| Previous changeset 13:98b4a5ec8e63 (2017-10-16) Next changeset 15:16c3c1b0362a (2017-10-16) |
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Commit message:
Deleted selected files |
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removed:
bin/html.pm |
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| diff -r 98b4a5ec8e63 -r 8b7000eac6a0 bin/html.pm --- a/bin/html.pm Mon Oct 16 03:34:16 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,907 +0,0 @@\n-package html;\n-\n-use strict;\n-use warnings;\n-use File::Basename;\n-\n-use Exporter;\n-our @ISA = qw( Exporter );\n-our @EXPORT_OK = qw( &main_page &details_pages &menu_page &ppp_page );\n-\n-sub main_page\n-{\n-\tmy ( $dir, $file, $list_mainTabP, $current, $ma, $ma_uni, $dir_root ) = @_;\n-\tmy ( $futHashP, $uniqueTabP, $randTabP, $pngTabP ) = get_genome ( $dir, $dir_root );\n-\n-\topen my $h, \'>\', $file || die "cannot create $file $!\\n";\n-\theader ( $h );\n-\tnavbar ( $h, $list_mainTabP, $current );\n-\tprint $h "<div class=\\"container\\"><p><a class=\\"btn\\" href=\\"$current-sub.html\\">View details »</a></p></div>\\n";\n-\tfuturette( $h, $current, $pngTabP, $futHashP );\n-\tprint $h "<div class=\\"container\\"><h2>mappers #: $ma</h2><h2>unique mappers #: $ma_uni</h2> </div>\\n";\n-\tcarousel2( $h, $uniqueTabP, $randTabP, $dir_root );\n-\tfooter($h);\n-\tclose $h;\n-}\n-\n-sub menu_page\n-{\n-\tmy ( $dir, $file, $list_mainTabP, $current, $min, $max, $simin, $simax, $pimin, $pimax, $dir_root ) = @_;\n- my $html_ref = $1 if $dir =~ /$dir_root(.*)/;\n-\topen my $h, \'>\', $file || die "cannot create $file $!\\n";\n- header($h);\n- navbar ( $h, $list_mainTabP, $current );\n- span( $h, $current, $min, $max, $simin, $simax, $pimin, $pimax );\n- print $h " <div class=\\"container\\"> <div class=\\"row text-center\\"> <img src=\\"$html_ref/pie_chart.png\\"/><br />\\n";\n- print $h " <A HREF=\\"$html_ref/repartition.txt\\">text file</A><br/>\\n </div></div>";\n- footer($h);\n- close $h;\n-}\n-\n-sub details_pages\n-{\n-\tmy ( $dir_details, $prefix, $list_mainTabP, $current, $misTE, $dir_root ) = @_;\n- my ($Hex, $HTE, $HG, $NonUniTE, $NonUniG, $UniG ) = get_subgroups( $dir_details, $current, $misTE, $dir_root );\n-\n- my $html_ref = $1.\'-PPP.html\' if $prefix =~ /$dir_root(.*)/;\n- open my $h, \'>\', $prefix.\'-TEs.html\' || die "cannot create $prefix-TEs.html $!\\n";\n- header($h);\n- navbar ( $h, $list_mainTabP, $current );\n- if ( $prefix =~ /bonafide_reads$/ )\n- {\n- \tprint $h " <div class=\\"container\\">";\n- \tprint $h " <p><a class=\\"btn\\" href=\\"$html_ref\\">Ping Pong Partners</a></p>\\n";\n- \tprint $h "</div>";\n- }\n- fut($h,\'Transposable elements\',$HTE);\n- carousel($h,$NonUniTE,$dir_root);\n- footer($h);\n- close $h;\n-\n- open $h, \'>\', $prefix.\'-genome.html\' || die "cannot create $prefix-genome.html $!\\n";\n- header($h);\n- navbar ( $h, $list_mainTabP, $current );\n- fut($h,\'Genome\',$HG);\n- carousel2($h,$UniG, $NonUniG,$dir_root);\n- footer($h);\n- close $h;\n-\n- open $h, \'>\', $prefix.\'-exons.html\' || die "cannot create $prefix-exons.html $!\\n";\n- header($h);\n- navbar ( $h, $list_mainTabP, $current );\n- fut($h,\'Exons\',$Hex);\n- footer($h);\n- close $h;\n-}\n-\n-sub ppp_page\n-{\n-\tmy ( $dir, $file, $list_mainTabP, $current, $ppp, $dir_root ) = @_;\n-\n-\tmy $ppp_file = $ppp.\'ppp.txt\';\n-\topen my $h, \'>\', $file || die "cannot create $file $!\\n";\n-\theader($h);\n- \tnavbar ( $h, $list_mainTabP, $current );\n- \tprint $h \'<div class="container"> <table class="wb-tables table table-striped table-hover">\'."\\n";\n- \tprint $h \'<thead>\n- <tr>\n- <th data-sortable="true">ID</th>\n- <th data-sortable="true">overlap sum</th>\n- <th data-sortable="true">ten overlap sum</th>\n- <th data-sortable="true">mean</th>\n- <th data-sortable="true">standard deviation</th>\n- \t<th data-sortable="true">z-score</th>\n- \t<th data-sortable="true">p-value</th>\n-\t</tr>\n- </thead>\n- <tbody>\';\n-\n- \topen my $f, \'<\', $ppp_file || die "cannot open $ppp_file $!\\n";\n- \twhile ( <$f> )\n- \t{\n- \t\tchomp;\n- \t\tprint $h \'<tr>\';\n- \t\tmy ( $id, $sum, $ten, $mean, $sd, $zscore, $prob) = split /\\t/, $_;\n- \t\tif( -d "$ppp/$id" ) \n- \t\t{\n- \t\t\tmy $sub_html = $ppp.$id.\'.html\';\n- my $sub_html_ref = $1.$id if $ppp =~ /$dir_root(.*)/;\n- \t\t\tprint $h "<td> <a href=\\"$sub_html_ref.html\\">$id</a> </td>";\n-\n- \t\t\topen my $sub, \'>\', $sub_html || die "cannot create $sub_html\\n";\n- \t\t\t{\n- \t\t\t\theader($sub);\n- \t\t\t\tprint $sub "\n-\t\t\t\t\t<div align=\\"center\\">\n-\t\t\t\t\t<h2>$id</h2>\n-\t\t\t\t\t<p> <img src=\\"$id/histogram.png\\" wi'..b'stri_TE\n-{\n- my ($dir, $name) = @_;\n- my (@out,@group);\n- my $group = $dir.\'/\'.$name.\'-subgroups-bonafide_reads-TE-*distribution-*.png\';\n- @group = glob $group;\n- foreach (my $g =0; $g <= $#group; $g++)\n- {\n- if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-TE-.*distribution-.*\\.png)/ )\n- {\n- my $tmp = $1;\n- push @out, $1;\n- }\n- }\n- return (\\@out);\n-}\n-\n-sub get_PPP\n-{\n- my ($dir,$name) = @_;\n- my (%distri,@group);\n- my $group = $dir.\'/\'.$name.\'-subgroups-bonafide_reads-TE-PPPartners-*\';\n- @group = glob $group;\n- \n- foreach (my $g =0; $g <= $#group; $g++)\n- {\n- if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-TE-PPPartners-.*)/ )\n- {\n- my $tmp = $1;\n- if ($tmp =~ /PPPartners-(.*?)-sens\\.txt$/)\n- {\n- $distri{$1} = [\'\',\'\',\'\',\'\',\'\',\'\'] unless exists $distri{$1};\n- $distri{$1}->[0] = $tmp;\n- }\n- elsif ($tmp =~ /PPPartners-(.*?)-antisens\\.txt$/)\n- {\n- $distri{$1} = [\'\',\'\',\'\',\'\',\'\',\'\'] unless exists $distri{$1};\n- $distri{$1}->[1] = $tmp;\n- }\n- elsif ($tmp =~ /PPPartners-(.*?)-sensPPP\\.txt$/)\n- {\n- $distri{$1} = [\'\',\'\',\'\',\'\',\'\',\'\'] unless exists $distri{$1};\n- $distri{$1}->[2] = $tmp;\n- }\n- elsif ($tmp =~ /PPPartners-(.*?)-antisensPPP\\.txt$/)\n- {\n- $distri{$1} = [\'\',\'\',\'\',\'\',\'\',\'\'] unless exists $distri{$1};\n- $distri{$1}->[3] = $tmp;\n- }\n- elsif ($tmp =~ /PPPartners-(.*?)-overlap_size\\.txt$/)\n- {\n- $distri{$1} = [\'\',\'\',\'\',\'\',\'\',\'\'] unless exists $distri{$1};\n- $distri{$1}->[4] = $tmp;\n- }\n- elsif ($tmp =~ /PPPartners-(.*?)-histogram\\.png$/)\n- {\n- $distri{$1} = [\'\',\'\',\'\',\'\',\'\',\'\'] unless exists $distri{$1};\n- $distri{$1}->[5] = $tmp;\n- }\n- }\n- }\n- return \\%distri;\n-}\n-\n-sub PPPrint\n-{\n- my ($h, $hash) = @_;\n- my $cmp = 0;\n- \n- print $h "<div class=\\"container\\">\\n";\n- print $h "<div class=\\"row text-center\\">";\n- while ( my ($k,$v) = each %{$hash} )\n- {\n- print $h "</div><div class=\\"row text-center\\">" if $cmp != 0 && $cmp % 2 == 0;\n- print $h "\n- \n- <div class=\\"span6\\">\n- <h2>$k</h2>\n- <p class=\\"featurette-p\\"> <img src=\\"$v->[5]\\"/></p>\n- <p class=\\"featurette-p\\"><a href=\\"$v->[4]\\">ping pong signature</a></p>\n- <p class=\\"featurette-p\\"><a href=\\"$v->[2]\\">sens reads with PPP</a></p>\n- <p class=\\"featurette-p\\"><a href=\\"$v->[3]\\">reverse reads with PPP</a></p>\n- <p class=\\"featurette-p\\"><a href=\\"$v->[0]\\">sens reads without PPP</a></p>\n- <p class=\\"featurette-p\\"><a href=\\"$v->[1]\\">reverse reads without PPP</a></p>\n- </div>\n- ";\n- $cmp++;\n- }\n- \n- print $h "</div></div>";\n-}\n-\n-sub printDistri\n-{\n- my ($h, $tab) = @_;\n- my ($txt, $name);\n- my $cmp = 0;\n- print $h "<div class=\\"container\\">\\n";\n- print $h "<div class=\\"row text-center\\">";\n- foreach my $k (@{$tab})\n- {\n- if ($k =~ /(.*)-(.*)\\.png$/)\n- {\n- $txt = $1.\'-\'.$2.\'.txt\';\n- $name = $2;\n- }\n- print $h "</div><div class=\\"row text-center\\">" if $cmp != 0 && $cmp % 2 == 0;\n- print $h "\n- \n- <div class=\\"span6\\">\n- <h2>$name</h2>\n- <p> <img src=\\"$k\\"/></p>\n- <p class=\\"featurette-p\\"><a href=\\"$txt\\">text file</a></p>\n- </div>\n- ";\n- $cmp++;\n- }\n- \n- print $h "</div></div>";\n-}\n-\n-sub mapnum\n-{\n- my $dupmapnum = shift;\n- my $dupnum_genome = shift;\n- open (my $dupTE, $dupmapnum) || die "cannot open ".$dupmapnum."\\n";\n- my %dupnum_TE = ();\n- my $header = <$dupTE>;\n- while (<$dupTE>)\n- {\n- chomp $_;\n- my @dupline = split /\\t/, $_;\n- $dupnum_TE{$dupline[0]} = $dupline[2];\n- }\n- close $dupTE;\n- open (my $du_TE, \'>\'.$dupmapnum) || die "cannot open to write ".$dupmapnum."\\n";\n- print $du_TE "sequence\\tduplicate\\tgenome map num\\tmap num\\n";\n- while (my ($k, $v) = each %dupnum_TE )\n- {\n- my $hashRef = ${$dupnum_genome}{$k};\n- print $du_TE "$k\\t$hashRef->[0]\\t$hashRef->[1]\\t$v\\n";\n- }\n- close $du_TE;\n-}\n-\n-1;\n' |