srnapipe: bin/html.pm annotate

annotate bin/html.pm @ 63:11708af40030 draft

planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit a461e07471d3897046e14389171a2c03d09b912d

author	pierre.pouchin
date	Thu, 24 Jan 2019 13:09:46 -0500
parents	9185ca0a7b43
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>";}
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><!--/.nav-collapse -->
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 <!-- FOOTER -->
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 <!-- Placed at the end of the document so the pages load faster -->
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

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