annotate bin/html.pm @ 26:b3be854a4273 draft

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author brasset_jensen
date Sun, 20 May 2018 16:55:31 -0400
parents 1df6aaac800e
children 360ec0ae04c9
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1
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1 package html;
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2
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3 use strict;
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4 use warnings;
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5 use File::Basename;
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6
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7 use Exporter;
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8 our @ISA = qw( Exporter );
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9 our @EXPORT_OK = qw( &main_page &details_pages &menu_page &ppp_page );
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10
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11 sub main_page
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12 {
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13 my ( $dir, $file, $list_mainTabP, $current, $ma, $ma_uni, $dir_root ) = @_;
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14 my ( $futHashP, $uniqueTabP, $randTabP, $pngTabP ) = get_genome ( $dir, $dir_root );
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15
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16 open my $h, '>', $file || die "cannot create $file $!\n";
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17 header ( $h );
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18 navbar ( $h, $list_mainTabP, $current );
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19 print $h "<div class=\"container\"><p><a class=\"btn\" href=\"$current-sub.html\">View details &raquo;</a></p></div>\n";
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20 futurette( $h, $current, $pngTabP, $futHashP );
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21 print $h "<div class=\"container\"><h2>mappers #: $ma</h2><h2>unique mappers #: $ma_uni</h2> </div>\n";
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22 carousel2( $h, $uniqueTabP, $randTabP, $dir_root );
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23 footer($h);
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24 close $h;
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25 }
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26
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27 sub menu_page
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28 {
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29 my ( $dir, $file, $list_mainTabP, $current, $min, $max, $simin, $simax, $pimin, $pimax, $dir_root ) = @_;
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30 my $html_ref = $1 if $dir =~ /$dir_root(.*)/;
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31 open my $h, '>', $file || die "cannot create $file $!\n";
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32 header($h);
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33 navbar ( $h, $list_mainTabP, $current );
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34 span( $h, $current, $min, $max, $simin, $simax, $pimin, $pimax );
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35 print $h " <div class=\"container\"> <div class=\"row text-center\"> <img src=\"$html_ref/pie_chart.png\"/><br />\n";
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36 print $h " <A HREF=\"$html_ref/repartition.txt\">text file</A><br/>\n </div></div>";
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37 footer($h);
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38 close $h;
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39 }
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40
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41 sub details_pages
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42 {
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43 my ( $dir_details, $prefix, $list_mainTabP, $current, $misTE, $dir_root, $ppp ) = @_;
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44 my ($Hex, $HTE, $HG, $NonUniTE, $NonUniG, $UniG ) = get_subgroups( $dir_details, $current, $misTE, $dir_root );
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45
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46 my $html_ref = $1.'-PPP.html' if $prefix =~ /$dir_root(.*)/;
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47 open my $h, '>', $prefix.'-TEs.html' || die "cannot create $prefix-TEs.html $!\n";
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48 header($h);
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49 navbar ( $h, $list_mainTabP, $current );
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50 if ( $prefix =~ /piRNAs$/ && $ppp eq 'true' )
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51 {
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52 print $h " <div class=\"container\">";
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53 print $h " <p><a class=\"btn\" href=\"$html_ref\">Ping Pong Partners</a></p>\n";
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54 print $h "</div>";
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55 }
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56 fut($h,'Transposable elements',$HTE);
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57 carousel($h,$NonUniTE,$dir_root);
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58 footer($h);
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59 close $h;
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60
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61 open $h, '>', $prefix.'-genome.html' || die "cannot create $prefix-genome.html $!\n";
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62 header($h);
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63 navbar ( $h, $list_mainTabP, $current );
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64 fut($h,'Genome',$HG);
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65 carousel2($h,$UniG, $NonUniG,$dir_root);
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66 footer($h);
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67 close $h;
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68
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69 open $h, '>', $prefix.'-transcripts.html' || die "cannot create $prefix-transcripts.html $!\n";
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70 header($h);
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71 navbar ( $h, $list_mainTabP, $current );
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72 fut($h,'transcripts',$Hex);
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73 footer($h);
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74 close $h;
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75 }
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76
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77 sub ppp_page
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78 {
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79 my ( $dir, $file, $list_mainTabP, $current, $ppp, $dir_root ) = @_;
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80
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81 my $ppp_file = $ppp.'ppp.txt';
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82 open my $h, '>', $file || die "cannot create $file $!\n";
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83 header($h);
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84 navbar ( $h, $list_mainTabP, $current );
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85 print $h '<div class="container"> <table class="wb-tables table table-striped table-hover">'."\n";
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86 print $h '<thead>
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87 <tr>
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88 <th data-sortable="true">ID</th>
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89 <th data-sortable="true">overlap sum</th>
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90 <th data-sortable="true">ten overlap sum</th>
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91 <th data-sortable="true">mean</th>
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92 <th data-sortable="true">standard deviation</th>
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93 <th data-sortable="true">z-score</th>
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94 <th data-sortable="true">p-value</th>
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95 </tr>
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96 </thead>
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97 <tbody>';
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98
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99 open my $f, '<', $ppp_file || die "cannot open $ppp_file $!\n";
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100 while ( <$f> )
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101 {
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102 chomp;
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103 print $h '<tr>';
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104 my ( $id, $sum, $ten, $mean, $sd, $zscore, $prob) = split /\t/, $_;
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105 if( -d "$ppp/$id" )
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106 {
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107 my $sub_html = $ppp.$id.'.html';
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108 my $sub_html_ref = $1.$id if $ppp =~ /$dir_root(.*)/;
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109 print $h "<td> <a href=\"$sub_html_ref.html\">$id</a> </td>";
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110
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111 open my $sub, '>', $sub_html || die "cannot create $sub_html\n";
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112 {
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113 header($sub);
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114 print $sub "
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115 <div align=\"center\">
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116 <h2>$id</h2>
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117 <p> <img class=\"featurette-image\" src=\"$id/histogram.png\"/></p>
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118 <p><a href=\"$id/overlap_size.txt\">ping pong signature</a></p>
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119 <p><a href=\"$id/sensPPP.txt\">sens reads with PPP</a></p>
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120 <p><a href=\"$id/antisensPPP.txt\">reverse reads with PPP</a></p>
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121 <p><a href=\"$id/sens.txt\">sens reads without PPP</a></p>
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122 <p><a href=\"$id/antisens.txt\">reverse reads without PPP</a></p>
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123 </div>";
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124 footer($sub);
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125 }
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126 close $sub;
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127
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128 }
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129 else { print $h "<td> $id </td>\n"; }
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130 print $h "<td> $sum </td><td> $ten </td><td> $mean </td><td> $sd </td><td> $zscore </td><td> $prob </td>\n";
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131
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132 print $h '</tr>';
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133 }
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134 close $f;
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135 print $h "</tbody></table></div>";
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136 footer($h);
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137 close $h;
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138 }
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139
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140 sub get_genome
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141 {
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142 my ( $dir, $dir_root ) = @_;
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143 my ( %hash, @group, @Unique, @NonUnique, @png );
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144
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145 my $fut = $dir.'/*';
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146 my @fut = glob $fut;
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147
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148
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149 foreach my $fr ( @fut )
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150 {
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151 my $f = $1 if $fr =~ /$dir_root(.*)/;
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152 if ( $fr =~ /.*Gviz/ )
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153 {
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154 my $nu = $fr.'/rand/*';
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155 @NonUnique = glob $nu;
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156 my $u = $fr.'/unique/*';
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157 @Unique = glob $u;
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158 }
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159 elsif ( $f =~ /.*distribution\.txt$/ ) { $hash{'mappers size distribution (txt)'} = $f; }
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160 elsif ( $f =~ /.*distribution\.png$/ ) { push @png, $f; }
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161 elsif ( $f =~ /.*unique\.fastq$/ ) { $hash{'unique mappers (fastq.gz)'} = $f.'.gz'; `gzip $fr`; }
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162 elsif ( $f =~ /.*rejected\.fastq$/ ) { $hash{'unmapped (fastq.gz)'} = $f.'.gz'; `gzip $fr`; }
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163 elsif ( $f =~ /.*all\.fastq$/ ) { $hash{'mappers (fastq.gz)'} = $f.'.gz'; `gzip $fr`; }
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164 elsif ( $f =~ /.*dup_unique\.txt$/ ) { $hash{'unique mappers (txt)'} = $f; }
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165 elsif ( $f =~ /.*dup_mapnum\.txt$/ ) { $hash{'mappers (txt)'} = $f; }
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166 elsif ( $f =~ /.*dup_nonmapp\.txt$/ ) { $hash{'unmapped (txt)'} = $f; }
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167 elsif ( $f =~ /.*_unique_sorted\.bam$/ ) { $hash{'unique alignment (bam)'} = $f; }
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168 elsif ( $f =~ /.*_sorted\.bam$/ ) { $hash{'alignment (bam)'} = $f; }
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169 elsif ( $f =~ /.*unique_plus.bedgraph/) { $hash{'bedgraph unique plus strand'} = $f; }
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170 elsif ( $f =~ /.*unique_minus.bedgraph/) { $hash{'bedgraph unique minus strand'} = $f; }
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171 elsif ( $f =~ /.*plus.bedgraph/) { $hash{'bedgraph plus strand'} = $f; }
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172 elsif ( $f =~ /.*minus.bedgraph/) { $hash{'bedgraph minus strand'} = $f; }
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173 else { unlink $fr; }
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174 }
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175 return (\%hash, \@Unique, \@NonUnique, \@png);
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176 }
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177
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178 sub span
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179 {
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180 my ( $file, $name, $min, $max, $simin, $simax, $pimin, $pimax ) = @_;
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181
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182 print $file "
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183 <div class=\"container text-center\">
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184 <div class=\"row-fluid\">
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185 <div class=\"span6\">
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186 <h2>Bonafide</h2>
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187 reads of size between $min and $max<br>with no mi, sn, t and r RNAs
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188 <p><a class=\"btn\" href=\"$name-bonafide_reads-genome.html\">Genome</a></p>
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189 <p><a class=\"btn\" href=\"$name-bonafide_reads-TEs.html\">TE</a></p>
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190 <p><a class=\"btn\" href=\"$name-bonafide_reads-transcripts.html\">Transcripts</a></p>
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191 <div class=\"row-fluid\">
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192 <div class=\"span6\">
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193 <h2>siRNAs</h2>
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194 bonafide reads of size between $simin and $simax
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195 <p><a class=\"btn\" href=\"$name-siRNAs-genome.html\">Genome</a></p>
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196 <p><a class=\"btn\" href=\"$name-siRNAs-TEs.html\">TE</a></p>
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197 <p><a class=\"btn\" href=\"$name-siRNAs-transcripts.html\">Transcripts</a></p>
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198 </div>
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199 <div class=\"span6\">
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200 <h2>piRNAs</h2>
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201 bonafide reads of size between $pimin and $pimax
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202 <p><a class=\"btn\" href=\"$name-piRNAs-genome.html\">Genome</a></p>
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203 <p><a class=\"btn\" href=\"$name-piRNAs-TEs.html\">TE</a></p>
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204 <p><a class=\"btn\" href=\"$name-piRNAs-transcripts.html\">Transcripts</a></p>
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205 </div>
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206 </div>
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207 </div>
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208 <div class=\"span6\">
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209 <h2>miRNAs</h2>
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210 <p><a class=\"btn\" href=\"$name-miRNAs-genome.html\">Genome</a></p>
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211 <p><a class=\"btn\" href=\"$name-miRNAs-TEs.html\">TE</a></p>
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212 <p><a class=\"btn\" href=\"$name-miRNAs-transcripts.html\">Transcripts</a></p>
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213 </div>
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214 </div>
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215 </div>
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216 ";
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217 }
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218
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219 sub get_subgroups
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220 {
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221 my ( $dir, $name, $misTE, $dir_root ) = @_;
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222 my (%Hex, %HTE, %HG, @group, @png, @pngTE, @NonUniTE, @UniG, @NonUniG );
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223
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224 my $fut = $dir.'/*';
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225 my @fut = glob $fut;
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226 my $f ='';
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227 foreach my $fr ( @fut )
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228 {
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229 $f = $1 if $fr =~ /$dir_root(.*)/;
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230
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231 if ( $f =~ /genome_unique_sorted\.bam$/ ) { $HG{'genome unique mappers (sorted bam)'} = $f; }
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232 elsif ( $f =~ /genome_sorted\.bam$/ ) { $HG{'genome mappers (sorted bam)'} = $f; }
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233 elsif ( $f =~ /miRNAs_reads_counts\.txt$/ ) { $HG{'miRNAs per type (txt)'} = $f; }
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234 elsif ( $f =~ /genome_unique_plus\.bedgraph$/) { $HG{'bedgraph unique plus strand'} = $f; }
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235 elsif ( $f =~ /genome_unique_minus\.bedgraph$/) { $HG{'bedgraph unique minus strand'} = $f; }
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236 elsif ( $f =~ /genome_plus\.bedgraph$/) { $HG{'bedgraph plus strand'} = $f; }
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237 elsif ( $f =~ /genome_minus\.bedgraph$/) { $HG{'bedgraph minus strand'} = $f; }
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238 elsif ( $f =~ /TEs_plus\.bedgraph$/) { $HTE{'bedgraph plus strand'} = $f; }
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239 elsif ( $f =~ /TEs_minus\.bedgraph$/) { $HTE{'bedgraph minus strand'} = $f; }
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240 elsif ( $f =~ /transcripts_sorted\.bam$/) { $Hex{'transcripts mappers (sorted bam)'} = $f;}
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241 elsif ( $f =~ /transcripts_unique_sorted\.bam$/) { $Hex{'transcripts unique mappers (sorted bam)'} = $f;}
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242 elsif ( $f =~ /transcripts_reads_counts\.txt$/) { $Hex{'read number per transcript (txt)'} = $f;}
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243 elsif ( $f =~ /TEs_reads_counts\.txt$/) { $HTE{"read number per TE 0 to $misTE mismatches (txt)"} = $f; }
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244 elsif ( $f =~ /TEs_reads_counts_mismatches\.txt$/) { $HTE{"read number per TE with 1 to $misTE mismatches (txt)"} = $f; }
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245 elsif ( $f =~ /TEs_reads_counts_nomismatches\.txt$/) { $HTE{'read number per TE with no mismatch (txt)'} = $f; }
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246 elsif ( $f =~ /TEs_unique_sorted\.bam$/) { $HTE{'TEs unique mappers (sorted bam)'} = $f; }
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247 elsif ( $f =~ /TEs_sorted\.bam$/) { $HTE{'TEs mappers (sorted bam)'} = $f; }
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brasset_jensen
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248 elsif ( $fr =~ /.*Gviz_TEs/ )
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brasset_jensen
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249 {
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250 my $nu = $fr.'/*';
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251 @NonUniTE = glob $nu;
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252 }
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253 elsif ( $fr =~ /.*Gviz_genome/ )
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brasset_jensen
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254 {
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255 my $nu = $fr.'/rand/*';
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256 @NonUniG = glob $nu;
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257 my $u = $fr.'/unique/*';
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258 @UniG = glob $u;
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259 }
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brasset_jensen
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260 else { unlink $fr; }
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261 }
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262 return (\%Hex, \%HTE, \%HG, \@NonUniTE, \@NonUniG, \@UniG);
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263 }
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264
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265 sub header
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266 {
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267 my $file = shift;
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268 print $file "
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269 <!DOCTYPE html>
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270 <html lang=\"en\">
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271 <head>
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272 <meta charset=\"utf-8\">
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273 <title>pipeline</title>
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274 <meta name=\"viewport\" content=\"width=device-width, initial-scale=1.0\">
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275 <meta name=\"description\" content=\"\">
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276 <meta name=\"author\" content=\"\">
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brasset_jensen
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277 <!-- Le styles -->
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278 <link href=\"css/bootstrap.css\" rel=\"stylesheet\">
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279 <link href=\"css/bootstrap-table.css\" rel=\"stylesheet\">
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280 <style type=\"text/css\">
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281 body {
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282 padding-top: 60px;
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283 padding-bottom: 40px;
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284 }
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285 div#page {
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286 width: 940px;
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287 background-color: #fff;
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288 margin: 0 auto;
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289 text-align: left;
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290 border-color: #fff;
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291 border-style: none solid solid;
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292 border-width: medium 1px 1px;
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293 }
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294
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295 div.content {
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296 display: none;
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297 float: right;
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brasset_jensen
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298 width: 550px;
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299 }
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brasset_jensen
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300 div.content a, div.navigation a {
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301 text-decoration: none;
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brasset_jensen
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302 color: #777;
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brasset_jensen
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303 }
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brasset_jensen
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304 div.content a:focus, div.content a:hover, div.content a:active {
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brasset_jensen
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305 text-decoration: underline;
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brasset_jensen
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306 }
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brasset_jensen
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307
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brasset_jensen
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308 div.controls {
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brasset_jensen
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309 margin-top: 5px;
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brasset_jensen
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310 height: 23px;
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311 }
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312
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313 div.controls a {
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314 padding: 5px;
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315 }
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brasset_jensen
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316 div.ss-controls {
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brasset_jensen
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317 float: left;
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brasset_jensen
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318 }
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brasset_jensen
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319 div.nav-controls {
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320 float: right;
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brasset_jensen
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321 }
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brasset_jensen
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322 div.slideshow-container {
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brasset_jensen
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323 position: relative;
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brasset_jensen
parents:
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324 clear: both;
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325 height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */
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brasset_jensen
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326 }
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brasset_jensen
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327 div.loader {
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328 position: absolute;
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329 top: 0;
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330 left: 0;
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brasset_jensen
parents:
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331 background-image: url('loader.gif');
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brasset_jensen
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332 background-repeat: no-repeat;
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brasset_jensen
parents:
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333 background-position: center;
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brasset_jensen
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334 width: 550px;
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brasset_jensen
parents:
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335 height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */
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brasset_jensen
parents:
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336 }
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brasset_jensen
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337 div.slideshow {
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brasset_jensen
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338
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339 }
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brasset_jensen
parents:
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340
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brasset_jensen
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341 div.slideshow span.image-wrapper {
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brasset_jensen
parents:
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342 display: block;
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brasset_jensen
parents:
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343 position: absolute;
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brasset_jensen
parents:
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344 top: 0;
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brasset_jensen
parents:
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345 left: 0;
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brasset_jensen
parents:
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346 }
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brasset_jensen
parents:
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347 div.slideshow a.advance-link {
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brasset_jensen
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348 display: block;
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brasset_jensen
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349 width: 550px;
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brasset_jensen
parents:
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350 height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */
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brasset_jensen
parents:
diff changeset
351 line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */
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brasset_jensen
parents:
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352 text-align: center;
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brasset_jensen
parents:
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353 }
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diff changeset
354 div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited {
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brasset_jensen
parents:
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355 text-decoration: none;
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brasset_jensen
parents:
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356 }
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brasset_jensen
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357 div.slideshow img {
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358 vertical-align: middle;
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brasset_jensen
parents:
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359 border: 1px solid #ccc;
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brasset_jensen
parents:
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360 }
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brasset_jensen
parents:
diff changeset
361
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brasset_jensen
parents:
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362 div.image-title {
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parents:
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363 font-weight: bold;
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brasset_jensen
parents:
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364 font-size: 1.4em;
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brasset_jensen
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365 }
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brasset_jensen
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366
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brasset_jensen
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367 div.image-desc {
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brasset_jensen
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diff changeset
368 line-height: 1.3em;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
369 padding-top: 12px;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
370 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
371 div.navigation {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
372
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
373 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
374 ul.thumbs {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
375 clear: both;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
376 margin: 0;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
377 padding: 0;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
378 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
379 ul.thumbs li {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
380 float: none;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
381 padding: 0;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
382 margin: 0;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
383 list-style: none;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
384 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
385 a.thumb {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
386 padding: 0;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
387 display: inline;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
388 border: none;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
389 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
390 ul.thumbs li.selected a.thumb {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
391 color: #000;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
392 font-weight: bold;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
393 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
394 a.thumb:focus {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
395 outline: none;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
396 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
397 ul.thumbs img {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
398 border: none;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
399 display: block;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
400 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
401 div.pagination {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
402 clear: both;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
403 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
404 div.navigation div.top {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
405 margin-bottom: 12px;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
406 height: 11px;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
407 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
408 div.navigation div.bottom {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
409 margin-top: 12px;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
410 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
411 div.pagination a, div.pagination span.current, div.pagination span.ellipsis {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
412 display: block;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
413 float: left;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
414 margin-right: 2px;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
415 padding: 4px 7px 2px 7px;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
416 border: 1px solid #ccc;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
417 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
418 div.pagination a:hover {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
419 background-color: #eee;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
420 text-decoration: none;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
421 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
422 div.pagination span.current {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
423 font-weight: bold;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
424 background-color: #000;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
425 border-color: #000;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
426 color: #fff;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
427 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
428 div.pagination span.ellipsis {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
429 border: none;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
430 padding: 5px 0 3px 2px;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
431 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
432
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
433 div.download {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
434 float: right;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
435 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
436
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
437 div.caption-container {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
438 position: relative;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
439 clear: left;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
440 height: 75px;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
441 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
442 span.image-caption {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
443 display: block;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
444 position: absolute;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
445 width: 550px;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
446 top: 0;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
447 left: 0;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
448 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
449 div.caption {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
450 padding: 12px;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
451 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
452
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
453 /* Featurettes
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
454 ------------------------- */
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
455
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
456 .featurette {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
457 padding-top: 20px; /* Vertically center images part 1: add padding above and below text. */
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
458 overflow: hidden; /* Vertically center images part 2: clear their floats. */
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
459 text-align: center;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
460 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
461
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
462 .featurette-p
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
463 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
464 text-align: left;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
465 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
466
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
467 .featurette-image {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
468 margin-top: 10px; /* Vertically center images part 3: negative margin up the image the same amount of the padding to center it. */
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
469 width: 450px;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
470 height: auto;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
471 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
472
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
473 </style>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
474 <link href=\"css/bootstrap-responsive.css\" rel=\"stylesheet\">
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
475 </head>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
476 <body>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
477 ";
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
478 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
479
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
480 sub navbar
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
481 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
482 my ( $file, $fastq, $actif ) = @_;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
483
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
484 print $file "
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
485 <div class=\"navbar navbar-inverse navbar-fixed-top\">
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
486 <div class=\"navbar-inner\">
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
487 <div class=\"container\">
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
488 <button type=\"button\" class=\"btn btn-navbar\" data-toggle=\"collapse\" data-target=\".nav-collapse\">
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
489 <span class=\"icon-bar\"></span>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
490 <span class=\"icon-bar\"></span>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
491 <span class=\"icon-bar\"></span>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
492 </button>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
493 <a class=\"brand\" href=\"report.txt\">Report</a>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
494 <div class=\"nav-collapse collapse\">
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
495 <ul class=\"nav\">
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
496 ";
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
497 for (my $i = 0 ; $i <= $#{$fastq}; $i++)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
498 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
499 # my $fa = basename($fastq->[$i],'.dat');
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
500 my $fa = $fastq->[$i];
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
501 if ($actif eq $fa){ print $file "<li class=\"active\"><a href=\"$fastq->[$i].html\">$fa</a></li>";}
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
502 else {print $file "<li><a href=\"$fastq->[$i].html\">$fa</a></li>" ;}
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
503 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
504 print $file "
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
505 </ul>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
506 </div><!--/.nav-collapse -->
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
507 </div>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
508 </div>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
509 </div>";
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
510 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
511
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
512 sub footer
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
513 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
514 my $file = shift;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
515 print $file "
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
516 <!-- FOOTER -->
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
517 <div class=\"container\">
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
518 <footer>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
519
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
520 </footer>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
521 </div>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
522 <!-- Le javascript
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
523 ================================================== -->
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
524 <!-- Placed at the end of the document so the pages load faster -->
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
525 <script type=\"text/javascript\" src=\"js/jquery.js\"></script>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
526 <script type=\"text/javascript\" src=\"js/jquery-1.3.2.js\"></script>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
527 <script type=\"text/javascript\" src=\"js/jquery.galleriffic.js\"></script>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
528 <script type=\"text/javascript\" src=\"js/jquery.opacityrollover.js\"></script>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
529 <script type=\"text/javascript\" src=\"js/bootstrap-table.js\"></script>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
530 <script type=\"text/javascript\" src=\"js/bootstrap.min.js\"></script>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
531 <script type=\"text/javascript\">
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
532 jQuery(document).ready(function(\$) {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
533 // We only want these styles applied when javascript is enabled
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
534 \$('div.navigation').css({'width' : '300px', 'float' : 'left'});
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
535 \$('div.content').css('display', 'block');
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
536
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
537 \$(\".each-gallery\").each(function(i){
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
538 // Initially set opacity on thumbs and add
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
539 // additional styling for hover effect on thumbs
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
540 var onMouseOutOpacity = 0.67;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
541 \$('#thumbs + i + ul.thumbs li').opacityrollover({
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
542 mouseOutOpacity: onMouseOutOpacity,
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
543 mouseOverOpacity: 1.0,
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
544 fadeSpeed: 'fast',
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
545 exemptionSelector: '.selected'
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
546 });
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
547
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
548 // Initialize Advanced Galleriffic Gallery
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
549 var gallery = \$('#thumbs'+i).galleriffic({
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
550 delay: 2500,
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
551 numThumbs: 22,
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
552 preloadAhead: 10,
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
553 enableTopPager: true,
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
554 enableBottomPager: true,
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
555 maxPagesToShow: 7,
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
556 imageContainerSel: '#slideshow'+ i,
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
557 controlsContainerSel: '#controls' + i,
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
558 captionContainerSel: '#caption' + i,
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
559 loadingContainerSel: '#loading' + i,
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
560 renderSSControls: true,
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
561 renderNavControls: true,
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
562 playLinkText: 'Play',
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
563 pauseLinkText: 'Pause',
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
564 prevLinkText: '&lsaquo; Previous',
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
565 nextLinkText: 'Next &rsaquo;',
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
566 nextPageLinkText: 'Next &rsaquo;',
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
567 prevPageLinkText: '&lsaquo; Prev',
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
568 enableHistory: false,
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
569 autoStart: false,
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
570 syncTransitions: true,
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
571 defaultTransitionDuration: 900,
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
572 onSlideChange: function(prevIndex, nextIndex) {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
573 // 'this' refers to the gallery, which is an extension of \$('#thumbs')
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
574 this.find('ul.thumbs').children()
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
575 .eq(prevIndex).fadeTo('fast', onMouseOutOpacity).end()
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
576 .eq(nextIndex).fadeTo('fast', 1.0);
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
577 },
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
578 onPageTransitionOut: function(callback) {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
579 this.fadeTo('fast', 0.0, callback);
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
580 },
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
581 onPageTransitionIn: function() {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
582 this.fadeTo('fast', 1.0);
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
583 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
584 });
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
585 });
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
586 });
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
587 </script>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
588 </body>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
589 </html>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
590 ";
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
591 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
592
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
593 sub carousel
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
594 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
595 my ($file, $non_unique, $dir_root) = @_;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
596 my $ac = 0;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
597 print $file "
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
598 <div id=\"page\">
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
599 <div id=\"container\">
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
600 <div class=\"each-gallery\">
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
601 <div id=\"gallery\" class=\"content\">
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
602 <div id=\"controls0\" class=\"controls\"></div>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
603 <div class=\"slideshow-container\">
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
604 <div id=\"loading0\" class=\"loader\"></div>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
605 <div id=\"slideshow0\" class=\"slideshow\"></div>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
606 </div>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
607 <div id=\"caption0\" class=\"caption-container\">Reads randomly assigned</div>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
608 </div>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
609 <div id=\"thumbs0\" class=\"navigation\">
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
610 <ul class=\"thumbs noscript\">
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
611 ";
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
612 foreach my $u (@{$non_unique})
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
613 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
614 my $name = basename($u,'.png');
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
615 $u = $1 if $u =~ /$dir_root(.*)/;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
616 print $file "
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
617 <li>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
618 <a class=\"thumb\" href=\"$u\" title=\"$name\">$name</a>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
619 </li>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
620 ";
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
621 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
622 print $file "
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
623 </ul>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
624 </div>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
625 <div style=\"clear: both;\"></div></div>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
626 </div>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
627 </div>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
628 ";
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
629 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
630
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
631 sub carousel2
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
632 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
633 my ($file, $unique, $non_unique, $dir_root) = @_;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
634 print $file "
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
635 <div id=\"page\">
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
636 <div id=\"container\">
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
637 <div class=\"each-gallery\">
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
638 <div id=\"gallery\" class=\"content\">
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
639 <div id=\"controls0\" class=\"controls\"></div>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
640 <div class=\"slideshow-container\">
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
641 <div id=\"loading0\" class=\"loader\"></div>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
642 <div id=\"slideshow0\" class=\"slideshow\"></div>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
643 </div>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
644 <div id=\"caption0\" class=\"caption-container\">Uniquely mapped reads</div>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
645 </div>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
646 <div id=\"thumbs0\" class=\"navigation\">
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
647 <ul class=\"thumbs noscript\">
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
648 ";
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
649
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
650 foreach my $u (@{$unique})
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
651 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
652 my $name = basename($u,'.png');
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
653 $u = $1 if $u =~ /$dir_root(.*)/;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
654 print $file "
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
655 <li>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
656 <a class=\"thumb\" href=\"$u\" title=\"$name\">$name</a>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
657 </li>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
658 ";
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
659 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
660 print $file "
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
661 </ul>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
662 </div>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
663 </div>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
664 <div id=\"page\">
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
665 <div id=\"container\">
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
666 <div class=\"each-gallery\">
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
667 <div id=\"gallery\" class=\"content\">
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
668 <div id=\"controls1\" class=\"controls\"></div>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
669 <div class=\"slideshow-container\">
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
670 <div id=\"loading1\" class=\"loader\"></div>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
671 <div id=\"slideshow1\" class=\"slideshow\"></div>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
672 </div>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
673 <div id=\"caption1\" class=\"caption-container\">Reads randomly assigned</div>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
674 </div>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
675 <div id=\"thumbs1\" class=\"navigation\">
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
676 <ul class=\"thumbs noscript\">
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
677 ";
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
678
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
679 foreach my $nu (@{$non_unique})
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
680 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
681 my $name = basename($nu,'.png');
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
682 $nu = $1 if $nu =~ /$dir_root(.*)/;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
683 print $file "
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
684 <li>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
685 <a class=\"thumb\" href=\"$nu\" title=\"$name\">$name</a>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
686 </li>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
687 ";
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
688 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
689 print $file "
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
690 </ul>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
691 </div>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
692 <div style=\"clear: both;\"></div></div>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
693 </div>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
694 </div>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
695 ";
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
696 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
697
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
698 sub futurette
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
699 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
700 my ($file, $name, $png, $hash) = @_;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
701 print $file "
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
702 <div class=\"container\">
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
703 <div class=\"featurette\">
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
704 <h1>$name</h1>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
705 <p class=\"featurette-p\">
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
706 ";
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
707 foreach my $k (sort keys %{$hash})
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
708 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
709 print $file "<A HREF=\"".${$hash}{$k}."\">$k</A><br/> \n" ;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
710 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
711
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
712 print $file "
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
713 </p>";
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
714
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
715 foreach my $pn (@{$png}){print $file "<img class=\"featurette-image\" src=\"$pn\"/><br />";}
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
716
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
717 print $file "
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
718 </div>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
719 </div>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
720 ";
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
721 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
722
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
723 sub fut
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
724 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
725 my ($file, $name, $hash) = @_;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
726 print $file "
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
727 <div class=\"container\">
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
728 <div class=\"featurette\">
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
729 <h1>$name</h1>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
730 <p class=\"featurette-p\">
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
731 ";
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
732
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
733 foreach my $k (sort { ${$hash}{$a} cmp ${$hash}{$b} } keys %{$hash})
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
734 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
735 print $file "<A HREF=\"".${$hash}{$k}."\">$k</A><br/> \n" ;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
736 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
737
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
738 print $file "
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
739 </p>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
740 </div>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
741 </div>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
742 ";
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
743 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
744
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
745 sub get_distri_exon
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
746 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
747 my ($dir, $name) = @_;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
748 my (@out,@group);
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
749 my $group = $dir.'/'.$name.'-subgroups-bonafide_reads-transcripts-*distribution-*.png';
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
750 @group = glob $group;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
751 foreach (my $g =0; $g <= $#group; $g++)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
752 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
753 if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-transcripts-.*distribution-.*\.png)/ )
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
754 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
755 my $tmp = $1;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
756 push @out, $1;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
757 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
758 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
759 return (\@out);
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
760 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
761
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
762 sub get_distri_TE
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
763 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
764 my ($dir, $name) = @_;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
765 my (@out,@group);
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
766 my $group = $dir.'/'.$name.'-subgroups-bonafide_reads-TE-*distribution-*.png';
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
767 @group = glob $group;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
768 foreach (my $g =0; $g <= $#group; $g++)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
769 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
770 if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-TE-.*distribution-.*\.png)/ )
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
771 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
772 my $tmp = $1;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
773 push @out, $1;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
774 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
775 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
776 return (\@out);
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
777 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
778
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
779 sub get_PPP
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
780 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
781 my ($dir,$name) = @_;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
782 my (%distri,@group);
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
783 my $group = $dir.'/'.$name.'-subgroups-bonafide_reads-TE-PPPartners-*';
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
784 @group = glob $group;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
785
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
786 foreach (my $g =0; $g <= $#group; $g++)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
787 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
788 if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-TE-PPPartners-.*)/ )
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
789 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
790 my $tmp = $1;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
791 if ($tmp =~ /PPPartners-(.*?)-sens\.txt$/)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
792 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
793 $distri{$1} = ['','','','','',''] unless exists $distri{$1};
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
794 $distri{$1}->[0] = $tmp;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
795 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
796 elsif ($tmp =~ /PPPartners-(.*?)-antisens\.txt$/)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
797 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
798 $distri{$1} = ['','','','','',''] unless exists $distri{$1};
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
799 $distri{$1}->[1] = $tmp;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
800 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
801 elsif ($tmp =~ /PPPartners-(.*?)-sensPPP\.txt$/)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
802 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
803 $distri{$1} = ['','','','','',''] unless exists $distri{$1};
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
804 $distri{$1}->[2] = $tmp;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
805 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
806 elsif ($tmp =~ /PPPartners-(.*?)-antisensPPP\.txt$/)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
807 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
808 $distri{$1} = ['','','','','',''] unless exists $distri{$1};
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
809 $distri{$1}->[3] = $tmp;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
810 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
811 elsif ($tmp =~ /PPPartners-(.*?)-overlap_size\.txt$/)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
812 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
813 $distri{$1} = ['','','','','',''] unless exists $distri{$1};
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
814 $distri{$1}->[4] = $tmp;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
815 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
816 elsif ($tmp =~ /PPPartners-(.*?)-histogram\.png$/)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
817 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
818 $distri{$1} = ['','','','','',''] unless exists $distri{$1};
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
819 $distri{$1}->[5] = $tmp;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
820 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
821 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
822 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
823 return \%distri;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
824 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
825
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
826 sub PPPrint
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
827 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
828 my ($h, $hash) = @_;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
829 my $cmp = 0;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
830
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
831 print $h "<div class=\"container\">\n";
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
832 print $h "<div class=\"row text-center\">";
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
833 while ( my ($k,$v) = each %{$hash} )
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
834 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
835 print $h "</div><div class=\"row text-center\">" if $cmp != 0 && $cmp % 2 == 0;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
836 print $h "
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
837
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
838 <div class=\"span6\">
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
839 <h2>$k</h2>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
840 <p class=\"featurette-p\"> <img src=\"$v->[5]\"/></p>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
841 <p class=\"featurette-p\"><a href=\"$v->[4]\">ping pong signature</a></p>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
842 <p class=\"featurette-p\"><a href=\"$v->[2]\">sens reads with PPP</a></p>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
843 <p class=\"featurette-p\"><a href=\"$v->[3]\">reverse reads with PPP</a></p>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
844 <p class=\"featurette-p\"><a href=\"$v->[0]\">sens reads without PPP</a></p>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
845 <p class=\"featurette-p\"><a href=\"$v->[1]\">reverse reads without PPP</a></p>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
846 </div>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
847 ";
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
848 $cmp++;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
849 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
850
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
851 print $h "</div></div>";
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
852 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
853
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
854 sub printDistri
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
855 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
856 my ($h, $tab) = @_;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
857 my ($txt, $name);
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
858 my $cmp = 0;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
859 print $h "<div class=\"container\">\n";
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
860 print $h "<div class=\"row text-center\">";
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
861 foreach my $k (@{$tab})
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
862 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
863 if ($k =~ /(.*)-(.*)\.png$/)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
864 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
865 $txt = $1.'-'.$2.'.txt';
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
866 $name = $2;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
867 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
868 print $h "</div><div class=\"row text-center\">" if $cmp != 0 && $cmp % 2 == 0;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
869 print $h "
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
870
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
871 <div class=\"span6\">
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
872 <h2>$name</h2>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
873 <p> <img src=\"$k\"/></p>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
874 <p class=\"featurette-p\"><a href=\"$txt\">text file</a></p>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
875 </div>
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
876 ";
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
877 $cmp++;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
878 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
879
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
880 print $h "</div></div>";
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
881 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
882
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
883 sub mapnum
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
884 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
885 my $dupmapnum = shift;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
886 my $dupnum_genome = shift;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
887 open (my $dupTE, $dupmapnum) || die "cannot open ".$dupmapnum."\n";
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
888 my %dupnum_TE = ();
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
889 my $header = <$dupTE>;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
890 while (<$dupTE>)
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
891 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
892 chomp $_;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
893 my @dupline = split /\t/, $_;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
894 $dupnum_TE{$dupline[0]} = $dupline[2];
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
895 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
896 close $dupTE;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
897 open (my $du_TE, '>'.$dupmapnum) || die "cannot open to write ".$dupmapnum."\n";
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
898 print $du_TE "sequence\tduplicate\tgenome map num\tmap num\n";
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
899 while (my ($k, $v) = each %dupnum_TE )
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
900 {
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
901 my $hashRef = ${$dupnum_genome}{$k};
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
902 print $du_TE "$k\t$hashRef->[0]\t$hashRef->[1]\t$v\n";
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
903 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
904 close $du_TE;
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
905 }
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
906
1df6aaac800e Deleted selected files
brasset_jensen
parents:
diff changeset
907 1;