

398 display: block;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

399 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

400 div.pagination {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

401 clear: both;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

402 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

403 div.navigation div.top {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

404 margin-bottom: 12px;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

405 height: 11px;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

406 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

407 div.navigation div.bottom {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

408 margin-top: 12px;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

409 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

410 div.pagination a, div.pagination span.current, div.pagination span.ellipsis {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

411 display: block;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

412 float: left;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

413 margin-right: 2px;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

414 padding: 4px 7px 2px 7px;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

415 border: 1px solid #ccc;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

416 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

417 div.pagination a:hover {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

418 background-color: #eee;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

419 text-decoration: none;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

420 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

421 div.pagination span.current {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

422 font-weight: bold;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

423 background-color: #000;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

424 border-color: #000;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

425 color: #fff;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

426 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

427 div.pagination span.ellipsis {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

428 border: none;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

429 padding: 5px 0 3px 2px;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

430 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

431

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

432 div.download {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

433 float: right;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

434 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

435

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

436 div.caption-container {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

437 position: relative;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

438 clear: left;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

439 height: 75px;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

440 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

441 span.image-caption {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

442 display: block;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

443 position: absolute;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

444 width: 550px;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

445 top: 0;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

446 left: 0;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

447 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

448 div.caption {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

449 padding: 12px;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

450 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

451

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

452 /* Featurettes

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

453 ------------------------- */

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

454

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

455 .featurette {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

456 padding-top: 20px; /* Vertically center images part 1: add padding above and below text. */

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

457 overflow: hidden; /* Vertically center images part 2: clear their floats. */

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

458 text-align: center;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

459 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

460

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

461 .featurette-p

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

462 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

463 text-align: left;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

464 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

465

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

466 .featurette-image {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

467 margin-top: 10px; /* Vertically center images part 3: negative margin up the image the same amount of the padding to center it. */

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

468 width: 450px;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

469 height: auto;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

470 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

471

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

472 </style>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

473 <link href=\"css/bootstrap-responsive.css\" rel=\"stylesheet\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

474 </head>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

475 <body>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

476 ";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

477 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

478

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

479 sub navbar

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

480 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

481 my ( $file, $fastq, $actif ) = @_;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

482

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

483 print $file "

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

484 <div class=\"navbar navbar-inverse navbar-fixed-top\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

485 <div class=\"navbar-inner\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

486 <div class=\"container\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

487 <button type=\"button\" class=\"btn btn-navbar\" data-toggle=\"collapse\" data-target=\".nav-collapse\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

488 <span class=\"icon-bar\"></span>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

489 <span class=\"icon-bar\"></span>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

490 <span class=\"icon-bar\"></span>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

491 </button>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

492 <a class=\"brand\" href=\"report.txt\">Report</a>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

493 <div class=\"nav-collapse collapse\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

494 <ul class=\"nav\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

495 ";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

496 for (my $i = 0 ; $i <= $#{$fastq}; $i++)

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

497 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

498 # my $fa = basename($fastq->[$i],'.dat');

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

499 my $fa = $fastq->[$i];

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

500 if ($actif eq $fa){ print $file "<li class=\"active\"><a href=\"$fastq->[$i].html\">$fa</a></li>";}

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

501 else {print $file "<li><a href=\"$fastq->[$i].html\">$fa</a></li>" ;}

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

502 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

503 print $file "

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

504 </ul>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

505 </div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

506 </div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

507 </div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

508 </div>";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

509 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

510

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

511 sub footer

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

512 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

513 my $file = shift;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

514 print $file "

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

515

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

516 <div class=\"container\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

517 <footer>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

518

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

519 </footer>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

520 </div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

521 <!-- Le javascript

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

522 ================================================== -->

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

523

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

524 <script type=\"text/javascript\" src=\"js/filter.js\"></script>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

525 <script type=\"text/javascript\" src=\"js/jquery.js\"></script>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

526 <script type=\"text/javascript\" src=\"js/jquery-1.3.2.js\"></script>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

527 <script type=\"text/javascript\" src=\"js/jquery.galleriffic.js\"></script>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

528 <script type=\"text/javascript\" src=\"js/jquery.opacityrollover.js\"></script>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

529 <script type=\"text/javascript\" src=\"js/bootstrap-table.js\"></script>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

530 <script type=\"text/javascript\" src=\"js/bootstrap.min.js\"></script>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

531 <script type=\"text/javascript\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

532 jQuery(document).ready(function(\$) {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

533 // We only want these styles applied when javascript is enabled

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

534 \$('div.navigation').css({'width' : '300px', 'float' : 'left'});

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

535 \$('div.content').css('display', 'block');

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

536

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

537 \$(\".each-gallery\").each(function(i){

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

538 // Initially set opacity on thumbs and add

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

539 // additional styling for hover effect on thumbs

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

540 var onMouseOutOpacity = 0.67;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

541 \$('#thumbs + i + ul.thumbs li').opacityrollover({

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

542 mouseOutOpacity: onMouseOutOpacity,

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

543 mouseOverOpacity: 1.0,

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

544 fadeSpeed: 'fast',

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

545 exemptionSelector: '.selected'

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

546 });

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

547

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

548 // Initialize Advanced Galleriffic Gallery

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

549 var gallery = \$('#thumbs'+i).galleriffic({

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

550 delay: 2500,

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

551 numThumbs: 22,

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

552 preloadAhead: 10,

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

553 enableTopPager: true,

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

554 enableBottomPager: true,

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

555 maxPagesToShow: 7,

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

556 imageContainerSel: '#slideshow'+ i,

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

557 controlsContainerSel: '#controls' + i,

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

558 captionContainerSel: '#caption' + i,

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

559 loadingContainerSel: '#loading' + i,

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

560 renderSSControls: true,

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

561 renderNavControls: true,

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

562 playLinkText: 'Play',

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

563 pauseLinkText: 'Pause',

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

564 prevLinkText: '&lsaquo; Previous',

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

565 nextLinkText: 'Next &rsaquo;',

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

566 nextPageLinkText: 'Next &rsaquo;',

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

567 prevPageLinkText: '&lsaquo; Prev',

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

568 enableHistory: false,

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

569 autoStart: false,

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

570 syncTransitions: true,

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

571 defaultTransitionDuration: 900,

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

572 onSlideChange: function(prevIndex, nextIndex) {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

573 // 'this' refers to the gallery, which is an extension of \$('#thumbs')

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

574 this.find('ul.thumbs').children()

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

575 .eq(prevIndex).fadeTo('fast', onMouseOutOpacity).end()

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

576 .eq(nextIndex).fadeTo('fast', 1.0);

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

577 },

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

578 onPageTransitionOut: function(callback) {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

579 this.fadeTo('fast', 0.0, callback);

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

580 },

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

581 onPageTransitionIn: function() {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

582 this.fadeTo('fast', 1.0);

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

583 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

584 });

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

585 });

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

586 });

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

587 </script>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

588 </body>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

589 </html>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

590 ";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

591 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

592

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

593 sub carousel

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

594 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

595 my ($file, $non_unique, $dir_root) = @_;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

596 my $ac = 0;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

597 print $file "

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

598 <div id=\"page\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

599 <div id=\"container\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

600 <div class=\"each-gallery\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

601 <div id=\"gallery\" class=\"content\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

602 <div id=\"controls0\" class=\"controls\"></div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

603 <div class=\"slideshow-container\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

604 <div id=\"loading0\" class=\"loader\"></div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

605 <div id=\"slideshow0\" class=\"slideshow\"></div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

606 </div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

607 <div id=\"caption0\" class=\"caption-container\">Reads randomly assigned</div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

608 </div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

609 <div id=\"thumbs0\" class=\"navigation\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

610 <input type=\"text\" id=\"myInput0\" onkeyup=\"search(this)\" placeholder=\"Search for names...\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

611 <ul class=\"thumbs noscript\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

612 ";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

613 foreach my $u (@{$non_unique})

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

614 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

615 my $name = basename($u,'.png');

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

616 $u = $1 if $u =~ /$dir_root(.*)/;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

617 print $file "

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

618 <li>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

619 <a class=\"thumb\" href=\"$u\" title=\"$name\">$name</a>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

620 </li>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

621 ";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

622 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

623 print $file "

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

624 </ul>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

625 </div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

626 <div style=\"clear: both;\"></div></div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

627 </div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

628 </div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

629 ";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

630 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

631

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

632 sub carousel2

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

633 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

634 my ($file, $unique, $non_unique, $dir_root) = @_;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

635 print $file "

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

636 <div id=\"page\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

637 <div id=\"container\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

638 <div class=\"each-gallery\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

639 <div id=\"gallery\" class=\"content\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

640 <div id=\"controls0\" class=\"controls\"></div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

641 <div class=\"slideshow-container\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

642 <div id=\"loading0\" class=\"loader\"></div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

643 <div id=\"slideshow0\" class=\"slideshow\"></div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

644 </div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

645 <div id=\"caption0\" class=\"caption-container\">Uniquely mapped reads</div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

646 </div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

647 <div id=\"thumbs0\" class=\"navigation\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

648 <input type=\"text\" id=\"myInput0\" onkeyup=\"search(this)\" placeholder=\"Search for names...\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

649 <ul class=\"thumbs noscript\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

650 ";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

651

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

652 foreach my $u (@{$unique})

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

653 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

654 my $name = basename($u,'.png');

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

655 $u = $1 if $u =~ /$dir_root(.*)/;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

656 print $file "

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

657 <li>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

658 <a class=\"thumb\" href=\"$u\" title=\"$name\">$name</a>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

659 </li>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

660 ";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

661 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

662 print $file "

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

663 </ul>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

664 </div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

665 </div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

666 <div id=\"page\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

667 <div id=\"container\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

668 <div class=\"each-gallery\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

669 <div id=\"gallery\" class=\"content\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

670 <div id=\"controls1\" class=\"controls\"></div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

671 <div class=\"slideshow-container\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

672 <div id=\"loading1\" class=\"loader\"></div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

673 <div id=\"slideshow1\" class=\"slideshow\"></div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

674 </div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

675 <div id=\"caption1\" class=\"caption-container\">Reads randomly assigned</div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

676 </div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

677 <div id=\"thumbs1\" class=\"navigation\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

678 <input type=\"text\" id=\"myInput1\" onkeyup=\"search(this)\" placeholder=\"Search for names...\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

679 <ul class=\"thumbs noscript\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

680 ";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

681

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

682 foreach my $nu (@{$non_unique})

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

683 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

684 my $name = basename($nu,'.png');

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

685 $nu = $1 if $nu =~ /$dir_root(.*)/;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

686 print $file "

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

687 <li>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

688 <a class=\"thumb\" href=\"$nu\" title=\"$name\">$name</a>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

689 </li>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

690 ";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

691 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

692 print $file "

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

693 </ul>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

694 </div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

695 <div style=\"clear: both;\"></div></div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

696 </div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

697 </div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

698 ";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

699 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

700

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

701 sub futurette

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

702 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

703 my ($file, $name, $png, $hash) = @_;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

704 print $file "

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

705 <div class=\"container\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

706 <div class=\"featurette\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

707 <h1>$name</h1>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

708 <p class=\"featurette-p\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

709 ";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

710 foreach my $k (sort keys %{$hash})

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

711 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

712 print $file "<A HREF=\"".${$hash}{$k}."\">$k</A><br/> \n" ;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

713 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

714

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

715 print $file "

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

716 </p>";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

717

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

718 foreach my $pn (@{$png}){print $file "<img class=\"featurette-image\" src=\"$pn\"/><br />";}

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

719

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

720 print $file "

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

721 </div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

722 </div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

723 ";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

724 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

725

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

726 sub fut

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

727 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

728 my ($file, $name, $hash) = @_;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

729 print $file "

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

730 <div class=\"container\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

731 <div class=\"featurette\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

732 <h1>$name</h1>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

733 <p class=\"featurette-p\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

734 ";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

735

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

736 foreach my $k (sort { ${$hash}{$a} cmp ${$hash}{$b} } keys %{$hash})

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

737 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

738 print $file "<A HREF=\"".${$hash}{$k}."\">$k</A><br/> \n" ;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

739 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

740

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

741 print $file "

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

742 </p>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

743 </div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

744 </div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

745 ";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

746 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

747

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

748 sub get_distri_exon

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

749 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

750 my ($dir, $name) = @_;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

751 my (@out,@group);

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

752 my $group = "'$dir'".'/'."'$name'".'-subgroups-bonafide_reads-transcripts-*distribution-*.png';

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

753 @group = glob $group;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

754 foreach (my $g =0; $g <= $#group; $g++)

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

755 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

756 if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-transcripts-.*distribution-.*\.png)/ )

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

757 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

758 my $tmp = $1;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

759 push @out, $1;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

760 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

761 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

762 return (\@out);

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

763 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

764

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

765 sub get_distri_TE

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

766 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

767 my ($dir, $name) = @_;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

768 my (@out,@group);

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

769 my $group = "'$dir'".'/'."'$name'".'-subgroups-bonafide_reads-TE-*distribution-*.png';

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

770 @group = glob $group;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

771 foreach (my $g =0; $g <= $#group; $g++)

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

772 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

773 if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-TE-.*distribution-.*\.png)/ )

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

774 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

775 my $tmp = $1;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

776 push @out, $1;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

777 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

778 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

779 return (\@out);

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

780 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

781

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

782 sub get_PPP

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

783 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

784 my ($dir,$name) = @_;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

785 my (%distri,@group);

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

786 my $group = "'$dir'".'/'."'$name'".'-subgroups-bonafide_reads-TE-PPPartners-*';

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

787 @group = glob $group;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

788

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

789 foreach (my $g =0; $g <= $#group; $g++)

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

790 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

791 if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-TE-PPPartners-.*)/ )

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

792 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

793 my $tmp = $1;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

794 if ($tmp =~ /PPPartners-(.*?)-sens\.txt$/)

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

795 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

796 $distri{$1} = ['','','','','',''] unless exists $distri{$1};

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

797 $distri{$1}->[0] = $tmp;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

798 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

799 elsif ($tmp =~ /PPPartners-(.*?)-antisens\.txt$/)

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

800 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

801 $distri{$1} = ['','','','','',''] unless exists $distri{$1};

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

802 $distri{$1}->[1] = $tmp;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

803 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

804 elsif ($tmp =~ /PPPartners-(.*?)-sensPPP\.txt$/)

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

805 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

806 $distri{$1} = ['','','','','',''] unless exists $distri{$1};

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

807 $distri{$1}->[2] = $tmp;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

808 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

809 elsif ($tmp =~ /PPPartners-(.*?)-antisensPPP\.txt$/)

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

810 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

811 $distri{$1} = ['','','','','',''] unless exists $distri{$1};

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

812 $distri{$1}->[3] = $tmp;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

813 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

814 elsif ($tmp =~ /PPPartners-(.*?)-overlap_size\.txt$/)

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

815 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

816 $distri{$1} = ['','','','','',''] unless exists $distri{$1};

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

817 $distri{$1}->[4] = $tmp;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

818 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

819 elsif ($tmp =~ /PPPartners-(.*?)-histogram\.png$/)

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

820 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

821 $distri{$1} = ['','','','','',''] unless exists $distri{$1};

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

822 $distri{$1}->[5] = $tmp;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

823 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

824 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

825 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

826 return \%distri;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

827 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

828

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

829 sub PPPrint

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

830 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

831 my ($h, $hash) = @_;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

832 my $cmp = 0;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

833

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

834 print $h "<div class=\"container\">\n";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

835 print $h "<div class=\"row text-center\">";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

836 while ( my ($k,$v) = each %{$hash} )

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

837 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

838 print $h "</div><div class=\"row text-center\">" if $cmp != 0 && $cmp % 2 == 0;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

839 print $h "

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

840

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

841 <div class=\"span6\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

842 <h2>$k</h2>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

843 <p class=\"featurette-p\"> <img src=\"$v->[5]\"/></p>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

844 <p class=\"featurette-p\"><a href=\"$v->[4]\">ping pong signature</a></p>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

845 <p class=\"featurette-p\"><a href=\"$v->[2]\">sense reads with PPP</a></p>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

846 <p class=\"featurette-p\"><a href=\"$v->[3]\">reverse reads with PPP</a></p>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

847 <p class=\"featurette-p\"><a href=\"$v->[0]\">sense reads without PPP</a></p>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

848 <p class=\"featurette-p\"><a href=\"$v->[1]\">reverse reads without PPP</a></p>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

849 </div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

850 ";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

851 $cmp++;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

852 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

853

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

854 print $h "</div></div>";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

855 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

856

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

857 sub printDistri

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

858 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

859 my ($h, $tab) = @_;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

860 my ($txt, $name);

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

861 my $cmp = 0;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

862 print $h "<div class=\"container\">\n";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

863 print $h "<div class=\"row text-center\">";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

864 foreach my $k (@{$tab})

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

865 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

866 if ($k =~ /(.*)-(.*)\.png$/)

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

867 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

868 $txt = $1.'-'.$2.'.txt';

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

869 $name = $2;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

870 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

871 print $h "</div><div class=\"row text-center\">" if $cmp != 0 && $cmp % 2 == 0;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

872 print $h "

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

873

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

874 <div class=\"span6\">

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

875 <h2>$name</h2>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

876 <p> <img src=\"$k\"/></p>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

877 <p class=\"featurette-p\"><a href=\"$txt\">text file</a></p>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

878 </div>

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

879 ";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

880 $cmp++;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

881 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

882

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

883 print $h "</div></div>";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

884 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

885

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

886 sub mapnum

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

887 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

888 my $dupmapnum = shift;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

889 my $dupnum_genome = shift;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

890 open (my $dupTE, $dupmapnum) || die "cannot open ".$dupmapnum."\n";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

891 my %dupnum_TE = ();

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

892 my $header = <$dupTE>;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

893 while (<$dupTE>)

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

894 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

895 chomp $_;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

896 my @dupline = split /\t/, $_;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

897 $dupnum_TE{$dupline[0]} = $dupline[2];

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

898 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

899 close $dupTE;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

900 open (my $du_TE, '>'.$dupmapnum) || die "cannot open to write ".$dupmapnum."\n";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

901 print $du_TE "sequence\tduplicate\tgenome map num\tmap num\n";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

902 while (my ($k, $v) = each %dupnum_TE )

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

903 {

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

904 my $hashRef = ${$dupnum_genome}{$k};

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

905 print $du_TE "$k\t$hashRef->[0]\t$hashRef->[1]\t$v\n";

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

906 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

907 close $du_TE;

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

908 }

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

909

9185ca0a7b43 Updated package according to recommendations.

pierre.pouchin

parents: 60

diff changeset

910 1;

Mercurial > repos > brasset_jensen > srnapipe

annotate bin/html.pm @ 61:9185ca0a7b43 draft