| Previous changeset 63:11708af40030 (2019-01-24) Next changeset 65:0e9adbd82bb4 (2019-01-30) |
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Commit message:
planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d |
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modified:
README.rst bin/sRNAPipe.pl sRNAPipe.xml |
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added:
lib/sRNAPipe.pm lib/sRNAPipe/Rcall.pm lib/sRNAPipe/align.pm lib/sRNAPipe/css/bootstrap-responsive.css lib/sRNAPipe/css/bootstrap-table.css lib/sRNAPipe/css/bootstrap.css lib/sRNAPipe/html.pm lib/sRNAPipe/js/bootstrap-table.js lib/sRNAPipe/js/bootstrap.min.js lib/sRNAPipe/js/filter.js lib/sRNAPipe/js/jquery.galleriffic.js lib/sRNAPipe/js/jquery.js lib/sRNAPipe/js/jquery.opacityrollover.js lib/sRNAPipe/ppp.pm lib/sRNAPipe/resize.pm lib/sRNAPipe/subgroups.pm |
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removed:
bin/Rcall.pm bin/align.pm bin/css/bootstrap-responsive.css bin/css/bootstrap-table.css bin/css/bootstrap.css bin/html.pm bin/js/bootstrap-table.js bin/js/bootstrap.min.js bin/js/filter.js bin/js/jquery.galleriffic.js bin/js/jquery.js bin/js/jquery.opacityrollover.js bin/ppp.pm bin/resize.pm bin/subgroups.pm |
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| diff -r 11708af40030 -r 967512924317 README.rst --- a/README.rst Thu Jan 24 13:09:46 2019 -0500 +++ b/README.rst Mon Jan 28 11:57:15 2019 -0500 |
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| @@ -15,7 +15,7 @@ Prerequisites ============= -1. Unix system with A Galaxy server (release july 2014 or later installed) +1. Unix system with A Galaxy server (release 16.01 or later installed) 2. Some tools are used by sRNAPipe and must be installed and added to the Path. |
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| diff -r 11708af40030 -r 967512924317 bin/Rcall.pm --- a/bin/Rcall.pm Thu Jan 24 13:09:46 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,136 +0,0 @@ -package Rcall; - -use strict; -use warnings; -use Statistics::R; - -use Exporter; -our @ISA = qw(Exporter); -our @EXPORT_OK = qw( &histogram &pie_chart &bg_to_png ); - -sub histogram -{ - my ($size_hashR, $out_png, $size) = @_; - my (@abs, @ord); - my $i = 0; - foreach my $k (sort {$a <=> $b} keys %{$size_hashR}) - { - my $percentage = 0; - $percentage = $size_hashR->{$k} * 100 / $size if $size != 0; - $abs[$i] = $k ; $ord[$i] = $percentage; $i++; - } - my $abs = join (",", @abs ); - my $ord = join (",", @ord ); - if (scalar(@abs) != 0) - { - - my $R = Statistics::R->new(); - $R->startR; - $R->send( - qq`library(ggplot2) - percentage = c($ord) - size =c($abs) - min = min(size) - max = max(size) - dat = data.frame(size,percentage) - png(filename=\"$out_png\", width = 640, height = 640) - c = ggplot(dat,aes(size,percentage)) - c + geom_bar(stat="identity") + scale_x_continuous(breaks=min:max)+theme( axis.text.x = element_text(angle=90, hjust=0.5, size=20), axis.text.y = element_text( size=20 ), axis.title.x = element_text( size=25, face="bold"), axis.title.y = element_text( size=25, face="bold") ) - dev.off()`); - $R->stopR(); - - } -} - -sub bg_to_png -{ - my ( $fai, $bgP, $bgM, $dir, $sb ) = @_; - my $R = Statistics::R->new(); - $R->startR; - $R->send( - qq`library('Sushi') - fai =read.table("$fai") - if ( file.info("$bgP")\$size !=0 ) - { - bgP = read.table("$bgP") - } else { bgP = data.frame(factor(),integer()) } - - if ( file.info("$bgM")\$size !=0 ) - { - bgM = read.table("$bgM") - } else { bgM = data.frame(factor(),integer()) } - - f_both = function(chr,end) { - jpeg( paste0("$dir",as.character(chr),".png"), quality=100) - par(mfrow=c(2,1),mar=c(1,10,1,3)) - plotBedgraph(bgP, chrom=chr,chromstart=0,chromend=end,transparency=.50, color=SushiColors(2)(2)[1]) - axis(side=2,las=2,tcl=.2) - mtext("Scaled Read Depth",side=2,line=4,cex=1,font=2) - plotBedgraph(bgM, chrom=chr,chromstart=0,chromend=end,transparency=.50, flip=TRUE, color=SushiColors(2)(2)[2]) - labelgenome(chrom=chr,chromstart=0,chromend=end,side=3,n=3,scale="$sb", line=0, chromline = 0.5, scaleline = 0.5, scaleadjust =1.05, chromadjust = -0.4) - axis(side=2,las=2,tcl=.2,at=pretty(par("yaxp")[c(1,2)]),labels=-1*pretty(par("yaxp")[c(1,2)])) - mtext("Scaled Read Depth",side=2,line=4.5,cex=1,font=2) - dev.off() - } - - f_plus = function(chr,end) { - jpeg( paste0("$dir",as.character(chr),".png"), quality=100) - plotBedgraph(bgP, chrom=chr,chromstart=0,chromend=end,transparency=.50, color=SushiColors(2)(2)[1]) - labelgenome(chrom=chr,chromstart=0,chromend=end,n=3,scale="$sb", line=0, chromline = 0.5, scaleline = 0.5, scaleadjust =1.05, chromadjust = -0.4) - axis(side=2,las=2,tcl=.2) - mtext("Scaled Read Depth",side=2,line=4,cex=1,font=2) - dev.off() - } - - f_minus = function(chr,end) { - jpeg( paste0("$dir",as.character(chr),".png"), quality=100) - plotBedgraph(bgM, chrom=chr,chromstart=0,chromend=end,transparency=.50, flip=TRUE, color=SushiColors(2)(2)[2]) - labelgenome(chrom=chr,chromstart=0,chromend=end,n=3,scale="$sb", line=0, chromline = 0.5, scaleline = 0.5, scaleadjust =1.05, chromadjust = -0.4) - axis(side=2,las=2,tcl=.2,at=pretty(par("yaxp")[c(1,2)]),labels=-1*pretty(par("yaxp")[c(1,2)])) - mtext("Scaled Read Depth",side=2,line=4.5,cex=1,font=2) - dev.off() - } - - fai_b = fai[fai\$V1 %in% intersect(bgM\$V1,bgP\$V1), ] - mapply( f_both, fai_b\$V1, fai_b\$V2) - - fai_p = fai[fai\$V1 %in% setdiff(bgP\$V1,bgM\$V1), ] - mapply( f_plus, fai_p\$V1, fai_p\$V2) - - fai_m = fai[fai\$V1 %in% setdiff(bgM\$V1,bgP\$V1), ] - mapply( f_minus, fai_m\$V1, fai_m\$V2) `); - - $R->stopR(); -} - -sub pie_chart -{ - my $dir = shift; - my $in = $dir.'repartition.txt'; - my $out = $dir.'pie_chart.png'; - - my $R = Statistics::R->new(); - $R->startR; - $R->send( - qq` - library(plotrix) - library(RColorBrewer) - R =read.table("$in",header=T) - values = round(R\$percentage) - keys = R\$type - lab = paste(values, "%", sep="") - png("$out") - colors <- brewer.pal(7,"Paired") - pie(values, col=colors, labels=lab, clockwise=TRUE) - legend("bottom", legend = keys, fill=colors, bty="n", ncol = 3) - par(mai = c(0,0,0,0)) - layout(c(1,2),heights=c(0.3,1)) - plot.new() - legend("bottom", legend = keys, fill=colors, bty="n",ncol = 3) - pie(values, col=colors, labels=lab, clockwise=TRUE) - dev.off()` - ); - $R->stopR(); -} - -1; |
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| diff -r 11708af40030 -r 967512924317 bin/align.pm --- a/bin/align.pm Thu Jan 24 13:09:46 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,551 +0,0 @@\n-package align;\n-\n-use strict;\n-use warnings;\n-use File::Basename;\n-use String::Random;\n-\n-use FindBin;\n-use lib $FindBin::Bin;\n-use Rcall qw ( histogram );\n-\n-use Exporter;\n-our @ISA = qw( Exporter );\n-our @EXPORT = qw( &rpms_rpkm_te &BWA_call &to_build &get_unique &sam_sorted_bam &get_hash_alignment &sam_to_bam_bg &sam_count &sam_count_mis &rpms_rpkm &get_fastq_seq &extract_sam );\n-\n-sub to_build\n-{\n- my ( $toBuildTabP, $log, $newdir ) = @_;\n-\n- foreach my $pairs ( @{ $toBuildTabP } )\n- {\n- if ( $pairs->[0] == 1 )\n- {\n- my $sym = $newdir.basename(${$pairs->[1]}).\'_symlink.fa\';\n- symlink( ${$pairs->[1]}, $sym );\n- ${$pairs->[1]} = $sym;\n- build_index ( ${$pairs->[1]}, $log );\n- }\n- }\n-}\n-\n-sub build_index\n-{\n- my $to_index = shift;\n- my $log = shift;\n- my $index_log = $to_index.\'_index.err\';\n- `bwa index \'$to_index\' 2> \'$index_log\'`;\n- print $log "Creating index for $to_index\\n";\n-}\n-\n-sub get_unique\n-{\n- my ( $sam, $s_uni, $out_prefix, $col_prefix, $details, $report ) = @_;\n-\n- my $fout = $col_prefix.\'_all_mappers.fastq\';\n- my $funi = $col_prefix.\'_unique_mappers.fastq\';\n- my $frej = $col_prefix.\'_unmapped.fastq\';\n- \n- my $repartition = $out_prefix.\'distribution.txt\';\n- my $png_rep = $out_prefix.\'distribution.png\';\n- my ( %duplicates, %genome_hits) ;\n-\n- #alignement to the first reference\n- my @return = sam_parse( $sam, $fout, $funi, $frej, $s_uni, \\%duplicates, \\%genome_hits, $report );\n- my $ref_fai = $return[4];\n- my $mappers = $return[5];\n- my $mappers_uni = $return[6];\n- my $size_mappedHashR = $return[7];\n-\n- if ( $details == 1 )\n- {\n- #print number of duplicates and hits number\n- my ($pourcentage, $total) =(0,0);\n-\n- $total += $_ foreach values %{$size_mappedHashR};\n- open (my $rep, \'>\'.$repartition) || die "cannot create $repartition $!\\n";\n- print $rep "size\\tnumber\\tpercentage\\n";\n- foreach my $k (sort{$a cmp $b} keys (%{$size_mappedHashR}))\n- {\n- $pourcentage = 0;\n- $pourcentage = $size_mappedHashR->{$k} / $total * 100 unless $total ==0;\n-\n- print $rep "$k\\t$size_mappedHashR->{$k}\\t";\n- printf $rep "%.2f\\n",$pourcentage;\n- }\n-\n- histogram($size_mappedHashR, $png_rep, $total);\n-\n-\n- my $dup = $out_prefix.\'dup_mapnum.txt\';\n- my $dup_u = $out_prefix .\'dup_unique.txt\';\n- my $dup_r = $out_prefix .\'dup_nonmapp.txt\';\n- open(my $tab,">".$dup) || die "cannot open output txt file\\n";\n- open(my $tab_r,">".$dup_r) || die "cannot open output txt file\\n";\n- open(my $tab_u,">".$dup_u) || die "cannot open output txt file\\n";\n- print $tab "sequence\\tcount\\tmapnum\\n";\n- print $tab_u "sequence\\tcount\\n";\n- print $tab_r "sequence\\tcount\\n";\n- foreach my $k (sort {$duplicates{$b} <=> $duplicates{$a}}keys %duplicates)\n- {\n- $duplicates{$k} = 0 unless exists($duplicates{$k});\n- $genome_hits{$k} = 0 unless exists($genome_hits{$k});\n- if ($genome_hits{$k} != 0) { print $tab $k."\\t".$duplicates{$k}."\\t".$genome_hits{$k}."\\n"; }\n- else {print $tab_r $k."\\t".$duplicates{$k}."\\n";}\n- if ($genome_hits{$k} == 1) { print $tab_u $k."\\t".$duplicates{$k}."\\n"; }\n- }\n- close $dup; close $dup_r; close $dup_u;\n- }\n- return ( $ref_fai, $mappers, $mappers_uni );\n-}\n-\n-sub sam_parse\n-{\n- my ( $sam, $fastq_accepted, $fastq_accepted_unique, $fastq_rejected, $sam_unique, $duplicate_hashR, $best_hit_number_hashR, $report ) = @_ ;\n- my ($reads, $mappers, $mappersUnique, @garbage, %size_num, %size_num_spe, %number, %numberSens, %numberReverse, %unique_number, %numberNM, %numberM, %size);\n- $mappers = $mappersUnique = $reads = 0;\n-\n- open my $fic, \'<\', $sam || die "cannot open $sam $!\\n";\n- open my $accepted, \'>\', $fastq_'..b'> \'$samse_err\' > \'$sam\'\\n";\n- `bwa aln -t $number_of_cpus -n $mismatches \'$index\' \'$fastq\' 2> \'$aln_err\' | bwa samse $index /dev/stdin \'$fastq\' 2> \'$samse_err\' > \'$sam\' `;\n-}\n-\n-sub rpms_rpkm\n-{\n- my ( $counthashR, $sizehashR, $mapped, $out_file, $piRNA_number, $miRNA_number, $bonafide_number ) =@_;\n- open(my $out, ">".$out_file) || die "cannot open normalized file $! \\n";\n- print $out "ID\\treads counts\\tRPKM";\n- print $out "\\tper million of piRNAs" if ($piRNA_number != 0);\n- print $out "\\tper million of miRNAs" if ($miRNA_number != 0);\n- print $out "\\tper million of bonafide reads" if ($bonafide_number != 0);\n- print $out "\\n";\n- foreach my $k ( sort keys %{$counthashR} )\n- {\n- my ($rpkm, $pirna, $mirna, $bonafide) = (0,0,0,0);\n- \n- $rpkm = ( $counthashR->{$k} * 1000000000) / ( $sizehashR->{$k} * $mapped) if ( $sizehashR->{$k} * $mapped) != 0 ;\n- print $out $k."\\t".$counthashR->{$k}."\\t"; printf $out "%.2f",$rpkm;\n- \n- if ($piRNA_number != 0 )\n- {\n- $pirna = ( $counthashR->{$k} * 1000000) / $piRNA_number;\n- printf $out "\\t%.2f",$pirna;\n- }\n- if ($miRNA_number != 0 )\n- {\n- $mirna = ( $counthashR->{$k} * 1000000) / $miRNA_number;\n- printf $out "\\t%.2f",$mirna;\n- }\n- if ($bonafide_number != 0 )\n- {\n- $bonafide = ( $counthashR->{$k} * 1000000) / $bonafide_number;\n- printf $out "\\t%.2f",$bonafide;\n- }\n- print $out "\\n";\n- }\n- close $out;\n-}\n-\n-sub extract_sam\n-{\n- my ( $hashRef, $sam_in, $sam_out, $sam_uni_out, $fastq_out, $fastq_uni_out ) = @_;\n- \n- open my $s_in, \'<\', $sam_in || die "cannot open $sam_in file $!\\n";\n-\n- open my $f_out, \'>\', $fastq_out || die "cannot create $fastq_out $!\\n";\n- open my $f_uni_out, \'>\', $fastq_uni_out || die "cannot create $fastq_uni_out $!\\n";\n- \n- open my $s_out, \'>\', $sam_out || die "cannot create $sam_out file $!\\n" if defined ($hashRef);\n- open my $s_uni_out, \'>\', $sam_uni_out || die "cannot create $sam_uni_out file $!\\n";\n-\n- my $sequence = \'\';\n- while(<$s_in>)\n- {\n- if ($_ =~ /^\\@[A-Za-z][A-Za-z](\\t[A-Za-z][A-Za-z0-9]:[ -~]+)+$/ || $_ =~ /^\\@CO\\t.*/ )\n- {\n- print $s_out $_ if defined ($hashRef);\n- print $s_uni_out $_;\n- next;\n- }\n- my @line = split (/\\t/,$_);\n- $sequence = $line[0];\n- if ( (! defined ($hashRef) )|| ( exists $hashRef->{$sequence} && $hashRef->{$sequence} == 1 ) )\n- {\n- my $arn = $line[9];\n- if ($line[1] & 16)\n- {\n- $arn =reverse($arn);\n- $arn =~ tr/atgcuATGCU/tacgaTACGA/;\n- }\n-\n- if ( ( $line[1] == 16 || $line[1] == 0 ) )\n- {\n- print $f_out "\\@".$line[0]."\\n".$arn."\\n+\\n".$line[10]."\\n" ;\n- print $s_out $_ if defined ($hashRef);\n- if ( $line[11] eq "XT:A:U" )\n- {\n- print $f_uni_out "\\@".$line[0]."\\n".$arn."\\n+\\n".$line[10]."\\n" ;\n- print $s_uni_out $_ ;\n- }\n- }\n- }\n- }\n- close $s_in; close $s_out if defined ($hashRef);\n- close $s_uni_out; close $f_out; close $f_uni_out;\n-}\n-\n-sub get_fastq_seq\n-{\n- my $fastq = shift;\n- my %hash; my $cmp = 0;\n-\n- open my $fic, \'<\', $fastq || die "cannot open input file $! \\n";\n- while(<$fic>)\n- {\n- chomp $_;\n- $cmp++;\n- if ($cmp % 4 == 1)\n- {\n- die "file do not contain a @ at line $cmp\\n" unless ($_ =~ /^\\@/ );\n- if ($_ =~ /^\\@(.*)\\s.*/) { $hash{$1} = 1;}\n- elsif ($_ =~ /^\\@(.*)/) { $hash{$1} = 1;}\n- }\n- elsif ($cmp % 4 == 3 )\n- {\n- die "file do not contain a + at line $cmp\\n" unless $_ =~ /^\\+/;\n- }\n- }\n- close $fic;\n- return \\%hash;\n-}\n-\n-1;\n' |
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| diff -r 11708af40030 -r 967512924317 bin/css/bootstrap-responsive.css --- a/bin/css/bootstrap-responsive.css Thu Jan 24 13:09:46 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,1109 +0,0 @@\n-/*!\n- * Bootstrap Responsive v2.3.2\n- *\n- * Copyright 2012 Twitter, Inc\n- * Licensed under the Apache License v2.0\n- * http://www.apache.org/licenses/LICENSE-2.0\n- *\n- * Designed and built with all the love in the world @twitter by @mdo and @fat.\n- */\n-\n-.clearfix {\n- *zoom: 1;\n-}\n-\n-.clearfix:before,\n-.clearfix:after {\n- display: table;\n- line-height: 0;\n- content: "";\n-}\n-\n-.clearfix:after {\n- clear: both;\n-}\n-\n-.hide-text {\n- font: 0/0 a;\n- color: transparent;\n- text-shadow: none;\n- background-color: transparent;\n- border: 0;\n-}\n-\n-.input-block-level {\n- display: block;\n- width: 100%;\n- min-height: 30px;\n- -webkit-box-sizing: border-box;\n- -moz-box-sizing: border-box;\n- box-sizing: border-box;\n-}\n-\n-@-ms-viewport {\n- width: device-width;\n-}\n-\n-.hidden {\n- display: none;\n- visibility: hidden;\n-}\n-\n-.visible-phone {\n- display: none !important;\n-}\n-\n-.visible-tablet {\n- display: none !important;\n-}\n-\n-.hidden-desktop {\n- display: none !important;\n-}\n-\n-.visible-desktop {\n- display: inherit !important;\n-}\n-\n-@media (min-width: 768px) and (max-width: 979px) {\n- .hidden-desktop {\n- display: inherit !important;\n- }\n- .visible-desktop {\n- display: none !important ;\n- }\n- .visible-tablet {\n- display: inherit !important;\n- }\n- .hidden-tablet {\n- display: none !important;\n- }\n-}\n-\n-@media (max-width: 767px) {\n- .hidden-desktop {\n- display: inherit !important;\n- }\n- .visible-desktop {\n- display: none !important;\n- }\n- .visible-phone {\n- display: inherit !important;\n- }\n- .hidden-phone {\n- display: none !important;\n- }\n-}\n-\n-.visible-print {\n- display: none !important;\n-}\n-\n-@media print {\n- .visible-print {\n- display: inherit !important;\n- }\n- .hidden-print {\n- display: none !important;\n- }\n-}\n-\n-@media (min-width: 1200px) {\n- .row {\n- margin-left: -30px;\n- *zoom: 1;\n- }\n- .row:before,\n- .row:after {\n- display: table;\n- line-height: 0;\n- content: "";\n- }\n- .row:after {\n- clear: both;\n- }\n- [class*="span"] {\n- float: left;\n- min-height: 1px;\n- margin-left: 30px;\n- }\n- .container,\n- .navbar-static-top .container,\n- .navbar-fixed-top .container,\n- .navbar-fixed-bottom .container {\n- width: 1170px;\n- }\n- .span12 {\n- width: 1170px;\n- }\n- .span11 {\n- width: 1070px;\n- }\n- .span10 {\n- width: 970px;\n- }\n- .span9 {\n- width: 870px;\n- }\n- .span8 {\n- width: 770px;\n- }\n- .span7 {\n- width: 670px;\n- }\n- .span6 {\n- width: 570px;\n- }\n- .span5 {\n- width: 470px;\n- }\n- .span4 {\n- width: 370px;\n- }\n- .span3 {\n- width: 270px;\n- }\n- .span2 {\n- width: 170px;\n- }\n- .span1 {\n- width: 70px;\n- }\n- .offset12 {\n- margin-left: 1230px;\n- }\n- .offset11 {\n- margin-left: 1130px;\n- }\n- .offset10 {\n- margin-left: 1030px;\n- }\n- .offset9 {\n- margin-left: 930px;\n- }\n- .offset8 {\n- margin-left: 830px;\n- }\n- .offset7 {\n- margin-left: 730px;\n- }\n- .offset6 {\n- margin-left: 630px;\n- }\n- .offset5 {\n- margin-left: 530px;\n- }\n- .offset4 {\n- margin-left: 430px;\n- }\n- .offset3 {\n- margin-left: 330px;\n- }\n- .offset2 {\n- margin-left: 230px;\n- }\n- .offset1 {\n- margin-left: 130px;\n- }\n- .row-fluid {\n- width: 100%;\n- *zoom: 1;\n- }\n- .row-fluid:before,\n- .row-fluid:after {\n- display: table;\n- line-height: 0;\n- content: "";\n- }\n- .row-fluid:after {\n- clear: both;\n- }\n- .row-fluid [class*="span"] {\n- display: block;\n- float: left;\n- width: 100%;\n- min-height: 30px;\n- margin-left: 2.564102564102564%;\n- *margin-left: 2.5109110747408616%;\n- -webkit-box-sizing: border-box;\n- -moz-box-sizing: border-box;\n- box-sizing: border-box;\n- }\n- .row-fluid [class*="span"]:first-child {\n- margin-left: 0;\n- }\n- .row-fluid .controls-row [class*="span"] + [class*="span"] {\n- margin-left: 2.564102564102564%;\n- }\n- .row-fluid .span12 {\n- width: 100%;\n- *width: 99.9468'..b'tic;\n- }\n-}\n-\n-@media (max-width: 979px) {\n- body {\n- padding-top: 0;\n- }\n- .navbar-fixed-top,\n- .navbar-fixed-bottom {\n- position: static;\n- }\n- .navbar-fixed-top {\n- margin-bottom: 20px;\n- }\n- .navbar-fixed-bottom {\n- margin-top: 20px;\n- }\n- .navbar-fixed-top .navbar-inner,\n- .navbar-fixed-bottom .navbar-inner {\n- padding: 5px;\n- }\n- .navbar .container {\n- width: auto;\n- padding: 0;\n- }\n- .navbar .brand {\n- padding-right: 10px;\n- padding-left: 10px;\n- margin: 0 0 0 -5px;\n- }\n- .nav-collapse {\n- clear: both;\n- }\n- .nav-collapse .nav {\n- float: none;\n- margin: 0 0 10px;\n- }\n- .nav-collapse .nav > li {\n- float: none;\n- }\n- .nav-collapse .nav > li > a {\n- margin-bottom: 2px;\n- }\n- .nav-collapse .nav > .divider-vertical {\n- display: none;\n- }\n- .nav-collapse .nav .nav-header {\n- color: #777777;\n- text-shadow: none;\n- }\n- .nav-collapse .nav > li > a,\n- .nav-collapse .dropdown-menu a {\n- padding: 9px 15px;\n- font-weight: bold;\n- color: #777777;\n- -webkit-border-radius: 3px;\n- -moz-border-radius: 3px;\n- border-radius: 3px;\n- }\n- .nav-collapse .btn {\n- padding: 4px 10px 4px;\n- font-weight: normal;\n- -webkit-border-radius: 4px;\n- -moz-border-radius: 4px;\n- border-radius: 4px;\n- }\n- .nav-collapse .dropdown-menu li + li a {\n- margin-bottom: 2px;\n- }\n- .nav-collapse .nav > li > a:hover,\n- .nav-collapse .nav > li > a:focus,\n- .nav-collapse .dropdown-menu a:hover,\n- .nav-collapse .dropdown-menu a:focus {\n- background-color: #f2f2f2;\n- }\n- .navbar-inverse .nav-collapse .nav > li > a,\n- .navbar-inverse .nav-collapse .dropdown-menu a {\n- color: #999999;\n- }\n- .navbar-inverse .nav-collapse .nav > li > a:hover,\n- .navbar-inverse .nav-collapse .nav > li > a:focus,\n- .navbar-inverse .nav-collapse .dropdown-menu a:hover,\n- .navbar-inverse .nav-collapse .dropdown-menu a:focus {\n- background-color: #111111;\n- }\n- .nav-collapse.in .btn-group {\n- padding: 0;\n- margin-top: 5px;\n- }\n- .nav-collapse .dropdown-menu {\n- position: static;\n- top: auto;\n- left: auto;\n- display: none;\n- float: none;\n- max-width: none;\n- padding: 0;\n- margin: 0 15px;\n- background-color: transparent;\n- border: none;\n- -webkit-border-radius: 0;\n- -moz-border-radius: 0;\n- border-radius: 0;\n- -webkit-box-shadow: none;\n- -moz-box-shadow: none;\n- box-shadow: none;\n- }\n- .nav-collapse .open > .dropdown-menu {\n- display: block;\n- }\n- .nav-collapse .dropdown-menu:before,\n- .nav-collapse .dropdown-menu:after {\n- display: none;\n- }\n- .nav-collapse .dropdown-menu .divider {\n- display: none;\n- }\n- .nav-collapse .nav > li > .dropdown-menu:before,\n- .nav-collapse .nav > li > .dropdown-menu:after {\n- display: none;\n- }\n- .nav-collapse .navbar-form,\n- .nav-collapse .navbar-search {\n- float: none;\n- padding: 10px 15px;\n- margin: 10px 0;\n- border-top: 1px solid #f2f2f2;\n- border-bottom: 1px solid #f2f2f2;\n- -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.1), 0 1px 0 rgba(255, 255, 255, 0.1);\n- -moz-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.1), 0 1px 0 rgba(255, 255, 255, 0.1);\n- box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.1), 0 1px 0 rgba(255, 255, 255, 0.1);\n- }\n- .navbar-inverse .nav-collapse .navbar-form,\n- .navbar-inverse .nav-collapse .navbar-search {\n- border-top-color: #111111;\n- border-bottom-color: #111111;\n- }\n- .navbar .nav-collapse .nav.pull-right {\n- float: none;\n- margin-left: 0;\n- }\n- .nav-collapse,\n- .nav-collapse.collapse {\n- height: 0;\n- overflow: hidden;\n- }\n- .navbar .btn-navbar {\n- display: block;\n- }\n- .navbar-static .navbar-inner {\n- padding-right: 10px;\n- padding-left: 10px;\n- }\n-}\n-\n-@media (min-width: 980px) {\n- .nav-collapse.collapse {\n- height: auto !important;\n- overflow: visible !important;\n- }\n-}\n' |
| b |
| diff -r 11708af40030 -r 967512924317 bin/css/bootstrap-table.css --- a/bin/css/bootstrap-table.css Thu Jan 24 13:09:46 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,313 +0,0 @@ -/** - * @author zhixin wen <wenzhixin2010@gmail.com> - * version: 1.11.1 - * https://github.com/wenzhixin/bootstrap-table/ - */ - -.bootstrap-table .table { - margin-bottom: 0 !important; - border-bottom: 1px solid #dddddd; - border-collapse: collapse !important; - border-radius: 1px; -} - -.bootstrap-table .table:not(.table-condensed), -.bootstrap-table .table:not(.table-condensed) > tbody > tr > th, -.bootstrap-table .table:not(.table-condensed) > tfoot > tr > th, -.bootstrap-table .table:not(.table-condensed) > thead > tr > td, -.bootstrap-table .table:not(.table-condensed) > tbody > tr > td, -.bootstrap-table .table:not(.table-condensed) > tfoot > tr > td { - padding: 8px; -} - -.bootstrap-table .table.table-no-bordered > thead > tr > th, -.bootstrap-table .table.table-no-bordered > tbody > tr > td { - border-right: 2px solid transparent; -} - -.bootstrap-table .table.table-no-bordered > tbody > tr > td:last-child { - border-right: none; -} - -.fixed-table-container { - position: relative; - clear: both; - border: 1px solid #dddddd; - border-radius: 4px; - -webkit-border-radius: 4px; - -moz-border-radius: 4px; -} - -.fixed-table-container.table-no-bordered { - border: 1px solid transparent; -} - -.fixed-table-footer, -.fixed-table-header { - overflow: hidden; -} - -.fixed-table-footer { - border-top: 1px solid #dddddd; -} - -.fixed-table-body { - overflow-x: auto; - overflow-y: auto; - height: 100%; -} - -.fixed-table-container table { - width: 100%; -} - -.fixed-table-container thead th { - height: 0; - padding: 0; - margin: 0; - border-left: 1px solid #dddddd; -} - -.fixed-table-container thead th:focus { - outline: 0 solid transparent; -} - -.fixed-table-container thead th:first-child { - border-left: none; - border-top-left-radius: 4px; - -webkit-border-top-left-radius: 4px; - -moz-border-radius-topleft: 4px; -} - -.fixed-table-container thead th .th-inner, -.fixed-table-container tbody td .th-inner { - padding: 8px; - line-height: 24px; - vertical-align: top; - overflow: hidden; - text-overflow: ellipsis; - white-space: nowrap; -} - -.fixed-table-container thead th .sortable { - cursor: pointer; - background-position: right; - background-repeat: no-repeat; - padding-right: 30px; -} - -.fixed-table-container thead th .both { - background-image: url('data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABMAAAATCAQAAADYWf5HAAAAkElEQVQoz7X QMQ5AQBCF4dWQSJxC5wwax1Cq1e7BAdxD5SL+Tq/QCM1oNiJidwox0355mXnG/DrEtIQ6azioNZQxI0ykPhTQIwhCR+BmBYtlK7kLJYwWCcJA9M4qdrZrd8pPjZWPtOqdRQy320YSV17OatFC4euts6z39GYMKRPCTKY9UnPQ6P+GtMRfGtPnBCiqhAeJPmkqAAAAAElFTkSuQmCC'); -} - -.fixed-table-container thead th .asc { - background-image: url('data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABMAAAATCAYAAAByUDbMAAAAZ0lEQVQ4y2NgGLKgquEuFxBPAGI2ahhWCsS/gDibUoO0gPgxEP8H4ttArEyuQYxAPBdqEAxPBImTY5gjEL9DM+wTENuQahAvEO9DMwiGdwAxOymGJQLxTyD+jgWDxCMZRsEoGAVoAADeemwtPcZI2wAAAABJRU5ErkJggg=='); -} - -.fixed-table-container thead th .desc { - background-image: url('data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABMAAAATCAYAAAByUDbMAAAAZUlEQVQ4y2NgGAWjYBSggaqGu5FA/BOIv2PBIPFEUgxjB+IdQPwfC94HxLykus4GiD+hGfQOiB3J8SojEE9EM2wuSJzcsFMG4ttQgx4DsRalkZENxL+AuJQaMcsGxBOAmGvopk8AVz1sLZgg0bsAAAAASUVORK5CYII= '); -} - -.fixed-table-container th.detail { - width: 30px; -} - -.fixed-table-container tbody td { - border-left: 1px solid #dddddd; -} - -.fixed-table-container tbody tr:first-child td { - border-top: none; -} - -.fixed-table-container tbody td:first-child { - border-left: none; -} - -/* the same color with .active */ -.fixed-table-container tbody .selected td { - background-color: #f5f5f5; -} - -.fixed-table-container .bs-checkbox { - text-align: center; -} - -.fixed-table-container .bs-checkbox .th-inner { - padding: 8px 0; -} - -.fixed-table-container input[type="radio"], -.fixed-table-container input[type="checkbox"] { - margin: 0 auto !important; -} - -.fixed-table-container .no-records-found { - text-align: center; -} - -.fixed-table-pagination div.pagination, -.fixed-table-pagination .pagination-detail { - margin-top: 10px; - margin-bottom: 10px; -} - -.fixed-table-pagination div.pagination .pagination { - margin: 0; -} - -.fixed-table-pagination .pagination a { - padding: 6px 12px; - line-height: 1.428571429; -} - -.fixed-table-pagination .pagination-info { - line-height: 34px; - margin-right: 5px; -} - -.fixed-table-pagination .btn-group { - position: relative; - display: inline-block; - vertical-align: middle; -} - -.fixed-table-pagination .dropup .dropdown-menu { - margin-bottom: 0; -} - -.fixed-table-pagination .page-list { - display: inline-block; -} - -.fixed-table-toolbar .columns-left { - margin-right: 5px; -} - -.fixed-table-toolbar .columns-right { - margin-left: 5px; -} - -.fixed-table-toolbar .columns label { - display: block; - padding: 3px 20px; - clear: both; - font-weight: normal; - line-height: 1.428571429; -} - -.fixed-table-toolbar .bs-bars, -.fixed-table-toolbar .search, -.fixed-table-toolbar .columns { - position: relative; - margin-top: 10px; - margin-bottom: 10px; - line-height: 34px; -} - -.fixed-table-pagination li.disabled a { - pointer-events: none; - cursor: default; -} - -.fixed-table-loading { - display: none; - position: absolute; - top: 42px; - right: 0; - bottom: 0; - left: 0; - z-index: 99; - background-color: #fff; - text-align: center; -} - -.fixed-table-body .card-view .title { - font-weight: bold; - display: inline-block; - min-width: 30%; - text-align: left !important; -} - -/* support bootstrap 2 */ -.fixed-table-body thead th .th-inner { - box-sizing: border-box; -} - -.table th, .table td { - vertical-align: middle; - box-sizing: border-box; -} - -.fixed-table-toolbar .dropdown-menu { - text-align: left; - max-height: 300px; - overflow: auto; -} - -.fixed-table-toolbar .btn-group > .btn-group { - display: inline-block; - margin-left: -1px !important; -} - -.fixed-table-toolbar .btn-group > .btn-group > .btn { - border-radius: 0; -} - -.fixed-table-toolbar .btn-group > .btn-group:first-child > .btn { - border-top-left-radius: 4px; - border-bottom-left-radius: 4px; -} - -.fixed-table-toolbar .btn-group > .btn-group:last-child > .btn { - border-top-right-radius: 4px; - border-bottom-right-radius: 4px; -} - -.bootstrap-table .table > thead > tr > th { - vertical-align: bottom; - border-bottom: 1px solid #ddd; -} - -/* support bootstrap 3 */ -.bootstrap-table .table thead > tr > th { - padding: 0; - margin: 0; -} - -.bootstrap-table .fixed-table-footer tbody > tr > td { - padding: 0 !important; -} - -.bootstrap-table .fixed-table-footer .table { - border-bottom: none; - border-radius: 0; - padding: 0 !important; -} - -.bootstrap-table .pull-right .dropdown-menu { - right: 0; - left: auto; -} - -/* calculate scrollbar width */ -p.fixed-table-scroll-inner { - width: 100%; - height: 200px; -} - -div.fixed-table-scroll-outer { - top: 0; - left: 0; - visibility: hidden; - width: 200px; - height: 150px; - overflow: hidden; -} - -/* for get correct heights */ -.fixed-table-toolbar:after, .fixed-table-pagination:after { - content: ""; - display: block; - clear: both; -} |
| b |
| diff -r 11708af40030 -r 967512924317 bin/css/bootstrap.css --- a/bin/css/bootstrap.css Thu Jan 24 13:09:46 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,6167 +0,0 @@\n-/*!\n- * Bootstrap v2.3.2\n- *\n- * Copyright 2012 Twitter, Inc\n- * Licensed under the Apache License v2.0\n- * http://www.apache.org/licenses/LICENSE-2.0\n- *\n- * Designed and built with all the love in the world @twitter by @mdo and @fat.\n- */\n-\n-.clearfix {\n- *zoom: 1;\n-}\n-\n-.clearfix:before,\n-.clearfix:after {\n- display: table;\n- line-height: 0;\n- content: "";\n-}\n-\n-.clearfix:after {\n- clear: both;\n-}\n-\n-.hide-text {\n- font: 0/0 a;\n- color: transparent;\n- text-shadow: none;\n- background-color: transparent;\n- border: 0;\n-}\n-\n-.input-block-level {\n- display: block;\n- width: 100%;\n- min-height: 30px;\n- -webkit-box-sizing: border-box;\n- -moz-box-sizing: border-box;\n- box-sizing: border-box;\n-}\n-\n-article,\n-aside,\n-details,\n-figcaption,\n-figure,\n-footer,\n-header,\n-hgroup,\n-nav,\n-section {\n- display: block;\n-}\n-\n-audio,\n-canvas,\n-video {\n- display: inline-block;\n- *display: inline;\n- *zoom: 1;\n-}\n-\n-audio:not([controls]) {\n- display: none;\n-}\n-\n-html {\n- font-size: 100%;\n- -webkit-text-size-adjust: 100%;\n- -ms-text-size-adjust: 100%;\n-}\n-\n-a:focus {\n- outline: thin dotted #333;\n- outline: 5px auto -webkit-focus-ring-color;\n- outline-offset: -2px;\n-}\n-\n-a:hover,\n-a:active {\n- outline: 0;\n-}\n-\n-sub,\n-sup {\n- position: relative;\n- font-size: 75%;\n- line-height: 0;\n- vertical-align: baseline;\n-}\n-\n-sup {\n- top: -0.5em;\n-}\n-\n-sub {\n- bottom: -0.25em;\n-}\n-\n-img {\n- width: auto\\9;\n- height: auto;\n- max-width: 100%;\n- vertical-align: middle;\n- border: 0;\n- -ms-interpolation-mode: bicubic;\n-}\n-\n-#map_canvas img,\n-.google-maps img {\n- max-width: none;\n-}\n-\n-button,\n-input,\n-select,\n-textarea {\n- margin: 0;\n- font-size: 100%;\n- vertical-align: middle;\n-}\n-\n-button,\n-input {\n- *overflow: visible;\n- line-height: normal;\n-}\n-\n-button::-moz-focus-inner,\n-input::-moz-focus-inner {\n- padding: 0;\n- border: 0;\n-}\n-\n-button,\n-html input[type="button"],\n-input[type="reset"],\n-input[type="submit"] {\n- cursor: pointer;\n- -webkit-appearance: button;\n-}\n-\n-label,\n-select,\n-button,\n-input[type="button"],\n-input[type="reset"],\n-input[type="submit"],\n-input[type="radio"],\n-input[type="checkbox"] {\n- cursor: pointer;\n-}\n-\n-input[type="search"] {\n- -webkit-box-sizing: content-box;\n- -moz-box-sizing: content-box;\n- box-sizing: content-box;\n- -webkit-appearance: textfield;\n-}\n-\n-input[type="search"]::-webkit-search-decoration,\n-input[type="search"]::-webkit-search-cancel-button {\n- -webkit-appearance: none;\n-}\n-\n-textarea {\n- overflow: auto;\n- vertical-align: top;\n-}\n-\n-@media print {\n- * {\n- color: #000 !important;\n- text-shadow: none !important;\n- background: transparent !important;\n- box-shadow: none !important;\n- }\n- a,\n- a:visited {\n- text-decoration: underline;\n- }\n- a[href]:after {\n- content: " (" attr(href) ")";\n- }\n- abbr[title]:after {\n- content: " (" attr(title) ")";\n- }\n- .ir a:after,\n- a[href^="javascript:"]:after,\n- a[href^="#"]:after {\n- content: "";\n- }\n- pre,\n- blockquote {\n- border: 1px solid #999;\n- page-break-inside: avoid;\n- }\n- thead {\n- display: table-header-group;\n- }\n- tr,\n- img {\n- page-break-inside: avoid;\n- }\n- img {\n- max-width: 100% !important;\n- }\n- @page {\n- margin: 0.5cm;\n- }\n- p,\n- h2,\n- h3 {\n- orphans: 3;\n- widows: 3;\n- }\n- h2,\n- h3 {\n- page-break-after: avoid;\n- }\n-}\n-\n-body {\n- margin: 0;\n- font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;\n- font-size: 14px;\n- line-height: 20px;\n- color: #333333;\n- background-color: #ffffff;\n-}\n-\n-a {\n- color: #0088cc;\n- text-decoration: none;\n-}\n-\n-a:hover,\n-a:focus {\n- color: #005580;\n- text-decoration: underline;\n-}\n-\n-.img-rounded {\n- -webkit-border-radius: 6px;\n- -moz-border-radius: 6px;\n- border-radius: 6px;\n-}\n-\n-.img-polaroid {\n- padding: 4px;\n- background-color: #fff;\n- border: 1px solid #ccc;\n- border: 1px solid rgba(0, 0, 0, 0.2);\n- -webkit-box-shadow: 0 1px 3'..b', 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);\n- background-image: linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);\n-}\n-\n-.accordion {\n- margin-bottom: 20px;\n-}\n-\n-.accordion-group {\n- margin-bottom: 2px;\n- border: 1px solid #e5e5e5;\n- -webkit-border-radius: 4px;\n- -moz-border-radius: 4px;\n- border-radius: 4px;\n-}\n-\n-.accordion-heading {\n- border-bottom: 0;\n-}\n-\n-.accordion-heading .accordion-toggle {\n- display: block;\n- padding: 8px 15px;\n-}\n-\n-.accordion-toggle {\n- cursor: pointer;\n-}\n-\n-.accordion-inner {\n- padding: 9px 15px;\n- border-top: 1px solid #e5e5e5;\n-}\n-\n-.carousel {\n- position: relative;\n- margin-bottom: 20px;\n- line-height: 1;\n-}\n-\n-.carousel-inner {\n- position: relative;\n- width: 100%;\n- overflow: hidden;\n-}\n-\n-.carousel-inner > .item {\n- position: relative;\n- display: none;\n- -webkit-transition: 0.6s ease-in-out left;\n- -moz-transition: 0.6s ease-in-out left;\n- -o-transition: 0.6s ease-in-out left;\n- transition: 0.6s ease-in-out left;\n-}\n-\n-.carousel-inner > .item > img,\n-.carousel-inner > .item > a > img {\n- display: block;\n- line-height: 1;\n-}\n-\n-.carousel-inner > .active,\n-.carousel-inner > .next,\n-.carousel-inner > .prev {\n- display: block;\n-}\n-\n-.carousel-inner > .active {\n- left: 0;\n-}\n-\n-.carousel-inner > .next,\n-.carousel-inner > .prev {\n- position: absolute;\n- top: 0;\n- width: 100%;\n-}\n-\n-.carousel-inner > .next {\n- left: 100%;\n-}\n-\n-.carousel-inner > .prev {\n- left: -100%;\n-}\n-\n-.carousel-inner > .next.left,\n-.carousel-inner > .prev.right {\n- left: 0;\n-}\n-\n-.carousel-inner > .active.left {\n- left: -100%;\n-}\n-\n-.carousel-inner > .active.right {\n- left: 100%;\n-}\n-\n-.carousel-control {\n- position: absolute;\n- top: 40%;\n- left: 15px;\n- width: 40px;\n- height: 40px;\n- margin-top: -20px;\n- font-size: 60px;\n- font-weight: 100;\n- line-height: 30px;\n- color: #ffffff;\n- text-align: center;\n- background: #222222;\n- border: 3px solid #ffffff;\n- -webkit-border-radius: 23px;\n- -moz-border-radius: 23px;\n- border-radius: 23px;\n- opacity: 0.5;\n- filter: alpha(opacity=50);\n-}\n-\n-.carousel-control.right {\n- right: 15px;\n- left: auto;\n-}\n-\n-.carousel-control:hover,\n-.carousel-control:focus {\n- color: #ffffff;\n- text-decoration: none;\n- opacity: 0.9;\n- filter: alpha(opacity=90);\n-}\n-\n-.carousel-indicators {\n- position: absolute;\n- top: 15px;\n- right: 15px;\n- z-index: 5;\n- margin: 0;\n- list-style: none;\n-}\n-\n-.carousel-indicators li {\n- display: block;\n- float: left;\n- width: 10px;\n- height: 10px;\n- margin-left: 5px;\n- text-indent: -999px;\n- background-color: #ccc;\n- background-color: rgba(255, 255, 255, 0.25);\n- border-radius: 5px;\n-}\n-\n-.carousel-indicators .active {\n- background-color: #fff;\n-}\n-\n-.carousel-caption {\n- position: absolute;\n- right: 0;\n- bottom: 0;\n- left: 0;\n- padding: 15px;\n- background: #333333;\n- background: rgba(0, 0, 0, 0.75);\n-}\n-\n-.carousel-caption h4,\n-.carousel-caption p {\n- line-height: 20px;\n- color: #ffffff;\n-}\n-\n-.carousel-caption h4 {\n- margin: 0 0 5px;\n-}\n-\n-.carousel-caption p {\n- margin-bottom: 0;\n-}\n-\n-.hero-unit {\n- padding: 60px;\n- margin-bottom: 30px;\n- font-size: 18px;\n- font-weight: 200;\n- line-height: 30px;\n- color: inherit;\n- background-color: #eeeeee;\n- -webkit-border-radius: 6px;\n- -moz-border-radius: 6px;\n- border-radius: 6px;\n-}\n-\n-.hero-unit h1 {\n- margin-bottom: 0;\n- font-size: 60px;\n- line-height: 1;\n- letter-spacing: -1px;\n- color: inherit;\n-}\n-\n-.hero-unit li {\n- line-height: 30px;\n-}\n-\n-.pull-right {\n- float: right;\n-}\n-\n-.pull-left {\n- float: left;\n-}\n-\n-.hide {\n- display: none;\n-}\n-\n-.show {\n- display: block;\n-}\n-\n-.invisible {\n- visibility: hidden;\n-}\n-\n-.affix {\n- position: fixed;\n-}\n' |
| b |
| diff -r 11708af40030 -r 967512924317 bin/html.pm --- a/bin/html.pm Thu Jan 24 13:09:46 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,910 +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- my ( $dir, $file, $list_mainTabP, $current, $ma, $ma_uni, $dir_root ) = @_;\n- my ( $futHashP, $uniqueTabP, $randTabP, $pngTabP ) = get_genome ( $dir, $dir_root );\n-\n- open my $h, \'>\', $file || die "cannot create $file $!\\n";\n- header ( $h );\n- navbar ( $h, $list_mainTabP, $current );\n- print $h "<div class=\\"container\\"><p><a class=\\"btn\\" href=\\"$current-sub.html\\">View details »</a></p></div>\\n";\n- futurette( $h, $current, $pngTabP, $futHashP );\n- print $h "<div class=\\"container\\"><h2>mappers #: $ma</h2><h2>unique mappers #: $ma_uni</h2> </div>\\n";\n- carousel2( $h, $uniqueTabP, $randTabP, $dir_root );\n- footer($h);\n- close $h;\n-}\n-\n-sub menu_page\n-{\n- my ( $dir, $file, $list_mainTabP, $current, $min, $max, $simin, $simax, $pimin, $pimax, $dir_root ) = @_;\n- my $html_ref = $1 if $dir =~ /$dir_root(.*)/;\n- open 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- my ( $dir_details, $prefix, $list_mainTabP, $current, $misTE, $dir_root, $ppp ) = @_;\n- my ($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 ( $prefix =~ /piRNAs$/ && $ppp eq \'true\' )\n- {\n- print $h " <div class=\\"container\\">";\n- print $h " <p><a class=\\"btn\\" href=\\"$html_ref\\">Ping Pong Partners</a></p>\\n";\n- print $h "</div>";\n- }\n- fut($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.\'-transcripts.html\' || die "cannot create $prefix-transcripts.html $!\\n";\n- header($h);\n- navbar ( $h, $list_mainTabP, $current );\n- fut($h,\'transcripts\',$Hex);\n- footer($h);\n- close $h;\n-}\n-\n-sub ppp_page\n-{\n- my ( $dir, $file, $list_mainTabP, $current, $ppp, $dir_root ) = @_;\n-\n- my $ppp_file = $ppp.\'ppp.txt\';\n- open my $h, \'>\', $file || die "cannot create $file $!\\n";\n- header($h);\n- navbar ( $h, $list_mainTabP, $current );\n- print $h \'<div class="container"> <table class="wb-tables table table-striped table-hover">\'."\\n";\n- print $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- open my $f, \'<\', $ppp_file || die "cannot open $ppp_file $!\\n";\n- while ( <$f> )\n- {\n- chomp;\n- print $h \'<tr>\';\n- my ( $id, $sum, $ten, $mean, $sd, $zscore, $prob) = split /\\t/, $_;\n- if( -d "$ppp/$id" )\n- {\n- my $sub_html = $ppp.$id.\'.html\';\n- my $sub_html_ref = $1.$id if $ppp =~ /$dir_root(.*)/;\n- print $h "<td> <a href=\\"$sub_html_ref.html\\">$id</a> </td>";\n-\n- open my $sub, \'>\', $sub_html || die "cannot create $sub_html\\n";\n- {\n- header($sub);\n- print $sub "\n-\t\t\t\t\t<div align=\\'..b'\n- my ($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=\\"$v->[2]\\">sense reads with PPP</a></p>\n- <p class=\\"featurette-p\\"><a href=\\"$v->[3]\\">reverse reads with PPP</a></p>\n- <p class=\\"featurette-p\\"><a href=\\"$v->[0]\\">sense reads without PPP</a></p>\n- <p class=\\"featurette-p\\"><a href=\\"$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 $du_TE;\n-}\n-\n-1;\n' |
| b |
| diff -r 11708af40030 -r 967512924317 bin/js/bootstrap-table.js --- a/bin/js/bootstrap-table.js Thu Jan 24 13:09:46 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b"@@ -1,3094 +0,0 @@\n-/**\n- * @author zhixin wen <wenzhixin2010@gmail.com>\n- * version: 1.11.1\n- * https://github.com/wenzhixin/bootstrap-table/\n- */\n-\n-(function ($) {\n- 'use strict';\n-\n- // TOOLS DEFINITION\n- // ======================\n-\n- var cachedWidth = null;\n-\n- // it only does '%s', and return '' when arguments are undefined\n- var sprintf = function (str) {\n- var args = arguments,\n- flag = true,\n- i = 1;\n-\n- str = str.replace(/%s/g, function () {\n- var arg = args[i++];\n-\n- if (typeof arg === 'undefined') {\n- flag = false;\n- return '';\n- }\n- return arg;\n- });\n- return flag ? str : '';\n- };\n-\n- var getPropertyFromOther = function (list, from, to, value) {\n- var result = '';\n- $.each(list, function (i, item) {\n- if (item[from] === value) {\n- result = item[to];\n- return false;\n- }\n- return true;\n- });\n- return result;\n- };\n-\n- var getFieldIndex = function (columns, field) {\n- var index = -1;\n-\n- $.each(columns, function (i, column) {\n- if (column.field === field) {\n- index = i;\n- return false;\n- }\n- return true;\n- });\n- return index;\n- };\n-\n- // http://jsfiddle.net/wenyi/47nz7ez9/3/\n- var setFieldIndex = function (columns) {\n- var i, j, k,\n- totalCol = 0,\n- flag = [];\n-\n- for (i = 0; i < columns[0].length; i++) {\n- totalCol += columns[0][i].colspan || 1;\n- }\n-\n- for (i = 0; i < columns.length; i++) {\n- flag[i] = [];\n- for (j = 0; j < totalCol; j++) {\n- flag[i][j] = false;\n- }\n- }\n-\n- for (i = 0; i < columns.length; i++) {\n- for (j = 0; j < columns[i].length; j++) {\n- var r = columns[i][j],\n- rowspan = r.rowspan || 1,\n- colspan = r.colspan || 1,\n- index = $.inArray(false, flag[i]);\n-\n- if (colspan === 1) {\n- r.fieldIndex = index;\n- // when field is undefined, use index instead\n- if (typeof r.field === 'undefined') {\n- r.field = index;\n- }\n- }\n-\n- for (k = 0; k < rowspan; k++) {\n- flag[i + k][index] = true;\n- }\n- for (k = 0; k < colspan; k++) {\n- flag[i][index + k] = true;\n- }\n- }\n- }\n- };\n-\n- var getScrollBarWidth = function () {\n- if (cachedWidth === null) {\n- var inner = $('<p/>').addClass('fixed-table-scroll-inner'),\n- outer = $('<div/>').addClass('fixed-table-scroll-outer'),\n- w1, w2;\n-\n- outer.append(inner);\n- $('body').append(outer);\n-\n- w1 = inner[0].offsetWidth;\n- outer.css('overflow', 'scroll');\n- w2 = inner[0].offsetWidth;\n-\n- if (w1 === w2) {\n- w2 = outer[0].clientWidth;\n- }\n-\n- outer.remove();\n- cachedWidth = w1 - w2;\n- }\n- return cachedWidth;\n- };\n-\n- var calculateObjectValue = function (self, name, args, defaultValue) {\n- var func = name;\n-\n- if (typeof name === 'string') {\n- // support obj.func1.func2\n- var names = name.split('.');\n-\n- if (names.length > 1) {\n- func = window;\n- $.each(names, function (i, f) {\n- func = func[f];\n- });\n- } else {\n- func = window[name];\n- }\n- }\n- if (typeof func === 'object') {\n- return func;\n- }\n- if (typeof func === 'function') {\n-"..b' i < trs.length; i++) {\n- this.expandRow_(true, $(trs[i]).data("index"));\n- }\n- }\n- };\n-\n- BootstrapTable.prototype.collapseAllRows = function (isSubTable) {\n- if (isSubTable) {\n- this.expandRow_(false, 0);\n- } else {\n- var trs = this.$body.children();\n- for (var i = 0; i < trs.length; i++) {\n- this.expandRow_(false, $(trs[i]).data("index"));\n- }\n- }\n- };\n-\n- BootstrapTable.prototype.updateFormatText = function (name, text) {\n- if (this.options[sprintf(\'format%s\', name)]) {\n- if (typeof text === \'string\') {\n- this.options[sprintf(\'format%s\', name)] = function () {\n- return text;\n- };\n- } else if (typeof text === \'function\') {\n- this.options[sprintf(\'format%s\', name)] = text;\n- }\n- }\n- this.initToolbar();\n- this.initPagination();\n- this.initBody();\n- };\n-\n- // BOOTSTRAP TABLE PLUGIN DEFINITION\n- // =======================\n-\n- var allowedMethods = [\n- \'getOptions\',\n- \'getSelections\', \'getAllSelections\', \'getData\',\n- \'load\', \'append\', \'prepend\', \'remove\', \'removeAll\',\n- \'insertRow\', \'updateRow\', \'updateCell\', \'updateByUniqueId\', \'removeByUniqueId\',\n- \'getRowByUniqueId\', \'showRow\', \'hideRow\', \'getHiddenRows\',\n- \'mergeCells\',\n- \'checkAll\', \'uncheckAll\', \'checkInvert\',\n- \'check\', \'uncheck\',\n- \'checkBy\', \'uncheckBy\',\n- \'refresh\',\n- \'resetView\',\n- \'resetWidth\',\n- \'destroy\',\n- \'showLoading\', \'hideLoading\',\n- \'showColumn\', \'hideColumn\', \'getHiddenColumns\', \'getVisibleColumns\',\n- \'showAllColumns\', \'hideAllColumns\',\n- \'filterBy\',\n- \'scrollTo\',\n- \'getScrollPosition\',\n- \'selectPage\', \'prevPage\', \'nextPage\',\n- \'togglePagination\',\n- \'toggleView\',\n- \'refreshOptions\',\n- \'resetSearch\',\n- \'expandRow\', \'collapseRow\', \'expandAllRows\', \'collapseAllRows\',\n- \'updateFormatText\'\n- ];\n-\n- $.fn.bootstrapTable = function (option) {\n- var value,\n- args = Array.prototype.slice.call(arguments, 1);\n-\n- this.each(function () {\n- var $this = $(this),\n- data = $this.data(\'bootstrap.table\'),\n- options = $.extend({}, BootstrapTable.DEFAULTS, $this.data(),\n- typeof option === \'object\' && option);\n-\n- if (typeof option === \'string\') {\n- if ($.inArray(option, allowedMethods) < 0) {\n- throw new Error("Unknown method: " + option);\n- }\n-\n- if (!data) {\n- return;\n- }\n-\n- value = data[option].apply(data, args);\n-\n- if (option === \'destroy\') {\n- $this.removeData(\'bootstrap.table\');\n- }\n- }\n-\n- if (!data) {\n- $this.data(\'bootstrap.table\', (data = new BootstrapTable(this, options)));\n- }\n- });\n-\n- return typeof value === \'undefined\' ? this : value;\n- };\n-\n- $.fn.bootstrapTable.Constructor = BootstrapTable;\n- $.fn.bootstrapTable.defaults = BootstrapTable.DEFAULTS;\n- $.fn.bootstrapTable.columnDefaults = BootstrapTable.COLUMN_DEFAULTS;\n- $.fn.bootstrapTable.locales = BootstrapTable.LOCALES;\n- $.fn.bootstrapTable.methods = allowedMethods;\n- $.fn.bootstrapTable.utils = {\n- sprintf: sprintf,\n- getFieldIndex: getFieldIndex,\n- compareObjects: compareObjects,\n- calculateObjectValue: calculateObjectValue,\n- getItemField: getItemField,\n- objectKeys: objectKeys,\n- isIEBrowser: isIEBrowser\n- };\n-\n- // BOOTSTRAP TABLE INIT\n- // =======================\n-\n- $(function () {\n- $(\'[data-toggle="table"]\').bootstrapTable();\n- });\n-})(jQuery);\n' |
| b |
| diff -r 11708af40030 -r 967512924317 bin/js/bootstrap.min.js --- a/bin/js/bootstrap.min.js Thu Jan 24 13:09:46 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,6 +0,0 @@\n-/**\n-* Bootstrap.js v2.3.2 by @fat & @mdo\n-* Copyright 2013 Twitter, Inc.\n-* http://www.apache.org/licenses/LICENSE-2.0.txt\n-*/\n-!function(e){"use strict";e(function(){e.support.transition=function(){var e=function(){var e=document.createElement("bootstrap"),t={WebkitTransition:"webkitTransitionEnd",MozTransition:"transitionend",OTransition:"oTransitionEnd otransitionend",transition:"transitionend"},n;for(n in t)if(e.style[n]!==undefined)return t[n]}();return e&&{end:e}}()})}(window.jQuery),!function(e){"use strict";var t=\'[data-dismiss="alert"]\',n=function(n){e(n).on("click",t,this.close)};n.prototype.close=function(t){function s(){i.trigger("closed").remove()}var n=e(this),r=n.attr("data-target"),i;r||(r=n.attr("href"),r=r&&r.replace(/.*(?=#[^\\s]*$)/,"")),i=e(r),t&&t.preventDefault(),i.length||(i=n.hasClass("alert")?n:n.parent()),i.trigger(t=e.Event("close"));if(t.isDefaultPrevented())return;i.removeClass("in"),e.support.transition&&i.hasClass("fade")?i.on(e.support.transition.end,s):s()};var r=e.fn.alert;e.fn.alert=function(t){return this.each(function(){var r=e(this),i=r.data("alert");i||r.data("alert",i=new n(this)),typeof t=="string"&&i[t].call(r)})},e.fn.alert.Constructor=n,e.fn.alert.noConflict=function(){return e.fn.alert=r,this},e(document).on("click.alert.data-api",t,n.prototype.close)}(window.jQuery),!function(e){"use strict";var t=function(t,n){this.$element=e(t),this.options=e.extend({},e.fn.button.defaults,n)};t.prototype.setState=function(e){var t="disabled",n=this.$element,r=n.data(),i=n.is("input")?"val":"html";e+="Text",r.resetText||n.data("resetText",n[i]()),n[i](r[e]||this.options[e]),setTimeout(function(){e=="loadingText"?n.addClass(t).attr(t,t):n.removeClass(t).removeAttr(t)},0)},t.prototype.toggle=function(){var e=this.$element.closest(\'[data-toggle="buttons-radio"]\');e&&e.find(".active").removeClass("active"),this.$element.toggleClass("active")};var n=e.fn.button;e.fn.button=function(n){return this.each(function(){var r=e(this),i=r.data("button"),s=typeof n=="object"&&n;i||r.data("button",i=new t(this,s)),n=="toggle"?i.toggle():n&&i.setState(n)})},e.fn.button.defaults={loadingText:"loading..."},e.fn.button.Constructor=t,e.fn.button.noConflict=function(){return e.fn.button=n,this},e(document).on("click.button.data-api","[data-toggle^=button]",function(t){var n=e(t.target);n.hasClass("btn")||(n=n.closest(".btn")),n.button("toggle")})}(window.jQuery),!function(e){"use strict";var t=function(t,n){this.$element=e(t),this.$indicators=this.$element.find(".carousel-indicators"),this.options=n,this.options.pause=="hover"&&this.$element.on("mouseenter",e.proxy(this.pause,this)).on("mouseleave",e.proxy(this.cycle,this))};t.prototype={cycle:function(t){return t||(this.paused=!1),this.interval&&clearInterval(this.interval),this.options.interval&&!this.paused&&(this.interval=setInterval(e.proxy(this.next,this),this.options.interval)),this},getActiveIndex:function(){return this.$active=this.$element.find(".item.active"),this.$items=this.$active.parent().children(),this.$items.index(this.$active)},to:function(t){var n=this.getActiveIndex(),r=this;if(t>this.$items.length-1||t<0)return;return this.sliding?this.$element.one("slid",function(){r.to(t)}):n==t?this.pause().cycle():this.slide(t>n?"next":"prev",e(this.$items[t]))},pause:function(t){return t||(this.paused=!0),this.$element.find(".next, .prev").length&&e.support.transition.end&&(this.$element.trigger(e.support.transition.end),this.cycle(!0)),clearInterval(this.interval),this.interval=null,this},next:function(){if(this.sliding)return;return this.slide("next")},prev:function(){if(this.sliding)return;return this.slide("prev")},slide:function(t,n){var r=this.$element.find(".item.active"),i=n||r[t](),s=this.interval,o=t=="next"?"left":"right",u=t=="next"?"first":"last",a=this,f;this.sliding=!0,s&&this.pause(),i=i.length?i:this.$element.find(".item")[u](),f=e.Event("slide",{relatedTarget:i[0],direction:o});if(i.hasClass("active"))return;this.$indicat'..b',next:function(t){var n=this.$menu.find(".active").removeClass("active"),r=n.next();r.length||(r=e(this.$menu.find("li")[0])),r.addClass("active")},prev:function(e){var 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r=e(this),i=r.data("typeahead"),s=typeof n=="object"&&n;i||r.data("typeahead",i=new t(this,s)),typeof n=="string"&&i[n]()})},e.fn.typeahead.defaults={source:[],items:8,menu:\'<ul class="typeahead dropdown-menu"></ul>\',item:\'<li><a href="#"></a></li>\',minLength:1},e.fn.typeahead.Constructor=t,e.fn.typeahead.noConflict=function(){return e.fn.typeahead=n,this},e(document).on("focus.typeahead.data-api",\'[data-provide="typeahead"]\',function(t){var n=e(this);if(n.data("typeahead"))return;n.typeahead(n.data())})}(window.jQuery),!function(e){"use strict";var t=function(t,n){this.options=e.extend({},e.fn.affix.defaults,n),this.$window=e(window).on("scroll.affix.data-api",e.proxy(this.checkPosition,this)).on("click.affix.data-api",e.proxy(function(){setTimeout(e.proxy(this.checkPosition,this),1)},this)),this.$element=e(t),this.checkPosition()};t.prototype.checkPosition=function(){if(!this.$element.is(":visible"))return;var 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t=e(this),n=t.data();n.offset=n.offset||{},n.offsetBottom&&(n.offset.bottom=n.offsetBottom),n.offsetTop&&(n.offset.top=n.offsetTop),t.affix(n)})})}(window.jQuery);\n\\ No newline at end of file\n' |
| b |
| diff -r 11708af40030 -r 967512924317 bin/js/filter.js --- a/bin/js/filter.js Thu Jan 24 13:09:46 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,20 +0,0 @@ -function search(input) { - // Declare variables - var elt, filter, uls, li, a, i; - elt = input.parentElement; - filter = input.value.toUpperCase(); - uls = elt.getElementsByClassName('thumbs'); - - // Loop through all list items, and hide those who don't match the search query - for (j = 0; j < uls.length; j++) { - li = uls[j].getElementsByTagName('li'); - for (i = 0; i < li.length; i++) { - a = li[i].getElementsByTagName("a")[0]; - if (a.innerHTML.toUpperCase().indexOf(filter) > -1) { - li[i].style.display = ""; - } else { - li[i].style.display = "none"; - } - } - } -} |
| b |
| diff -r 11708af40030 -r 967512924317 bin/js/jquery.galleriffic.js --- a/bin/js/jquery.galleriffic.js Thu Jan 24 13:09:46 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b"@@ -1,979 +0,0 @@\n-/**\r\n- * jQuery Galleriffic plugin\r\n- *\r\n- * Copyright (c) 2008 Trent Foley (http://trentacular.com)\r\n- * Licensed under the MIT License:\r\n- * http://www.opensource.org/licenses/mit-license.php\r\n- *\r\n- * Much thanks to primary contributer Ponticlaro (http://www.ponticlaro.com)\r\n- */\r\n-;(function($) {\r\n-\t// Globally keep track of all images by their unique hash. Each item is an image data object.\r\n-\tvar allImages = {};\r\n-\tvar imageCounter = 0;\r\n-\n-\t// Galleriffic static class\r\n-\t$.galleriffic = {\n-\t\tversion: '2.0.1',\n-\n-\t\t// Strips invalid characters and any leading # characters\n-\t\tnormalizeHash: function(hash) {\r\n-\t\t\treturn hash.replace(/^.*#/, '').replace(/\\?.*$/, '');\n-\t\t},\n-\n-\t\tgetImage: function(hash) {\n-\t\t\tif (!hash)\n-\t\t\t\treturn undefined;\n-\n-\t\t\thash = $.galleriffic.normalizeHash(hash);\r\n-\t\t\treturn allImages[hash];\n-\t\t},\n-\r\n-\t\t// Global function that looks up an image by its hash and displays the image.\n-\t\t// Returns false when an image is not found for the specified hash.\n-\t\t// @param {String} hash This is the unique hash value assigned to an image.\n-\t\tgotoImage: function(hash) {\r\n-\t\t\tvar imageData = $.galleriffic.getImage(hash);\r\n-\t\t\tif (!imageData)\n-\t\t\t\treturn false;\r\n-\n-\t\t\tvar gallery = imageData.gallery;\n-\t\t\tgallery.gotoImage(imageData);\n-\t\t\t\n-\t\t\treturn true;\r\n-\t\t},\n-\n-\t\t// Removes an image from its respective gallery by its hash.\n-\t\t// Returns false when an image is not found for the specified hash or the\n-\t\t// specified owner gallery does match the located images gallery.\n-\t\t// @param {String} hash This is the unique hash value assigned to an image.\n-\t\t// @param {Object} ownerGallery (Optional) When supplied, the located images\n-\t\t// gallery is verified to be the same as the specified owning gallery before\n-\t\t// performing the remove operation.\n-\t\tremoveImageByHash: function(hash, ownerGallery) {\n-\t\t\tvar imageData = $.galleriffic.getImage(hash);\n-\t\t\tif (!imageData)\n-\t\t\t\treturn false;\n-\n-\t\t\tvar gallery = imageData.gallery;\n-\t\t\tif (ownerGallery && ownerGallery != gallery)\n-\t\t\t\treturn false;\n-\n-\t\t\treturn gallery.removeImageByIndex(imageData.index);\n-\t\t}\r\n-\t};\n-\r\n-\tvar defaults = {\r\n-\t\tdelay: 3000,\r\n-\t\tnumThumbs: 20,\r\n-\t\tpreloadAhead: 40, // Set to -1 to preload all images\r\n-\t\tenableTopPager: false,\r\n-\t\tenableBottomPager: true,\r\n-\t\tmaxPagesToShow: 7,\r\n-\t\timageContainerSel: '',\r\n-\t\tcaptionContainerSel: '',\r\n-\t\tcontrolsContainerSel: '',\r\n-\t\tloadingContainerSel: '',\r\n-\t\trenderSSControls: true,\r\n-\t\trenderNavControls: true,\r\n-\t\tplayLinkText: 'Play',\r\n-\t\tpauseLinkText: 'Pause',\r\n-\t\tprevLinkText: 'Previous',\r\n-\t\tnextLinkText: 'Next',\r\n-\t\tnextPageLinkText: 'Next ›',\r\n-\t\tprevPageLinkText: '‹ Prev',\r\n-\t\tenableHistory: false,\n-\t\tenableKeyboardNavigation: true,\r\n-\t\tautoStart: false,\r\n-\t\tsyncTransitions: false,\r\n-\t\tdefaultTransitionDuration: 1000,\r\n-\t\tonSlideChange: undefined, // accepts a delegate like such: function(prevIndex, nextIndex) { ... }\r\n-\t\tonTransitionOut: undefined, // accepts a delegate like such: function(slide, caption, isSync, callback) { ... }\r\n-\t\tonTransitionIn: undefined, // accepts a delegate like such: function(slide, caption, isSync) { ... }\r\n-\t\tonPageTransitionOut: undefined, // accepts a delegate like such: function(callback) { ... }\r\n-\t\tonPageTransitionIn: undefined, // accepts a delegate like such: function() { ... }\n-\t\tonImageAdded: undefined, // accepts a delegate like such: function(imageData, $li) { ... }\n-\t\tonImageRemoved: undefined // accepts a delegate like such: function(imageData, $li) { ... }\r\n-\t};\r\n-\n-\t// Primary Galleriffic initialization function that should be called on the thumbnail container.\r\n-\t$.fn.galleriffic = function(settings) {\r\n-\t\t// Extend Gallery O"..b'display all thumbnails.\r\n-\t\t\tbuildPageLink: function(pager, pageNum, numPages) {\r\n-\t\t\t\tvar pageLabel = pageNum + 1;\r\n-\t\t\t\tvar currentPage = this.getCurrentPage();\r\n-\t\t\t\tif (pageNum == currentPage)\r\n-\t\t\t\t\tpager.append(\'<span class="current">\'+pageLabel+\'</span>\');\r\n-\t\t\t\telse if (pageNum < numPages) {\r\n-\t\t\t\t\tvar imageIndex = pageNum*this.numThumbs;\r\n-\t\t\t\t\tpager.append(\'<a rel="history" href="#\'+this.data[imageIndex].hash+\'" title="\'+pageLabel+\'">\'+pageLabel+\'</a>\');\r\n-\t\t\t\t}\n-\t\t\t\t\n-\t\t\t\treturn this;\r\n-\t\t\t}\r\n-\t\t});\r\n-\r\n-\t\t// Now initialize the gallery\r\n-\t\t$.extend(this, defaults, settings);\r\n-\t\t\r\n-\t\t// Verify the history plugin is available\r\n-\t\tif (this.enableHistory && !$.historyInit)\r\n-\t\t\tthis.enableHistory = false;\r\n-\t\t\r\n-\t\t// Select containers\r\n-\t\tif (this.imageContainerSel) this.$imageContainer = $(this.imageContainerSel);\r\n-\t\tif (this.captionContainerSel) this.$captionContainer = $(this.captionContainerSel);\r\n-\t\tif (this.loadingContainerSel) this.$loadingContainer = $(this.loadingContainerSel);\r\n-\n-\t\t// Initialize the thumbails\r\n-\t\tthis.initializeThumbs();\r\n-\t\t\r\n-\t\tif (this.maxPagesToShow < 3)\r\n-\t\t\tthis.maxPagesToShow = 3;\r\n-\r\n-\t\tthis.displayedPage = -1;\n-\t\tthis.currentImage = this.data[0];\r\n-\t\tvar gallery = this;\r\n-\r\n-\t\t// Hide the loadingContainer\r\n-\t\tif (this.$loadingContainer)\r\n-\t\t\tthis.$loadingContainer.hide();\r\n-\r\n-\t\t// Setup controls\r\n-\t\tif (this.controlsContainerSel) {\r\n-\t\t\tthis.$controlsContainer = $(this.controlsContainerSel).empty();\r\n-\t\t\t\r\n-\t\t\tif (this.renderSSControls) {\r\n-\t\t\t\tif (this.autoStart) {\r\n-\t\t\t\t\tthis.$controlsContainer\r\n-\t\t\t\t\t\t.append(\'<div class="ss-controls"><a href="#pause" class="pause" title="\'+this.pauseLinkText+\'">\'+this.pauseLinkText+\'</a></div>\');\r\n-\t\t\t\t} else {\r\n-\t\t\t\t\tthis.$controlsContainer\r\n-\t\t\t\t\t\t.append(\'<div class="ss-controls"><a href="#play" class="play" title="\'+this.playLinkText+\'">\'+this.playLinkText+\'</a></div>\');\r\n-\t\t\t\t}\r\n-\r\n-\t\t\t\tthis.$controlsContainer.find(\'div.ss-controls a\')\r\n-\t\t\t\t\t.click(function(e) {\r\n-\t\t\t\t\t\tgallery.toggleSlideshow();\r\n-\t\t\t\t\t\te.preventDefault();\r\n-\t\t\t\t\t\treturn false;\r\n-\t\t\t\t\t});\r\n-\t\t\t}\r\n-\t\t\r\n-\t\t\tif (this.renderNavControls) {\r\n-\t\t\t\tthis.$controlsContainer\r\n-\t\t\t\t\t.append(\'<div class="nav-controls"><a class="prev" rel="history" title="\'+this.prevLinkText+\'">\'+this.prevLinkText+\'</a><a class="next" rel="history" title="\'+this.nextLinkText+\'">\'+this.nextLinkText+\'</a></div>\')\r\n-\t\t\t\t\t.find(\'div.nav-controls a\')\r\n-\t\t\t\t\t.click(function(e) {\r\n-\t\t\t\t\t\tgallery.clickHandler(e, this);\r\n-\t\t\t\t\t});\r\n-\t\t\t}\r\n-\t\t}\r\n-\n-\t\tvar initFirstImage = !this.enableHistory || !location.hash;\n-\t\tif (this.enableHistory && location.hash) {\n-\t\t\tvar hash = $.galleriffic.normalizeHash(location.hash);\n-\t\t\tvar imageData = allImages[hash];\r\n-\t\t\tif (!imageData)\n-\t\t\t\tinitFirstImage = true;\n-\t\t}\n-\r\n-\t\t// Setup gallery to show the first image\n-\t\tif (initFirstImage)\r\n-\t\t\tthis.gotoIndex(0, false, true);\r\n-\n-\t\t// Setup Keyboard Navigation\n-\t\tif (this.enableKeyboardNavigation) {\n-\t\t\t$(document).keydown(function(e) {\n-\t\t\t\tvar key = e.charCode ? e.charCode : e.keyCode ? e.keyCode : 0;\n-\t\t\t\tswitch(key) {\n-\t\t\t\t\tcase 32: // space\n-\t\t\t\t\t\tgallery.next();\n-\t\t\t\t\t\te.preventDefault();\n-\t\t\t\t\t\tbreak;\n-\t\t\t\t\tcase 33: // Page Up\n-\t\t\t\t\t\tgallery.previousPage();\n-\t\t\t\t\t\te.preventDefault();\n-\t\t\t\t\t\tbreak;\n-\t\t\t\t\tcase 34: // Page Down\n-\t\t\t\t\t\tgallery.nextPage();\n-\t\t\t\t\t\te.preventDefault();\n-\t\t\t\t\t\tbreak;\n-\t\t\t\t\tcase 35: // End\n-\t\t\t\t\t\tgallery.gotoIndex(gallery.data.length-1);\n-\t\t\t\t\t\te.preventDefault();\n-\t\t\t\t\t\tbreak;\n-\t\t\t\t\tcase 36: // Home\n-\t\t\t\t\t\tgallery.gotoIndex(0);\n-\t\t\t\t\t\te.preventDefault();\n-\t\t\t\t\t\tbreak;\n-\t\t\t\t\tcase 37: // left arrow\n-\t\t\t\t\t\tgallery.previous();\n-\t\t\t\t\t\te.preventDefault();\n-\t\t\t\t\t\tbreak;\n-\t\t\t\t\tcase 39: // right arrow\n-\t\t\t\t\t\tgallery.next();\n-\t\t\t\t\t\te.preventDefault();\n-\t\t\t\t\t\tbreak;\n-\t\t\t\t}\n-\t\t\t});\n-\t\t}\n-\n-\t\t// Auto start the slideshow\r\n-\t\tif (this.autoStart)\r\n-\t\t\tthis.play();\r\n-\r\n-\t\t// Kickoff Image Preloader after 1 second\r\n-\t\tsetTimeout(function() { gallery.preloadInit(); }, 1000);\r\n-\r\n-\t\treturn this;\r\n-\t};\r\n-})(jQuery);\r\n' |
| b |
| diff -r 11708af40030 -r 967512924317 bin/js/jquery.js --- a/bin/js/jquery.js Thu Jan 24 13:09:46 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,5 +0,0 @@\n-/*! jQuery v1.9.1 | (c) 2005, 2012 jQuery Foundation, Inc. | jquery.org/license\n-//@ sourceMappingURL=jquery.min.map\n-*/(function(e,t){var n,r,i=typeof t,o=e.document,a=e.location,s=e.jQuery,u=e.$,l={},c=[],p="1.9.1",f=c.concat,d=c.push,h=c.slice,g=c.indexOf,m=l.toString,y=l.hasOwnProperty,v=p.trim,b=function(e,t){return new b.fn.init(e,t,r)},x=/[+-]?(?:\\d*\\.|)\\d+(?:[eE][+-]?\\d+|)/.source,w=/\\S+/g,T=/^[\\s\\uFEFF\\xA0]+|[\\s\\uFEFF\\xA0]+$/g,N=/^(?:(<[\\w\\W]+>)[^>]*|#([\\w-]*))$/,C=/^<(\\w+)\\s*\\/?>(?:<\\/\\1>|)$/,k=/^[\\],:{}\\s]*$/,E=/(?:^|:|,)(?:\\s*\\[)+/g,S=/\\\\(?:["\\\\\\/bfnrt]|u[\\da-fA-F]{4})/g,A=/"[^"\\\\\\r\\n]*"|true|false|null|-?(?:\\d+\\.|)\\d+(?:[eE][+-]?\\d+|)/g,j=/^-ms-/,D=/-([\\da-z])/gi,L=function(e,t){return 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e,n=b.timers,r=0;for(Xn=b.now();n.length>r;r++)e=n[r],e()||n[r]!==e||n.splice(r--,1);n.length||b.fx.stop(),Xn=t},b.fx.timer=function(e){e()&&b.timers.push(e)&&b.fx.start()},b.fx.interval=13,b.fx.start=function(){Un||(Un=setInterval(b.fx.tick,b.fx.interval))},b.fx.stop=function(){clearInterval(Un),Un=null},b.fx.speeds={slow:600,fast:200,_default:400},b.fx.step={},b.expr&&b.expr.filters&&(b.expr.filters.animated=function(e){return b.grep(b.timers,function(t){return e===t.elem}).length}),b.fn.offset=function(e){if(arguments.length)return e===t?this:this.each(function(t){b.offset.setOffset(this,e,t)});var n,r,o={top:0,left:0},a=this[0],s=a&&a.ownerDocument;if(s)return n=s.documentElement,b.contains(n,a)?(typeof a.getBoundingClientRect!==i&&(o=a.getBoundingClientRect()),r=or(s),{top:o.top+(r.pageYOffset||n.scrollTop)-(n.clientTop||0),left:o.left+(r.pageXOffset||n.scrollLeft)-(n.clientLeft||0)}):o},b.offset={setOffset:function(e,t,n){var r=b.css(e,"position");"static"===r&&(e.style.position="relative");var i=b(e),o=i.offset(),a=b.css(e,"top"),s=b.css(e,"left"),u=("absolute"===r||"fixed"===r)&&b.inArray("auto",[a,s])>-1,l={},c={},p,f;u?(c=i.position(),p=c.top,f=c.left):(p=parseFloat(a)||0,f=parseFloat(s)||0),b.isFunction(t)&&(t=t.call(e,n,o)),null!=t.top&&(l.top=t.top-o.top+p),null!=t.left&&(l.left=t.left-o.left+f),"using"in t?t.using.call(e,l):i.css(l)}},b.fn.extend({position:function(){if(this[0]){var e,t,n={top:0,left:0},r=this[0];return"fixed"===b.css(r,"position")?t=r.getBoundingClientRect():(e=this.offsetParent(),t=this.offset(),b.nodeName(e[0],"html")||(n=e.offset()),n.top+=b.css(e[0],"borderTopWidth",!0),n.left+=b.css(e[0],"borderLeftWidth",!0)),{top:t.top-n.top-b.css(r,"marginTop",!0),left:t.left-n.left-b.css(r,"marginLeft",!0)}}},offsetParent:function(){return this.map(function(){var e=this.offsetParent||o.documentElement;while(e&&!b.nodeName(e,"html")&&"static"===b.css(e,"position"))e=e.offsetParent;return e||o.documentElement})}}),b.each({scrollLeft:"pageXOffset",scrollTop:"pageYOffset"},function(e,n){var r=/Y/.test(n);b.fn[e]=function(i){return b.access(this,function(e,i,o){var a=or(e);return o===t?a?n in a?a[n]:a.document.documentElement[i]:e[i]:(a?a.scrollTo(r?b(a).scrollLeft():o,r?o:b(a).scrollTop()):e[i]=o,t)},e,i,arguments.length,null)}});function or(e){return b.isWindow(e)?e:9===e.nodeType?e.defaultView||e.parentWindow:!1}b.each({Height:"height",Width:"width"},function(e,n){b.each({padding:"inner"+e,content:n,"":"outer"+e},function(r,i){b.fn[i]=function(i,o){var a=arguments.length&&(r||"boolean"!=typeof i),s=r||(i===!0||o===!0?"margin":"border");return b.access(this,function(n,r,i){var o;return b.isWindow(n)?n.document.documentElement["client"+e]:9===n.nodeType?(o=n.documentElement,Math.max(n.body["scroll"+e],o["scroll"+e],n.body["offset"+e],o["offset"+e],o["client"+e])):i===t?b.css(n,r,s):b.style(n,r,i,s)},n,a?i:t,a,null)}})}),e.jQuery=e.$=b,"function"==typeof define&&define.amd&&define.amd.jQuery&&define("jquery",[],function(){return b})})(window);\n\\ No newline at end of file\n' |
| b |
| diff -r 11708af40030 -r 967512924317 bin/js/jquery.opacityrollover.js --- a/bin/js/jquery.opacityrollover.js Thu Jan 24 13:09:46 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,42 +0,0 @@ -/** - * jQuery Opacity Rollover plugin - * - * Copyright (c) 2009 Trent Foley (http://trentacular.com) - * Licensed under the MIT License: - * http://www.opensource.org/licenses/mit-license.php - */ -;(function($) { - var defaults = { - mouseOutOpacity: 0.67, - mouseOverOpacity: 1.0, - fadeSpeed: 'fast', - exemptionSelector: '.selected' - }; - - $.fn.opacityrollover = function(settings) { - // Initialize the effect - $.extend(this, defaults, settings); - - var config = this; - - function fadeTo(element, opacity) { - var $target = $(element); - - if (config.exemptionSelector) - $target = $target.not(config.exemptionSelector); - - $target.fadeTo(config.fadeSpeed, opacity); - } - - this.css('opacity', this.mouseOutOpacity) - .hover( - function () { - fadeTo(this, config.mouseOverOpacity); - }, - function () { - fadeTo(this, config.mouseOutOpacity); - }); - - return this; - }; -})(jQuery); |
| b |
| diff -r 11708af40030 -r 967512924317 bin/ppp.pm --- a/bin/ppp.pm Thu Jan 24 13:09:46 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,230 +0,0 @@\n-package ppp;\n-\n-use strict;\n-use warnings;\n-use FindBin;\n-use lib $FindBin::Bin;\n-use Rcall qw ( histogram );\n-use Math::CDF;\n-\n-use Exporter;\n-our @ISA = qw( Exporter );\n-our @EXPORT_OK = qw( &ping_pong_partners );\n-\n-sub ping_pong_partners\n-{\n- my ( $TE_fai, $sam, $dir, $max ) = @_;\n- my ( $hashRef, $dupRef, $hasPpp ) = count_mapped ( $TE_fai, $sam );\n- my ( %num_per_overlap_size, $overlap_number, $reverseR, $begRev, $endRev, $sensR, $begSens, $endSens, $snum, $rnum, $overlap );\n- my ( $SP, $AP, $SN, $AN, $txt );\n- my $flag = 0;\n- my @distri_overlap = (); my @overlaps_names = ();\n-\n- open my $ppp_f, \'>\', $dir."ppp.txt" || die "cannot create ppp.txt $!\\n";\n- foreach my $k ( sort keys %{$hashRef} )\n- {\n- my $v = $hashRef->{$k};\n- my $TE_dir = $dir.$k.\'/\';\n-\n- %num_per_overlap_size = (); $overlap_number = 0;\n- $flag = 0;\n- for ( my $i = 0; $i <= $#{$v->[1]} ; $i++ )\n- {\n- $reverseR = ${$v->[1]}[$i] ;\n- $begRev = $reverseR->[0];\n- $endRev = $begRev + length($reverseR->[1]) - 1;\n-\n- my $revR = reverse($reverseR->[1]);\n- $revR =~ tr/atgcuATGCU/tacgaTACGA/;\n-\n- for ( my $j = 0; $j <= $#{$v->[0]}; $j++ )\n- {\n- $sensR = ${$v->[0]}[$j];\n- $begSens = $sensR->[0];\n- $endSens = $begSens + length($sensR->[1]) - 1;\n-\n- if ( $begSens <= $endRev && $endSens > $endRev )\n- {\n- $flag = 1;\n- mkdir $TE_dir;\n- open $txt, \'>\', $TE_dir.\'overlap_size.txt\' || die "cannot open repartition\\n";\n-\n- $overlap = $endRev - $begSens + 1;\n- $snum = $dupRef->{$sensR->[0].$sensR->[1].$sensR->[2].$sensR->[3]};\n- $rnum = $dupRef->{$reverseR->[0].$reverseR->[1].$reverseR->[2].$reverseR->[3]};\n-\n- if ( $overlap == 10 )\n- {\n- $hasPpp->{ $sensR->[0].$sensR->[1].$sensR->[2].$sensR->[3] } = 1;\n- $hasPpp->{ $reverseR->[0].$reverseR->[1].$reverseR->[2].$reverseR->[3] } = 1;\n- }\n- next if $overlap > $max;\n- if ( $snum < $rnum )\n- {\n- $num_per_overlap_size{$overlap} += $snum;\n- $overlap_number += $snum;\n- }\n- else\n- {\n- $num_per_overlap_size{$overlap} += $rnum ;\n- $overlap_number += $rnum ;\n- }\n- }\n- }\n- }\n- if ( $max != 0 )\n- {\n- my @overlaps = ();\n- push @overlaps_names, $k;\n- for my $i (1..$max)\n- {\n- $num_per_overlap_size{$i} = 0 unless exists( $num_per_overlap_size{$i} );\n- push @overlaps, $num_per_overlap_size{$i};\n- }\n- push @distri_overlap, \\@overlaps;\n- }\n-\n- if ( $flag == 1 )\n- {\n- open $AP, \'>\', $TE_dir."antisensPPP.txt" || die "cannot create antisensPPP\\n";\n- open $AN, \'>\', $TE_dir."antisens.txt" || die "cannot create antisens\\n";\n- for ( my $i = 0; $i <= $#{$v->[1]} ; $i++ )\n- {\n- $reverseR = ${$v->[1]}[$i] ;\n- my $revR = reverse($reverseR->[1]);\n- $revR =~ tr/atgcuATGCU/tacgaTACGA/;\n- $rnum = $dupRef->{$reverseR->[0].$reverseR->[1].$reverseR->[2].$reverseR->[3]};\n- if ( $hasPpp->{ $reverseR->[0].$reverseR->[1].$reverseR->[2].$reverseR->[3] } == 1 )\n- {\n- print $AP ">$reverseR->[0]|$reverseR->[2]|$reverseR->[3]|$rnum\\n$revR\\n";\n- }\n- else\n- {\n- print $AN ">$reverseR->[0]|$reverseR->[2]|$reverseR->[3]|$r'..b' open $SP, \'>\', $TE_dir."sensPPP.txt" || die "cannot create sensPPP\\n";\n- open $SN, \'>\', $TE_dir."sens.txt" || die "cannot create sens\\n";\n- for ( my $j = 0; $j <= $#{$v->[0]}; $j++ )\n- {\n- $sensR = ${$v->[0]}[$j];\n- $snum = $dupRef->{$sensR->[0].$sensR->[1].$sensR->[2].$sensR->[3]};\n- if ( $hasPpp->{ $sensR->[0].$sensR->[1].$sensR->[2].$sensR->[3] } == 1 )\n- {\n- print $SP ">$sensR->[0]|$sensR->[2]|$sensR->[3]|$snum\\n$sensR->[1]\\n";\n- }\n- else\n- {\n- print $SN ">$sensR->[0]|$sensR->[2]|$sensR->[3]|$snum\\n$sensR->[1]\\n";\n- }\n- }\n- close $SP; close $SN;\n-\n- my $histo_png = $TE_dir.\'histogram.png\';\n- histogram( \\%num_per_overlap_size, $histo_png, $overlap_number );\n- print $txt "size\\tnumber\\tpercentage of the total overlap number\\n";\n- foreach my $k ( sort {$a <=> $b} keys %num_per_overlap_size )\n- {\n- my $percentage = 0;\n- $percentage = $num_per_overlap_size{$k} * 100 / $overlap_number unless $overlap_number == 0;\n- print $txt "$k\\t$num_per_overlap_size{$k}\\t"; printf $txt "%.2f\\n",$percentage;\n- }\n- close $txt;\n- }\n- }\n-\n- foreach my $tabP ( @distri_overlap )\n- {\n- my $sum = sum($tabP);\n- my $ten = $tabP->[9];\n- my $mean = mean($tabP);\n- my $std = standard_deviation($tabP, $mean);\n- my $zsc = z_significance($ten, $mean, $std);\n- my $name = shift @overlaps_names;\n- my $prob = \'NA\';\n- $prob = 1 - &Math::CDF::pnorm( $zsc ) if $zsc ne \'NA\';\n- print $ppp_f (join ("\\t", $name, $sum, $ten, $mean, $std, $zsc, $prob ),"\\n" );\n- }\n- close $ppp_f;\n-}\n-\n-sub count_mapped\n-{\n- my ( $fai, $in_file ) = @_;\n- my ( %mapped, %dup, %has_ppp );\n-\n- open my $f, \'<\', $fai || die "cannot open $fai $! \\n";\n- while(<$f>)\n- {\n- if ($_ =~ /(.*)\\t(\\d+)\\n/)\n- {\n- $mapped{$1} = [];\n- $mapped{$1}->[0] = []; $mapped{$1}->[1] = [];\n- }\n- }\n- close $f;\n-\n- open my $infile, "samtools view \'$in_file\' |"|| die "cannot open input file $! \\n";\n- while(<$infile>)\n- {\n- unless ($_ =~ /^\\@[A-Za-z][A-Za-z](\\t[A-Za-z][A-Za-z0-9]:[ -~]+)+$/ || $_ =~ /^\\@CO\\t.*/ )\n- {\n- my @line = split (/\\t/,$_);\n- if ($line[1] == 0)\n- {\n- unless ( exists ($dup{$line[3].$line[9].$line[1].$line[2]}) )\n- {\n- push @{$mapped{$line[2]}->[0]} , [$line[3], $line[9], $line[1], $line[2]];\n- $has_ppp {$line[3].$line[9].$line[1].$line[2]} = 0;\n- }\n- $dup{$line[3].$line[9].$line[1].$line[2]}+=1;\n- }\n- elsif ($line[1] == 16)\n- {\n- unless ( exists ($dup{$line[3].$line[9].$line[1].$line[2]}) )\n- {\n- push @{$mapped{$line[2]}->[1]} , [$line[3], $line[9], $line[1], $line[2]];\n- $has_ppp{$line[3].$line[9].$line[1].$line[2]} = 0;\n- }\n- $dup{$line[3].$line[9].$line[1].$line[2]}+=1\n- }\n- }\n- }\n- close $infile;\n- return (\\%mapped, \\%dup, \\%has_ppp );\n-}\n-\n-sub sum\n-{\n- my $arrayref = shift;\n- my $result = 0;\n- foreach (@$arrayref) {$result += $_}\n- return $result;\n-}\n-\n-sub mean\n-{\n- my $arrayref = shift;\n- my $result;\n- foreach (@$arrayref) {$result += $_}\n- return $result / scalar(@$arrayref);\n-}\n-\n-sub standard_deviation\n-{\n- my ($arrayref, $mean) = @_;\n- return sqrt ( mean ( [map $_**2 , @$arrayref ]) - ($mean**2));\n-}\n-\n-sub z_significance\n-{\n- my ($ten, $mean, $std) = @_;\n- my $z = \'NA\';\n- $z = (($ten - $mean) / $std) if $std != 0;\n- return $z;\n-}\n-\n-1;\n-\n' |
| b |
| diff -r 11708af40030 -r 967512924317 bin/resize.pm --- a/bin/resize.pm Thu Jan 24 13:09:46 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,101 +0,0 @@ -package resize; - -use strict; -use warnings; - -use FindBin; -use lib $FindBin::Bin; -use Rcall qw ( histogram ); - -use Exporter; -our @ISA = qw( Exporter ); -our @EXPORT_OK = qw( &size_distribution ); - -sub size_distribution -{ - my ( $fastq, $fastq_out, $dir, $min, $max ) = @_; - - my ( %fragments_size, %duplicates ) ; - my $num = size($min, $max, $fastq, $fastq_out, \%fragments_size, \%duplicates); - - my $png = $dir.'histogram.png'; - histogram(\%fragments_size, $png, $num); - - my $size = $dir.'reads_size.txt'; - - - my $pourcentage; - open my $o, '>', $size || die "cannot open $size $!\n"; - print $o "size\tnumber\tpercentage\n"; - foreach my $k (sort { $a <=> $b } keys %fragments_size ) - { - $pourcentage = $fragments_size{$k} / $num * 100; - - print $o "$k\t$fragments_size{$k}\t"; - printf $o "%.2f\n",$pourcentage; - } - close $o; - - my $dup = $dir.'duplicates.txt' ; - open $o, '>', $dup || die "cannot open $size $!\n"; - print $o "size\tnumber\n"; - foreach my $k (sort { $duplicates{$b} <=> $duplicates{$a} } keys %duplicates ) - { - print $o "$k\t$duplicates{$k}\n"; - } - close $o; -} - -sub size -{ - my ($min, $max, $in_file, $out_file, $sizeHashR, $duplicateHashR) = @_; - my ($numreads, $size, $cmp, $ok, $line) = (0, 0, 0, 0); - my @fastq; - open (my $in, $in_file) || die "cannot open $in_file $!\n"; - open (my $out, ">".$out_file) || die "cannot create $out_file $!\n"; - while(<$in>) - { - chomp $_; - $cmp++; $line++; - if ($cmp == 1) - { - die "file do not contain a @ at line $line\n" unless ($_ =~ /^\@/ ); - $ok = 0; @fastq = (); - push(@fastq,$_); - } - elsif ($cmp == 2) - { - #die "unrecognized symbol at line $line\n" unless ($_ =~ /[atcgATCGnN]+/ || $_ =~ /^$/ ); - push(@fastq,$_); - $size = length($_); - if ($size >= $min && $size <= $max) - { - $numreads++; - ${$sizeHashR}{$size}+=1; - ${$duplicateHashR}{$_}+=1 if (defined($duplicateHashR)); - $ok = 1; - } - } - elsif ($cmp == 3 ) - { - die "file do not contain a + at line $line\n" unless $_ =~ /^\+/; - push(@fastq,$_); - } - elsif ($cmp == 4 ) - { - push(@fastq,$_); - $cmp = 0; - if ($ok == 1) - { - foreach my $t (@fastq) - { - print $out $t."\n"; - } - } - } - } - close $in; close $out; - return $numreads; -} - -1; |
| b |
| diff -r 11708af40030 -r 967512924317 bin/sRNAPipe.pl --- a/bin/sRNAPipe.pl Thu Jan 24 13:09:46 2019 -0500 +++ b/bin/sRNAPipe.pl Mon Jan 28 11:57:15 2019 -0500 |
| [ |
| @@ -1,20 +1,21 @@ -#!/usr/bin/perl +#!/usr/bin/env perl +package main; use strict; use warnings; use Getopt::Long; use Parallel::ForkManager; use File::Basename; -use File::Copy::Recursive qw( dircopy ); +use File::Copy; use POSIX; use FindBin; -use lib $FindBin::Bin; -use resize qw ( size_distribution ); -use subgroups qw (subgroups ); -use ppp qw ( ping_pong_partners ); -use Rcall qw (pie_chart bg_to_png ); -use align qw ( to_build get_unique sam_count sam_count_mis sam_sorted_bam rpms_rpkm rpms_rpkm_te BWA_call get_fastq_seq extract_sam sam_to_bam_bg ); -use html qw ( main_page details_pages menu_page ppp_page ); -use File::Copy; +use lib "$FindBin::Bin/../lib"; +use sRNAPipe; +use sRNAPipe::resize qw ( size_distribution ); +use sRNAPipe::subgroups qw ( subgroups ); +use sRNAPipe::ppp qw ( ping_pong_partners ); +use sRNAPipe::Rcall qw (pie_chart bg_to_png ); +use sRNAPipe::align qw ( to_build get_unique sam_count sam_count_mis sam_sorted_bam rpms_rpkm rpms_rpkm_te BWA_call get_fastq_seq extract_sam sam_to_bam_bg ); +use sRNAPipe::html qw ( main_page details_pages menu_page ppp_page copy_css copy_js ); if(@ARGV) { my ( @fastq, @fastq_n, $dir, $min, $max, $mis, $misTE, $help, $Pcheck, $mapnumf, $html_out); @@ -62,8 +63,8 @@ mkdir $dir; mkdir $fq_collection; $dir = $dir.'/' unless $dir =~ /\/$/; mkdir $dir.'/css';mkdir $dir.'/js'; - dircopy( $FindBin::Bin.'/css', $dir.'/css' ); - dircopy( $FindBin::Bin.'/js', $dir.'/js' ); + copy_css( $dir ); + copy_js( $dir ); my $file = $dir.'report.txt'; open my $report, '>', $file or die "Cannot open $file $!\n"; @@ -273,5 +274,34 @@ print $report "Job done!\n"; close $report; } else { - print "sRNAPipe v1.1\n"; + print "sRNAPipe version $sRNAPipe::VERSION + +Usage: + +sRNAPipe --fastq <fastq file 1> --fastq_n <name 1> [--fastq <fastq file 2> --fastq_n <name 2> --fastq <fastq file 3> -- fastq_n <name 3> ...] --ref <reference genome> [--build_index] --transcripts <transcripts> [--build_transcripts] --TE <transposable elements> [--build_TE] --miRNAs <miRNAs> [--build_miRNAs] --snRNAs <snRNAs> [--build_snRNAs] --rRNAs <rRNAs> [--build_rRNAs] --tRNAs <tRNAs> [--buid_tRNAs] [options] + +Arguments: +--fastq <fastq file>\t\tFastq file to process +--fastq_n <name>\t\tName of the content to process +--ref <reference>\t\tFasta file containing the reference genome +--transcripts <transcripts>\tFasta file containing the transcripts +--TE <TE>\t\t\tFasta file containing the transposable elements +--miRNAs <miRNAs>\t\tFasta file containing the miRNAs +--snRNAs <snRNAs>\t\tFasta file containing the snRNAs +--rRNAs <rRNAs>\t\t\tFasta file containing the rRNAs +--tRNAs <tRNAS>\t\t\tFasta file containing the tRNAs + +For any fasta file, if a bwa index is not provided, you should build it through the corresponding '--build_[element]' argument + +Options: +--min <INT>\t\t\tMinimum read size (default: 18) +--max <INT>\t\t\tMaximum read size (default: 29) +--si_min <INT>\t\t\tLower bound of siRNA range (default: 21) +--si_max <INT>\t\t\tHigher bound of siRNA range (default: 21) +--pi_min <INT>\t\t\tLower bound of piRNA range (default: 23) +--pi_max <INT>\t\t\tHigher bound of piRNA range (default: 29) +--mis <INT>\t\t\tMaximal genome mismatches (default: 0) +--misTE <INT>\t\t\tMaximal TE mismatches (default: 3) +--PPPon <true|false>\t\tPing-pong partners (default: true) +"; } |
| b |
| diff -r 11708af40030 -r 967512924317 bin/subgroups.pm --- a/bin/subgroups.pm Thu Jan 24 13:09:46 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,174 +0,0 @@ -package subgroups; - -use strict; -use warnings; -use Exporter; -our @ISA = qw( Exporter ); -our @EXPORT_OK = qw( &subgroups ); - -use POSIX; -use File::Copy; -use FindBin; -use lib $FindBin::Bin; -use align qw ( get_hash_alignment ); - -sub subgroups -{ - my ($fin, $dir, $mis, $mis_TE, $proc, $tRNAs, $rRNAs, $snRNAs, $miRNAs, $transcripts, $TE, $min_si, $max_si, $min_pi, $max_pi, $report ) = @_; - my (@files, $sum, $pie, $repar, %ismapped, %isjunk, %repartition, @junk_ref, @all_ref ); - - srand(); - print $report "----------------------------\n"; - print $report "Create subgroups:\nfastq_in: $fin\ndirectory_out: $dir\nmismatches: $mis\nmismatches TE: $mis_TE\n"; - - mkdir $dir; - $dir = $dir.'/' unless $dir =~ /(.*)\/$/; - - my $accept_miRNas = $dir.'miRNAs.fastq'; - my $reject_miRNAs = $dir.'miRNAs_rejected.fastq'; - my $sam_miRNAs = $dir.'miRNAs.sam'; - my @tmp = get_hash_alignment($miRNAs, $mis, 1, 1, $accept_miRNas, $reject_miRNAs, $fin, $proc, 'miRNAs',$sam_miRNAs, $report); - my $mi = $tmp[0]; my $sam = ''; - $repartition{'miRNAs'} = $mi; - - - my $reject_rRNAs = $dir.'rRNAs_rejected.fastq'; - if ( $rRNAs eq 'None') - { - move($reject_miRNAs,$reject_rRNAs); - } - else - { - $sam = new String::Random; - $sam = $sam->randpattern("CCcccccc"); - @tmp = get_hash_alignment($rRNAs, $mis, 0, 1, 'NA', $reject_rRNAs, $reject_miRNAs, $proc, 'rRNAs', $sam, $report); - $repartition{'rRNAs'} = $tmp[0]; - unlink $sam, $sam.'_aln.err', $sam.'_samse.err'; - } - - my $reject_tRNAs = $dir.'rRNAs_rejected.fastq'; - if ( $rRNAs eq 'None') - { - move($reject_rRNAs,$reject_tRNAs); - } - else - { - $sam = new String::Random; - $sam = $sam->randpattern("CCcccccc"); - @tmp = get_hash_alignment($tRNAs, $mis, 0, 1, 'NA', $reject_tRNAs, $reject_rRNAs, $proc, 'tRNAs', $sam, $report); - $repartition{'tRNAs'} = $tmp[0]; - unlink $sam, $sam.'_aln.err', $sam.'_samse.err'; - } - - - my $bonafide = $dir.'bonafide_reads.fastq'; - if ( $rRNAs eq 'None') - { - move($reject_tRNAs,$bonafide); - } - else - { - $sam = new String::Random; - $sam = $sam->randpattern("CCcccccc"); - @tmp = get_hash_alignment($snRNAs, $mis, 0, 1, 'NA', $bonafide, $reject_tRNAs, $proc, 'snRNAs', $sam, $report); - $repartition{'snRNAs'} = $tmp[0]; - - unlink $sam, $sam.'_aln.err', $sam.'_samse.err'; - } - my $bo = $tmp[1]; - - my $sam_transcripts = $dir.'transcripts.sam'; - my $reject_transcripts = $dir.'rejected_transcripts.fastq'; - @tmp = get_hash_alignment($transcripts, $mis, 0, 1, 'NA', $reject_transcripts, $bonafide, $proc, 'transcripts', $sam_transcripts, $report, $dir.'transcripts.fai'); - $repartition{'transcripts'} = $tmp[0]; - - - my $sam_TEs = $dir.'TEs.sam'; - my $reject_TEs = $dir.'rejected.fastq'; - @tmp = get_hash_alignment($TE, $mis_TE, 0, 1, 'NA', $reject_TEs, $reject_transcripts, $proc, 'TEs', $sam_TEs, $report, $dir.'TEs.fai' ); - $repartition{'TEs'} = $tmp[0] ; $repartition{'others'} = $tmp[1]; - unlink $sam, $sam.'_aln.err', $sam.'_samse.err'; - unlink $reject_transcripts; - unlink $reject_rRNAs; - unlink $reject_miRNAs; - unlink $reject_tRNAs; - - #create repartition - my $pi = fastqSubgroups($bonafide, $dir, $min_si, $max_si, $min_pi, $max_pi ); - - open (my $re, '>'.$dir.'repartition.txt') || die "cannot open $dir repartition.txt $!\n"; - print $re "type\tnumber\tpercentage\n"; - $sum += $_ foreach values %repartition; - foreach my $k ( sort keys %repartition ) - { - my $prct = 0; - $prct = $repartition{$k} / $sum * 100 if $sum != 0; - print $re "$k\t$repartition{$k}\t"; printf $re "%.2f\n",$prct; - } - return ( $bo, $mi, $pi); -} - -sub fastqSubgroups -{ - my ( $fastq, $output_directory, $min_si, $max_si, $min_pi, $max_pi ) = @_; - my $fastq_siRNA = $output_directory."siRNAs.fastq"; - my $fastq_piRNA = $output_directory."piRNAs.fastq"; - - open my $fic, '<', $fastq || die "cannot open input file $! \n"; - open my $si, '>', $fastq_siRNA || die "cannot open siRNA.fastq $! \n"; - open my $pi, '>', $fastq_piRNA || die "cannot open piRNA.fastq $! \n"; - - my ($length, $cmp, $type, $siRNA_number, $miRNA_h_number, $piRNA_number, $not_pi_number) = (0,0,0,0,0,0,0); - my (@fastq) =(); my $seq_name; - my $out; - while(<$fic>) - { - chomp $_; - $cmp++; - if ($cmp == 1) - { - die "file do not contain a @ at line $cmp\n" unless ($_ =~ /^\@/ ); - $type = 0; @fastq = (); - if ($_ =~ /^\@(.*)\s.*/) { $seq_name = $1;} - elsif ($_ =~ /^\@(.*)/) {$seq_name = $1;} - push(@fastq,$_); - } - elsif ($cmp == 2) - { - #die "unrecognized symbol at line $cmp\n" unless $_ =~ /[atcgATCGnN]+/; - push(@fastq,$_); - $length = length($_); - $type = 0; - if ( $length >= $min_si && $length <= $max_si ) - { - $type = 2; - $siRNA_number++; - } - if ($length >= $min_pi && $length <= $max_pi ) - { - $type += 4; - $piRNA_number++; - } - } - elsif ($cmp == 3 ) - { - die "file do not contain a + at line $cmp\n" unless $_ =~ /^\+/; - push(@fastq,$_); - } - elsif ($cmp == 4 ) - { - push(@fastq,$_); - $cmp = 0; - if ($type != 0) - { - if ($type & 4 ) { foreach my $t (@fastq) { print $pi $t."\n";} } - if ($type & 2 ) { foreach my $t (@fastq) { print $si $t."\n";} } - } - } - } - close $fic; - close $si; close $pi; - return ($piRNA_number); -} - -1; |
| b |
| diff -r 11708af40030 -r 967512924317 lib/sRNAPipe.pm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/sRNAPipe.pm Mon Jan 28 11:57:15 2019 -0500 |
| b |
| @@ -0,0 +1,5 @@ +package sRNAPipe; + +our $VERSION = '1.1'; + +1; |
| b |
| diff -r 11708af40030 -r 967512924317 lib/sRNAPipe/Rcall.pm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/sRNAPipe/Rcall.pm Mon Jan 28 11:57:15 2019 -0500 |
| [ |
| @@ -0,0 +1,136 @@ +package sRNAPipe::Rcall; + +use strict; +use warnings; +use Statistics::R; + +use Exporter; +our @ISA = qw(Exporter); +our @EXPORT_OK = qw( &histogram &pie_chart &bg_to_png ); + +sub histogram +{ + my ($size_hashR, $out_png, $size) = @_; + my (@abs, @ord); + my $i = 0; + foreach my $k (sort {$a <=> $b} keys %{$size_hashR}) + { + my $percentage = 0; + $percentage = $size_hashR->{$k} * 100 / $size if $size != 0; + $abs[$i] = $k ; $ord[$i] = $percentage; $i++; + } + my $abs = join (",", @abs ); + my $ord = join (",", @ord ); + if (scalar(@abs) != 0) + { + + my $R = Statistics::R->new(); + $R->startR; + $R->send( + qq`library(ggplot2) + percentage = c($ord) + size =c($abs) + min = min(size) + max = max(size) + dat = data.frame(size,percentage) + png(filename=\"$out_png\", width = 640, height = 640) + c = ggplot(dat,aes(size,percentage)) + c + geom_bar(stat="identity") + scale_x_continuous(breaks=min:max)+theme( axis.text.x = element_text(angle=90, hjust=0.5, size=20), axis.text.y = element_text( size=20 ), axis.title.x = element_text( size=25, face="bold"), axis.title.y = element_text( size=25, face="bold") ) + dev.off()`); + $R->stopR(); + + } +} + +sub bg_to_png +{ + my ( $fai, $bgP, $bgM, $dir, $sb ) = @_; + my $R = Statistics::R->new(); + $R->startR; + $R->send( + qq`library('Sushi') + fai =read.table("$fai") + if ( file.info("$bgP")\$size !=0 ) + { + bgP = read.table("$bgP") + } else { bgP = data.frame(factor(),integer()) } + + if ( file.info("$bgM")\$size !=0 ) + { + bgM = read.table("$bgM") + } else { bgM = data.frame(factor(),integer()) } + + f_both = function(chr,end) { + jpeg( paste0("$dir",as.character(chr),".png"), quality=100) + par(mfrow=c(2,1),mar=c(1,10,1,3)) + plotBedgraph(bgP, chrom=chr,chromstart=0,chromend=end,transparency=.50, color=SushiColors(2)(2)[1]) + axis(side=2,las=2,tcl=.2) + mtext("Scaled Read Depth",side=2,line=4,cex=1,font=2) + plotBedgraph(bgM, chrom=chr,chromstart=0,chromend=end,transparency=.50, flip=TRUE, color=SushiColors(2)(2)[2]) + labelgenome(chrom=chr,chromstart=0,chromend=end,side=3,n=3,scale="$sb", line=0, chromline = 0.5, scaleline = 0.5, scaleadjust =1.05, chromadjust = -0.4) + axis(side=2,las=2,tcl=.2,at=pretty(par("yaxp")[c(1,2)]),labels=-1*pretty(par("yaxp")[c(1,2)])) + mtext("Scaled Read Depth",side=2,line=4.5,cex=1,font=2) + dev.off() + } + + f_plus = function(chr,end) { + jpeg( paste0("$dir",as.character(chr),".png"), quality=100) + plotBedgraph(bgP, chrom=chr,chromstart=0,chromend=end,transparency=.50, color=SushiColors(2)(2)[1]) + labelgenome(chrom=chr,chromstart=0,chromend=end,n=3,scale="$sb", line=0, chromline = 0.5, scaleline = 0.5, scaleadjust =1.05, chromadjust = -0.4) + axis(side=2,las=2,tcl=.2) + mtext("Scaled Read Depth",side=2,line=4,cex=1,font=2) + dev.off() + } + + f_minus = function(chr,end) { + jpeg( paste0("$dir",as.character(chr),".png"), quality=100) + plotBedgraph(bgM, chrom=chr,chromstart=0,chromend=end,transparency=.50, flip=TRUE, color=SushiColors(2)(2)[2]) + labelgenome(chrom=chr,chromstart=0,chromend=end,n=3,scale="$sb", line=0, chromline = 0.5, scaleline = 0.5, scaleadjust =1.05, chromadjust = -0.4) + axis(side=2,las=2,tcl=.2,at=pretty(par("yaxp")[c(1,2)]),labels=-1*pretty(par("yaxp")[c(1,2)])) + mtext("Scaled Read Depth",side=2,line=4.5,cex=1,font=2) + dev.off() + } + + fai_b = fai[fai\$V1 %in% intersect(bgM\$V1,bgP\$V1), ] + mapply( f_both, fai_b\$V1, fai_b\$V2) + + fai_p = fai[fai\$V1 %in% setdiff(bgP\$V1,bgM\$V1), ] + mapply( f_plus, fai_p\$V1, fai_p\$V2) + + fai_m = fai[fai\$V1 %in% setdiff(bgM\$V1,bgP\$V1), ] + mapply( f_minus, fai_m\$V1, fai_m\$V2) `); + + $R->stopR(); +} + +sub pie_chart +{ + my $dir = shift; + my $in = $dir.'repartition.txt'; + my $out = $dir.'pie_chart.png'; + + my $R = Statistics::R->new(); + $R->startR; + $R->send( + qq` + library(plotrix) + library(RColorBrewer) + R =read.table("$in",header=T) + values = round(R\$percentage) + keys = R\$type + lab = paste(values, "%", sep="") + png("$out") + colors <- brewer.pal(7,"Paired") + pie(values, col=colors, labels=lab, clockwise=TRUE) + legend("bottom", legend = keys, fill=colors, bty="n", ncol = 3) + par(mai = c(0,0,0,0)) + layout(c(1,2),heights=c(0.3,1)) + plot.new() + legend("bottom", legend = keys, fill=colors, bty="n",ncol = 3) + pie(values, col=colors, labels=lab, clockwise=TRUE) + dev.off()` + ); + $R->stopR(); +} + +1; |
| b |
| diff -r 11708af40030 -r 967512924317 lib/sRNAPipe/align.pm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/sRNAPipe/align.pm Mon Jan 28 11:57:15 2019 -0500 |
| [ |
| b'@@ -0,0 +1,551 @@\n+package sRNAPipe::align;\n+\n+use strict;\n+use warnings;\n+use File::Basename;\n+use String::Random;\n+\n+use FindBin;\n+use lib "$FindBin::Bin/../lib";\n+use sRNAPipe::Rcall qw ( histogram );\n+\n+use Exporter;\n+our @ISA = qw( Exporter );\n+our @EXPORT = qw( &rpms_rpkm_te &BWA_call &to_build &get_unique &sam_sorted_bam &get_hash_alignment &sam_to_bam_bg &sam_count &sam_count_mis &rpms_rpkm &get_fastq_seq &extract_sam );\n+\n+sub to_build\n+{\n+ my ( $toBuildTabP, $log, $newdir ) = @_;\n+\n+ foreach my $pairs ( @{ $toBuildTabP } )\n+ {\n+ if ( $pairs->[0] == 1 )\n+ {\n+ my $sym = $newdir.basename(${$pairs->[1]}).\'_symlink.fa\';\n+ symlink( ${$pairs->[1]}, $sym );\n+ ${$pairs->[1]} = $sym;\n+ build_index ( ${$pairs->[1]}, $log );\n+ }\n+ }\n+}\n+\n+sub build_index\n+{\n+ my $to_index = shift;\n+ my $log = shift;\n+ my $index_log = $to_index.\'_index.err\';\n+ `bwa index \'$to_index\' 2> \'$index_log\'`;\n+ print $log "Creating index for $to_index\\n";\n+}\n+\n+sub get_unique\n+{\n+ my ( $sam, $s_uni, $out_prefix, $col_prefix, $details, $report ) = @_;\n+\n+ my $fout = $col_prefix.\'_all_mappers.fastq\';\n+ my $funi = $col_prefix.\'_unique_mappers.fastq\';\n+ my $frej = $col_prefix.\'_unmapped.fastq\';\n+ \n+ my $repartition = $out_prefix.\'distribution.txt\';\n+ my $png_rep = $out_prefix.\'distribution.png\';\n+ my ( %duplicates, %genome_hits) ;\n+\n+ #alignement to the first reference\n+ my @return = sam_parse( $sam, $fout, $funi, $frej, $s_uni, \\%duplicates, \\%genome_hits, $report );\n+ my $ref_fai = $return[4];\n+ my $mappers = $return[5];\n+ my $mappers_uni = $return[6];\n+ my $size_mappedHashR = $return[7];\n+\n+ if ( $details == 1 )\n+ {\n+ #print number of duplicates and hits number\n+ my ($pourcentage, $total) =(0,0);\n+\n+ $total += $_ foreach values %{$size_mappedHashR};\n+ open (my $rep, \'>\'.$repartition) || die "cannot create $repartition $!\\n";\n+ print $rep "size\\tnumber\\tpercentage\\n";\n+ foreach my $k (sort{$a cmp $b} keys (%{$size_mappedHashR}))\n+ {\n+ $pourcentage = 0;\n+ $pourcentage = $size_mappedHashR->{$k} / $total * 100 unless $total ==0;\n+\n+ print $rep "$k\\t$size_mappedHashR->{$k}\\t";\n+ printf $rep "%.2f\\n",$pourcentage;\n+ }\n+\n+ histogram($size_mappedHashR, $png_rep, $total);\n+\n+\n+ my $dup = $out_prefix.\'dup_mapnum.txt\';\n+ my $dup_u = $out_prefix .\'dup_unique.txt\';\n+ my $dup_r = $out_prefix .\'dup_nonmapp.txt\';\n+ open(my $tab,">".$dup) || die "cannot open output txt file\\n";\n+ open(my $tab_r,">".$dup_r) || die "cannot open output txt file\\n";\n+ open(my $tab_u,">".$dup_u) || die "cannot open output txt file\\n";\n+ print $tab "sequence\\tcount\\tmapnum\\n";\n+ print $tab_u "sequence\\tcount\\n";\n+ print $tab_r "sequence\\tcount\\n";\n+ foreach my $k (sort {$duplicates{$b} <=> $duplicates{$a}}keys %duplicates)\n+ {\n+ $duplicates{$k} = 0 unless exists($duplicates{$k});\n+ $genome_hits{$k} = 0 unless exists($genome_hits{$k});\n+ if ($genome_hits{$k} != 0) { print $tab $k."\\t".$duplicates{$k}."\\t".$genome_hits{$k}."\\n"; }\n+ else {print $tab_r $k."\\t".$duplicates{$k}."\\n";}\n+ if ($genome_hits{$k} == 1) { print $tab_u $k."\\t".$duplicates{$k}."\\n"; }\n+ }\n+ close $dup; close $dup_r; close $dup_u;\n+ }\n+ return ( $ref_fai, $mappers, $mappers_uni );\n+}\n+\n+sub sam_parse\n+{\n+ my ( $sam, $fastq_accepted, $fastq_accepted_unique, $fastq_rejected, $sam_unique, $duplicate_hashR, $best_hit_number_hashR, $report ) = @_ ;\n+ my ($reads, $mappers, $mappersUnique, @garbage, %size_num, %size_num_spe, %number, %numberSens, %numberReverse, %unique_number, %numberNM, %numberM, %size);\n+ $mappers = $mappersUnique = $reads = 0;\n+\n+ open my $fic, \'<\', $sam || die "cannot open $sam $!\\n";\n+ op'..b'> \'$samse_err\' > \'$sam\'\\n";\n+ `bwa aln -t $number_of_cpus -n $mismatches \'$index\' \'$fastq\' 2> \'$aln_err\' | bwa samse $index /dev/stdin \'$fastq\' 2> \'$samse_err\' > \'$sam\' `;\n+}\n+\n+sub rpms_rpkm\n+{\n+ my ( $counthashR, $sizehashR, $mapped, $out_file, $piRNA_number, $miRNA_number, $bonafide_number ) =@_;\n+ open(my $out, ">".$out_file) || die "cannot open normalized file $! \\n";\n+ print $out "ID\\treads counts\\tRPKM";\n+ print $out "\\tper million of piRNAs" if ($piRNA_number != 0);\n+ print $out "\\tper million of miRNAs" if ($miRNA_number != 0);\n+ print $out "\\tper million of bonafide reads" if ($bonafide_number != 0);\n+ print $out "\\n";\n+ foreach my $k ( sort keys %{$counthashR} )\n+ {\n+ my ($rpkm, $pirna, $mirna, $bonafide) = (0,0,0,0);\n+ \n+ $rpkm = ( $counthashR->{$k} * 1000000000) / ( $sizehashR->{$k} * $mapped) if ( $sizehashR->{$k} * $mapped) != 0 ;\n+ print $out $k."\\t".$counthashR->{$k}."\\t"; printf $out "%.2f",$rpkm;\n+ \n+ if ($piRNA_number != 0 )\n+ {\n+ $pirna = ( $counthashR->{$k} * 1000000) / $piRNA_number;\n+ printf $out "\\t%.2f",$pirna;\n+ }\n+ if ($miRNA_number != 0 )\n+ {\n+ $mirna = ( $counthashR->{$k} * 1000000) / $miRNA_number;\n+ printf $out "\\t%.2f",$mirna;\n+ }\n+ if ($bonafide_number != 0 )\n+ {\n+ $bonafide = ( $counthashR->{$k} * 1000000) / $bonafide_number;\n+ printf $out "\\t%.2f",$bonafide;\n+ }\n+ print $out "\\n";\n+ }\n+ close $out;\n+}\n+\n+sub extract_sam\n+{\n+ my ( $hashRef, $sam_in, $sam_out, $sam_uni_out, $fastq_out, $fastq_uni_out ) = @_;\n+ \n+ open my $s_in, \'<\', $sam_in || die "cannot open $sam_in file $!\\n";\n+\n+ open my $f_out, \'>\', $fastq_out || die "cannot create $fastq_out $!\\n";\n+ open my $f_uni_out, \'>\', $fastq_uni_out || die "cannot create $fastq_uni_out $!\\n";\n+ \n+ open my $s_out, \'>\', $sam_out || die "cannot create $sam_out file $!\\n" if defined ($hashRef);\n+ open my $s_uni_out, \'>\', $sam_uni_out || die "cannot create $sam_uni_out file $!\\n";\n+\n+ my $sequence = \'\';\n+ while(<$s_in>)\n+ {\n+ if ($_ =~ /^\\@[A-Za-z][A-Za-z](\\t[A-Za-z][A-Za-z0-9]:[ -~]+)+$/ || $_ =~ /^\\@CO\\t.*/ )\n+ {\n+ print $s_out $_ if defined ($hashRef);\n+ print $s_uni_out $_;\n+ next;\n+ }\n+ my @line = split (/\\t/,$_);\n+ $sequence = $line[0];\n+ if ( (! defined ($hashRef) )|| ( exists $hashRef->{$sequence} && $hashRef->{$sequence} == 1 ) )\n+ {\n+ my $arn = $line[9];\n+ if ($line[1] & 16)\n+ {\n+ $arn =reverse($arn);\n+ $arn =~ tr/atgcuATGCU/tacgaTACGA/;\n+ }\n+\n+ if ( ( $line[1] == 16 || $line[1] == 0 ) )\n+ {\n+ print $f_out "\\@".$line[0]."\\n".$arn."\\n+\\n".$line[10]."\\n" ;\n+ print $s_out $_ if defined ($hashRef);\n+ if ( $line[11] eq "XT:A:U" )\n+ {\n+ print $f_uni_out "\\@".$line[0]."\\n".$arn."\\n+\\n".$line[10]."\\n" ;\n+ print $s_uni_out $_ ;\n+ }\n+ }\n+ }\n+ }\n+ close $s_in; close $s_out if defined ($hashRef);\n+ close $s_uni_out; close $f_out; close $f_uni_out;\n+}\n+\n+sub get_fastq_seq\n+{\n+ my $fastq = shift;\n+ my %hash; my $cmp = 0;\n+\n+ open my $fic, \'<\', $fastq || die "cannot open input file $! \\n";\n+ while(<$fic>)\n+ {\n+ chomp $_;\n+ $cmp++;\n+ if ($cmp % 4 == 1)\n+ {\n+ die "file do not contain a @ at line $cmp\\n" unless ($_ =~ /^\\@/ );\n+ if ($_ =~ /^\\@(.*)\\s.*/) { $hash{$1} = 1;}\n+ elsif ($_ =~ /^\\@(.*)/) { $hash{$1} = 1;}\n+ }\n+ elsif ($cmp % 4 == 3 )\n+ {\n+ die "file do not contain a + at line $cmp\\n" unless $_ =~ /^\\+/;\n+ }\n+ }\n+ close $fic;\n+ return \\%hash;\n+}\n+\n+1;\n' |
| b |
| diff -r 11708af40030 -r 967512924317 lib/sRNAPipe/css/bootstrap-responsive.css --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/sRNAPipe/css/bootstrap-responsive.css Mon Jan 28 11:57:15 2019 -0500 |
| [ |
| b'@@ -0,0 +1,1109 @@\n+/*!\n+ * Bootstrap Responsive v2.3.2\n+ *\n+ * Copyright 2012 Twitter, Inc\n+ * Licensed under the Apache License v2.0\n+ * http://www.apache.org/licenses/LICENSE-2.0\n+ *\n+ * Designed and built with all the love in the world @twitter by @mdo and @fat.\n+ */\n+\n+.clearfix {\n+ *zoom: 1;\n+}\n+\n+.clearfix:before,\n+.clearfix:after {\n+ display: table;\n+ line-height: 0;\n+ content: "";\n+}\n+\n+.clearfix:after {\n+ clear: both;\n+}\n+\n+.hide-text {\n+ font: 0/0 a;\n+ color: transparent;\n+ text-shadow: none;\n+ background-color: transparent;\n+ border: 0;\n+}\n+\n+.input-block-level {\n+ display: block;\n+ width: 100%;\n+ min-height: 30px;\n+ -webkit-box-sizing: border-box;\n+ -moz-box-sizing: border-box;\n+ box-sizing: border-box;\n+}\n+\n+@-ms-viewport {\n+ width: device-width;\n+}\n+\n+.hidden {\n+ display: none;\n+ visibility: hidden;\n+}\n+\n+.visible-phone {\n+ display: none !important;\n+}\n+\n+.visible-tablet {\n+ display: none !important;\n+}\n+\n+.hidden-desktop {\n+ display: none !important;\n+}\n+\n+.visible-desktop {\n+ display: inherit !important;\n+}\n+\n+@media (min-width: 768px) and (max-width: 979px) {\n+ .hidden-desktop {\n+ display: inherit !important;\n+ }\n+ .visible-desktop {\n+ display: none !important ;\n+ }\n+ .visible-tablet {\n+ display: inherit !important;\n+ }\n+ .hidden-tablet {\n+ display: none !important;\n+ }\n+}\n+\n+@media (max-width: 767px) {\n+ .hidden-desktop {\n+ display: inherit !important;\n+ }\n+ .visible-desktop {\n+ display: none !important;\n+ }\n+ .visible-phone {\n+ display: inherit !important;\n+ }\n+ .hidden-phone {\n+ display: none !important;\n+ }\n+}\n+\n+.visible-print {\n+ display: none !important;\n+}\n+\n+@media print {\n+ .visible-print {\n+ display: inherit !important;\n+ }\n+ .hidden-print {\n+ display: none !important;\n+ }\n+}\n+\n+@media (min-width: 1200px) {\n+ .row {\n+ margin-left: -30px;\n+ *zoom: 1;\n+ }\n+ .row:before,\n+ .row:after {\n+ display: table;\n+ line-height: 0;\n+ content: "";\n+ }\n+ .row:after {\n+ clear: both;\n+ }\n+ [class*="span"] {\n+ float: left;\n+ min-height: 1px;\n+ margin-left: 30px;\n+ }\n+ .container,\n+ .navbar-static-top .container,\n+ .navbar-fixed-top .container,\n+ .navbar-fixed-bottom .container {\n+ width: 1170px;\n+ }\n+ .span12 {\n+ width: 1170px;\n+ }\n+ .span11 {\n+ width: 1070px;\n+ }\n+ .span10 {\n+ width: 970px;\n+ }\n+ .span9 {\n+ width: 870px;\n+ }\n+ .span8 {\n+ width: 770px;\n+ }\n+ .span7 {\n+ width: 670px;\n+ }\n+ .span6 {\n+ width: 570px;\n+ }\n+ .span5 {\n+ width: 470px;\n+ }\n+ .span4 {\n+ width: 370px;\n+ }\n+ .span3 {\n+ width: 270px;\n+ }\n+ .span2 {\n+ width: 170px;\n+ }\n+ .span1 {\n+ width: 70px;\n+ }\n+ .offset12 {\n+ margin-left: 1230px;\n+ }\n+ .offset11 {\n+ margin-left: 1130px;\n+ }\n+ .offset10 {\n+ margin-left: 1030px;\n+ }\n+ .offset9 {\n+ margin-left: 930px;\n+ }\n+ .offset8 {\n+ margin-left: 830px;\n+ }\n+ .offset7 {\n+ margin-left: 730px;\n+ }\n+ .offset6 {\n+ margin-left: 630px;\n+ }\n+ .offset5 {\n+ margin-left: 530px;\n+ }\n+ .offset4 {\n+ margin-left: 430px;\n+ }\n+ .offset3 {\n+ margin-left: 330px;\n+ }\n+ .offset2 {\n+ margin-left: 230px;\n+ }\n+ .offset1 {\n+ margin-left: 130px;\n+ }\n+ .row-fluid {\n+ width: 100%;\n+ *zoom: 1;\n+ }\n+ .row-fluid:before,\n+ .row-fluid:after {\n+ display: table;\n+ line-height: 0;\n+ content: "";\n+ }\n+ .row-fluid:after {\n+ clear: both;\n+ }\n+ .row-fluid [class*="span"] {\n+ display: block;\n+ float: left;\n+ width: 100%;\n+ min-height: 30px;\n+ margin-left: 2.564102564102564%;\n+ *margin-left: 2.5109110747408616%;\n+ -webkit-box-sizing: border-box;\n+ -moz-box-sizing: border-box;\n+ box-sizing: border-box;\n+ }\n+ .row-fluid [class*="span"]:first-child {\n+ margin-left: 0;\n+ }\n+ .row-fluid .controls-row [class*="span"] + [class*="span"] {\n+ margin-left: 2.564102564102564%;\n+ }\n+ .row-fluid .span12 {\n+ width: 100%;\n+ *width: 99.9468'..b'tic;\n+ }\n+}\n+\n+@media (max-width: 979px) {\n+ body {\n+ padding-top: 0;\n+ }\n+ .navbar-fixed-top,\n+ .navbar-fixed-bottom {\n+ position: static;\n+ }\n+ .navbar-fixed-top {\n+ margin-bottom: 20px;\n+ }\n+ .navbar-fixed-bottom {\n+ margin-top: 20px;\n+ }\n+ .navbar-fixed-top .navbar-inner,\n+ .navbar-fixed-bottom .navbar-inner {\n+ padding: 5px;\n+ }\n+ .navbar .container {\n+ width: auto;\n+ padding: 0;\n+ }\n+ .navbar .brand {\n+ padding-right: 10px;\n+ padding-left: 10px;\n+ margin: 0 0 0 -5px;\n+ }\n+ .nav-collapse {\n+ clear: both;\n+ }\n+ .nav-collapse .nav {\n+ float: none;\n+ margin: 0 0 10px;\n+ }\n+ .nav-collapse .nav > li {\n+ float: none;\n+ }\n+ .nav-collapse .nav > li > a {\n+ margin-bottom: 2px;\n+ }\n+ .nav-collapse .nav > .divider-vertical {\n+ display: none;\n+ }\n+ .nav-collapse .nav .nav-header {\n+ color: #777777;\n+ text-shadow: none;\n+ }\n+ .nav-collapse .nav > li > a,\n+ .nav-collapse .dropdown-menu a {\n+ padding: 9px 15px;\n+ font-weight: bold;\n+ color: #777777;\n+ -webkit-border-radius: 3px;\n+ -moz-border-radius: 3px;\n+ border-radius: 3px;\n+ }\n+ .nav-collapse .btn {\n+ padding: 4px 10px 4px;\n+ font-weight: normal;\n+ -webkit-border-radius: 4px;\n+ -moz-border-radius: 4px;\n+ border-radius: 4px;\n+ }\n+ .nav-collapse .dropdown-menu li + li a {\n+ margin-bottom: 2px;\n+ }\n+ .nav-collapse .nav > li > a:hover,\n+ .nav-collapse .nav > li > a:focus,\n+ .nav-collapse .dropdown-menu a:hover,\n+ .nav-collapse .dropdown-menu a:focus {\n+ background-color: #f2f2f2;\n+ }\n+ .navbar-inverse .nav-collapse .nav > li > a,\n+ .navbar-inverse .nav-collapse .dropdown-menu a {\n+ color: #999999;\n+ }\n+ .navbar-inverse .nav-collapse .nav > li > a:hover,\n+ .navbar-inverse .nav-collapse .nav > li > a:focus,\n+ .navbar-inverse .nav-collapse .dropdown-menu a:hover,\n+ .navbar-inverse .nav-collapse .dropdown-menu a:focus {\n+ background-color: #111111;\n+ }\n+ .nav-collapse.in .btn-group {\n+ padding: 0;\n+ margin-top: 5px;\n+ }\n+ .nav-collapse .dropdown-menu {\n+ position: static;\n+ top: auto;\n+ left: auto;\n+ display: none;\n+ float: none;\n+ max-width: none;\n+ padding: 0;\n+ margin: 0 15px;\n+ background-color: transparent;\n+ border: none;\n+ -webkit-border-radius: 0;\n+ -moz-border-radius: 0;\n+ border-radius: 0;\n+ -webkit-box-shadow: none;\n+ -moz-box-shadow: none;\n+ box-shadow: none;\n+ }\n+ .nav-collapse .open > .dropdown-menu {\n+ display: block;\n+ }\n+ .nav-collapse .dropdown-menu:before,\n+ .nav-collapse .dropdown-menu:after {\n+ display: none;\n+ }\n+ .nav-collapse .dropdown-menu .divider {\n+ display: none;\n+ }\n+ .nav-collapse .nav > li > .dropdown-menu:before,\n+ .nav-collapse .nav > li > .dropdown-menu:after {\n+ display: none;\n+ }\n+ .nav-collapse .navbar-form,\n+ .nav-collapse .navbar-search {\n+ float: none;\n+ padding: 10px 15px;\n+ margin: 10px 0;\n+ border-top: 1px solid #f2f2f2;\n+ border-bottom: 1px solid #f2f2f2;\n+ -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.1), 0 1px 0 rgba(255, 255, 255, 0.1);\n+ -moz-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.1), 0 1px 0 rgba(255, 255, 255, 0.1);\n+ box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.1), 0 1px 0 rgba(255, 255, 255, 0.1);\n+ }\n+ .navbar-inverse .nav-collapse .navbar-form,\n+ .navbar-inverse .nav-collapse .navbar-search {\n+ border-top-color: #111111;\n+ border-bottom-color: #111111;\n+ }\n+ .navbar .nav-collapse .nav.pull-right {\n+ float: none;\n+ margin-left: 0;\n+ }\n+ .nav-collapse,\n+ .nav-collapse.collapse {\n+ height: 0;\n+ overflow: hidden;\n+ }\n+ .navbar .btn-navbar {\n+ display: block;\n+ }\n+ .navbar-static .navbar-inner {\n+ padding-right: 10px;\n+ padding-left: 10px;\n+ }\n+}\n+\n+@media (min-width: 980px) {\n+ .nav-collapse.collapse {\n+ height: auto !important;\n+ overflow: visible !important;\n+ }\n+}\n' |
| b |
| diff -r 11708af40030 -r 967512924317 lib/sRNAPipe/css/bootstrap-table.css --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/sRNAPipe/css/bootstrap-table.css Mon Jan 28 11:57:15 2019 -0500 |
| [ |
| @@ -0,0 +1,313 @@ +/** + * @author zhixin wen <wenzhixin2010@gmail.com> + * version: 1.11.1 + * https://github.com/wenzhixin/bootstrap-table/ + */ + +.bootstrap-table .table { + margin-bottom: 0 !important; + border-bottom: 1px solid #dddddd; + border-collapse: collapse !important; + border-radius: 1px; +} + +.bootstrap-table .table:not(.table-condensed), +.bootstrap-table .table:not(.table-condensed) > tbody > tr > th, +.bootstrap-table .table:not(.table-condensed) > tfoot > tr > th, +.bootstrap-table .table:not(.table-condensed) > thead > tr > td, +.bootstrap-table .table:not(.table-condensed) > tbody > tr > td, +.bootstrap-table .table:not(.table-condensed) > tfoot > tr > td { + padding: 8px; +} + +.bootstrap-table .table.table-no-bordered > thead > tr > th, +.bootstrap-table .table.table-no-bordered > tbody > tr > td { + border-right: 2px solid transparent; +} + +.bootstrap-table .table.table-no-bordered > tbody > tr > td:last-child { + border-right: none; +} + +.fixed-table-container { + position: relative; + clear: both; + border: 1px solid #dddddd; + border-radius: 4px; + -webkit-border-radius: 4px; + -moz-border-radius: 4px; +} + +.fixed-table-container.table-no-bordered { + border: 1px solid transparent; +} + +.fixed-table-footer, +.fixed-table-header { + overflow: hidden; +} + +.fixed-table-footer { + border-top: 1px solid #dddddd; +} + +.fixed-table-body { + overflow-x: auto; + overflow-y: auto; + height: 100%; +} + +.fixed-table-container table { + width: 100%; +} + +.fixed-table-container thead th { + height: 0; + padding: 0; + margin: 0; + border-left: 1px solid #dddddd; +} + +.fixed-table-container thead th:focus { + outline: 0 solid transparent; +} + +.fixed-table-container thead th:first-child { + border-left: none; + border-top-left-radius: 4px; + -webkit-border-top-left-radius: 4px; + -moz-border-radius-topleft: 4px; +} + +.fixed-table-container thead th .th-inner, +.fixed-table-container tbody td .th-inner { + padding: 8px; + line-height: 24px; + vertical-align: top; + overflow: hidden; + text-overflow: ellipsis; + white-space: nowrap; +} + +.fixed-table-container thead th .sortable { + cursor: pointer; + background-position: right; + background-repeat: no-repeat; + padding-right: 30px; +} + +.fixed-table-container thead th .both { + background-image: url('data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABMAAAATCAQAAADYWf5HAAAAkElEQVQoz7X QMQ5AQBCF4dWQSJxC5wwax1Cq1e7BAdxD5SL+Tq/QCM1oNiJidwox0355mXnG/DrEtIQ6azioNZQxI0ykPhTQIwhCR+BmBYtlK7kLJYwWCcJA9M4qdrZrd8pPjZWPtOqdRQy320YSV17OatFC4euts6z39GYMKRPCTKY9UnPQ6P+GtMRfGtPnBCiqhAeJPmkqAAAAAElFTkSuQmCC'); +} + +.fixed-table-container thead th .asc { + background-image: url('data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABMAAAATCAYAAAByUDbMAAAAZ0lEQVQ4y2NgGLKgquEuFxBPAGI2ahhWCsS/gDibUoO0gPgxEP8H4ttArEyuQYxAPBdqEAxPBImTY5gjEL9DM+wTENuQahAvEO9DMwiGdwAxOymGJQLxTyD+jgWDxCMZRsEoGAVoAADeemwtPcZI2wAAAABJRU5ErkJggg=='); +} + +.fixed-table-container thead th .desc { + background-image: url('data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABMAAAATCAYAAAByUDbMAAAAZUlEQVQ4y2NgGAWjYBSggaqGu5FA/BOIv2PBIPFEUgxjB+IdQPwfC94HxLykus4GiD+hGfQOiB3J8SojEE9EM2wuSJzcsFMG4ttQgx4DsRalkZENxL+AuJQaMcsGxBOAmGvopk8AVz1sLZgg0bsAAAAASUVORK5CYII= '); +} + +.fixed-table-container th.detail { + width: 30px; +} + +.fixed-table-container tbody td { + border-left: 1px solid #dddddd; +} + +.fixed-table-container tbody tr:first-child td { + border-top: none; +} + +.fixed-table-container tbody td:first-child { + border-left: none; +} + +/* the same color with .active */ +.fixed-table-container tbody .selected td { + background-color: #f5f5f5; +} + +.fixed-table-container .bs-checkbox { + text-align: center; +} + +.fixed-table-container .bs-checkbox .th-inner { + padding: 8px 0; +} + +.fixed-table-container input[type="radio"], +.fixed-table-container input[type="checkbox"] { + margin: 0 auto !important; +} + +.fixed-table-container .no-records-found { + text-align: center; +} + +.fixed-table-pagination div.pagination, +.fixed-table-pagination .pagination-detail { + margin-top: 10px; + margin-bottom: 10px; +} + +.fixed-table-pagination div.pagination .pagination { + margin: 0; +} + +.fixed-table-pagination .pagination a { + padding: 6px 12px; + line-height: 1.428571429; +} + +.fixed-table-pagination .pagination-info { + line-height: 34px; + margin-right: 5px; +} + +.fixed-table-pagination .btn-group { + position: relative; + display: inline-block; + vertical-align: middle; +} + +.fixed-table-pagination .dropup .dropdown-menu { + margin-bottom: 0; +} + +.fixed-table-pagination .page-list { + display: inline-block; +} + +.fixed-table-toolbar .columns-left { + margin-right: 5px; +} + +.fixed-table-toolbar .columns-right { + margin-left: 5px; +} + +.fixed-table-toolbar .columns label { + display: block; + padding: 3px 20px; + clear: both; + font-weight: normal; + line-height: 1.428571429; +} + +.fixed-table-toolbar .bs-bars, +.fixed-table-toolbar .search, +.fixed-table-toolbar .columns { + position: relative; + margin-top: 10px; + margin-bottom: 10px; + line-height: 34px; +} + +.fixed-table-pagination li.disabled a { + pointer-events: none; + cursor: default; +} + +.fixed-table-loading { + display: none; + position: absolute; + top: 42px; + right: 0; + bottom: 0; + left: 0; + z-index: 99; + background-color: #fff; + text-align: center; +} + +.fixed-table-body .card-view .title { + font-weight: bold; + display: inline-block; + min-width: 30%; + text-align: left !important; +} + +/* support bootstrap 2 */ +.fixed-table-body thead th .th-inner { + box-sizing: border-box; +} + +.table th, .table td { + vertical-align: middle; + box-sizing: border-box; +} + +.fixed-table-toolbar .dropdown-menu { + text-align: left; + max-height: 300px; + overflow: auto; +} + +.fixed-table-toolbar .btn-group > .btn-group { + display: inline-block; + margin-left: -1px !important; +} + +.fixed-table-toolbar .btn-group > .btn-group > .btn { + border-radius: 0; +} + +.fixed-table-toolbar .btn-group > .btn-group:first-child > .btn { + border-top-left-radius: 4px; + border-bottom-left-radius: 4px; +} + +.fixed-table-toolbar .btn-group > .btn-group:last-child > .btn { + border-top-right-radius: 4px; + border-bottom-right-radius: 4px; +} + +.bootstrap-table .table > thead > tr > th { + vertical-align: bottom; + border-bottom: 1px solid #ddd; +} + +/* support bootstrap 3 */ +.bootstrap-table .table thead > tr > th { + padding: 0; + margin: 0; +} + +.bootstrap-table .fixed-table-footer tbody > tr > td { + padding: 0 !important; +} + +.bootstrap-table .fixed-table-footer .table { + border-bottom: none; + border-radius: 0; + padding: 0 !important; +} + +.bootstrap-table .pull-right .dropdown-menu { + right: 0; + left: auto; +} + +/* calculate scrollbar width */ +p.fixed-table-scroll-inner { + width: 100%; + height: 200px; +} + +div.fixed-table-scroll-outer { + top: 0; + left: 0; + visibility: hidden; + width: 200px; + height: 150px; + overflow: hidden; +} + +/* for get correct heights */ +.fixed-table-toolbar:after, .fixed-table-pagination:after { + content: ""; + display: block; + clear: both; +} |
| b |
| diff -r 11708af40030 -r 967512924317 lib/sRNAPipe/css/bootstrap.css --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/sRNAPipe/css/bootstrap.css Mon Jan 28 11:57:15 2019 -0500 |
| [ |
| b'@@ -0,0 +1,6167 @@\n+/*!\n+ * Bootstrap v2.3.2\n+ *\n+ * Copyright 2012 Twitter, Inc\n+ * Licensed under the Apache License v2.0\n+ * http://www.apache.org/licenses/LICENSE-2.0\n+ *\n+ * Designed and built with all the love in the world @twitter by @mdo and @fat.\n+ */\n+\n+.clearfix {\n+ *zoom: 1;\n+}\n+\n+.clearfix:before,\n+.clearfix:after {\n+ display: table;\n+ line-height: 0;\n+ content: "";\n+}\n+\n+.clearfix:after {\n+ clear: both;\n+}\n+\n+.hide-text {\n+ font: 0/0 a;\n+ color: transparent;\n+ text-shadow: none;\n+ background-color: transparent;\n+ border: 0;\n+}\n+\n+.input-block-level {\n+ display: block;\n+ width: 100%;\n+ min-height: 30px;\n+ -webkit-box-sizing: border-box;\n+ -moz-box-sizing: border-box;\n+ box-sizing: border-box;\n+}\n+\n+article,\n+aside,\n+details,\n+figcaption,\n+figure,\n+footer,\n+header,\n+hgroup,\n+nav,\n+section {\n+ display: block;\n+}\n+\n+audio,\n+canvas,\n+video {\n+ display: inline-block;\n+ *display: inline;\n+ *zoom: 1;\n+}\n+\n+audio:not([controls]) {\n+ display: none;\n+}\n+\n+html {\n+ font-size: 100%;\n+ -webkit-text-size-adjust: 100%;\n+ -ms-text-size-adjust: 100%;\n+}\n+\n+a:focus {\n+ outline: thin dotted #333;\n+ outline: 5px auto -webkit-focus-ring-color;\n+ outline-offset: -2px;\n+}\n+\n+a:hover,\n+a:active {\n+ outline: 0;\n+}\n+\n+sub,\n+sup {\n+ position: relative;\n+ font-size: 75%;\n+ line-height: 0;\n+ vertical-align: baseline;\n+}\n+\n+sup {\n+ top: -0.5em;\n+}\n+\n+sub {\n+ bottom: -0.25em;\n+}\n+\n+img {\n+ width: auto\\9;\n+ height: auto;\n+ max-width: 100%;\n+ vertical-align: middle;\n+ border: 0;\n+ -ms-interpolation-mode: bicubic;\n+}\n+\n+#map_canvas img,\n+.google-maps img {\n+ max-width: none;\n+}\n+\n+button,\n+input,\n+select,\n+textarea {\n+ margin: 0;\n+ font-size: 100%;\n+ vertical-align: middle;\n+}\n+\n+button,\n+input {\n+ *overflow: visible;\n+ line-height: normal;\n+}\n+\n+button::-moz-focus-inner,\n+input::-moz-focus-inner {\n+ padding: 0;\n+ border: 0;\n+}\n+\n+button,\n+html input[type="button"],\n+input[type="reset"],\n+input[type="submit"] {\n+ cursor: pointer;\n+ -webkit-appearance: button;\n+}\n+\n+label,\n+select,\n+button,\n+input[type="button"],\n+input[type="reset"],\n+input[type="submit"],\n+input[type="radio"],\n+input[type="checkbox"] {\n+ cursor: pointer;\n+}\n+\n+input[type="search"] {\n+ -webkit-box-sizing: content-box;\n+ -moz-box-sizing: content-box;\n+ box-sizing: content-box;\n+ -webkit-appearance: textfield;\n+}\n+\n+input[type="search"]::-webkit-search-decoration,\n+input[type="search"]::-webkit-search-cancel-button {\n+ -webkit-appearance: none;\n+}\n+\n+textarea {\n+ overflow: auto;\n+ vertical-align: top;\n+}\n+\n+@media print {\n+ * {\n+ color: #000 !important;\n+ text-shadow: none !important;\n+ background: transparent !important;\n+ box-shadow: none !important;\n+ }\n+ a,\n+ a:visited {\n+ text-decoration: underline;\n+ }\n+ a[href]:after {\n+ content: " (" attr(href) ")";\n+ }\n+ abbr[title]:after {\n+ content: " (" attr(title) ")";\n+ }\n+ .ir a:after,\n+ a[href^="javascript:"]:after,\n+ a[href^="#"]:after {\n+ content: "";\n+ }\n+ pre,\n+ blockquote {\n+ border: 1px solid #999;\n+ page-break-inside: avoid;\n+ }\n+ thead {\n+ display: table-header-group;\n+ }\n+ tr,\n+ img {\n+ page-break-inside: avoid;\n+ }\n+ img {\n+ max-width: 100% !important;\n+ }\n+ @page {\n+ margin: 0.5cm;\n+ }\n+ p,\n+ h2,\n+ h3 {\n+ orphans: 3;\n+ widows: 3;\n+ }\n+ h2,\n+ h3 {\n+ page-break-after: avoid;\n+ }\n+}\n+\n+body {\n+ margin: 0;\n+ font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;\n+ font-size: 14px;\n+ line-height: 20px;\n+ color: #333333;\n+ background-color: #ffffff;\n+}\n+\n+a {\n+ color: #0088cc;\n+ text-decoration: none;\n+}\n+\n+a:hover,\n+a:focus {\n+ color: #005580;\n+ text-decoration: underline;\n+}\n+\n+.img-rounded {\n+ -webkit-border-radius: 6px;\n+ -moz-border-radius: 6px;\n+ border-radius: 6px;\n+}\n+\n+.img-polaroid {\n+ padding: 4px;\n+ background-color: #fff;\n+ border: 1px solid #ccc;\n+ border: 1px solid rgba(0, 0, 0, 0.2);\n+ -webkit-box-shadow: 0 1px 3'..b', 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);\n+ background-image: linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);\n+}\n+\n+.accordion {\n+ margin-bottom: 20px;\n+}\n+\n+.accordion-group {\n+ margin-bottom: 2px;\n+ border: 1px solid #e5e5e5;\n+ -webkit-border-radius: 4px;\n+ -moz-border-radius: 4px;\n+ border-radius: 4px;\n+}\n+\n+.accordion-heading {\n+ border-bottom: 0;\n+}\n+\n+.accordion-heading .accordion-toggle {\n+ display: block;\n+ padding: 8px 15px;\n+}\n+\n+.accordion-toggle {\n+ cursor: pointer;\n+}\n+\n+.accordion-inner {\n+ padding: 9px 15px;\n+ border-top: 1px solid #e5e5e5;\n+}\n+\n+.carousel {\n+ position: relative;\n+ margin-bottom: 20px;\n+ line-height: 1;\n+}\n+\n+.carousel-inner {\n+ position: relative;\n+ width: 100%;\n+ overflow: hidden;\n+}\n+\n+.carousel-inner > .item {\n+ position: relative;\n+ display: none;\n+ -webkit-transition: 0.6s ease-in-out left;\n+ -moz-transition: 0.6s ease-in-out left;\n+ -o-transition: 0.6s ease-in-out left;\n+ transition: 0.6s ease-in-out left;\n+}\n+\n+.carousel-inner > .item > img,\n+.carousel-inner > .item > a > img {\n+ display: block;\n+ line-height: 1;\n+}\n+\n+.carousel-inner > .active,\n+.carousel-inner > .next,\n+.carousel-inner > .prev {\n+ display: block;\n+}\n+\n+.carousel-inner > .active {\n+ left: 0;\n+}\n+\n+.carousel-inner > .next,\n+.carousel-inner > .prev {\n+ position: absolute;\n+ top: 0;\n+ width: 100%;\n+}\n+\n+.carousel-inner > .next {\n+ left: 100%;\n+}\n+\n+.carousel-inner > .prev {\n+ left: -100%;\n+}\n+\n+.carousel-inner > .next.left,\n+.carousel-inner > .prev.right {\n+ left: 0;\n+}\n+\n+.carousel-inner > .active.left {\n+ left: -100%;\n+}\n+\n+.carousel-inner > .active.right {\n+ left: 100%;\n+}\n+\n+.carousel-control {\n+ position: absolute;\n+ top: 40%;\n+ left: 15px;\n+ width: 40px;\n+ height: 40px;\n+ margin-top: -20px;\n+ font-size: 60px;\n+ font-weight: 100;\n+ line-height: 30px;\n+ color: #ffffff;\n+ text-align: center;\n+ background: #222222;\n+ border: 3px solid #ffffff;\n+ -webkit-border-radius: 23px;\n+ -moz-border-radius: 23px;\n+ border-radius: 23px;\n+ opacity: 0.5;\n+ filter: alpha(opacity=50);\n+}\n+\n+.carousel-control.right {\n+ right: 15px;\n+ left: auto;\n+}\n+\n+.carousel-control:hover,\n+.carousel-control:focus {\n+ color: #ffffff;\n+ text-decoration: none;\n+ opacity: 0.9;\n+ filter: alpha(opacity=90);\n+}\n+\n+.carousel-indicators {\n+ position: absolute;\n+ top: 15px;\n+ right: 15px;\n+ z-index: 5;\n+ margin: 0;\n+ list-style: none;\n+}\n+\n+.carousel-indicators li {\n+ display: block;\n+ float: left;\n+ width: 10px;\n+ height: 10px;\n+ margin-left: 5px;\n+ text-indent: -999px;\n+ background-color: #ccc;\n+ background-color: rgba(255, 255, 255, 0.25);\n+ border-radius: 5px;\n+}\n+\n+.carousel-indicators .active {\n+ background-color: #fff;\n+}\n+\n+.carousel-caption {\n+ position: absolute;\n+ right: 0;\n+ bottom: 0;\n+ left: 0;\n+ padding: 15px;\n+ background: #333333;\n+ background: rgba(0, 0, 0, 0.75);\n+}\n+\n+.carousel-caption h4,\n+.carousel-caption p {\n+ line-height: 20px;\n+ color: #ffffff;\n+}\n+\n+.carousel-caption h4 {\n+ margin: 0 0 5px;\n+}\n+\n+.carousel-caption p {\n+ margin-bottom: 0;\n+}\n+\n+.hero-unit {\n+ padding: 60px;\n+ margin-bottom: 30px;\n+ font-size: 18px;\n+ font-weight: 200;\n+ line-height: 30px;\n+ color: inherit;\n+ background-color: #eeeeee;\n+ -webkit-border-radius: 6px;\n+ -moz-border-radius: 6px;\n+ border-radius: 6px;\n+}\n+\n+.hero-unit h1 {\n+ margin-bottom: 0;\n+ font-size: 60px;\n+ line-height: 1;\n+ letter-spacing: -1px;\n+ color: inherit;\n+}\n+\n+.hero-unit li {\n+ line-height: 30px;\n+}\n+\n+.pull-right {\n+ float: right;\n+}\n+\n+.pull-left {\n+ float: left;\n+}\n+\n+.hide {\n+ display: none;\n+}\n+\n+.show {\n+ display: block;\n+}\n+\n+.invisible {\n+ visibility: hidden;\n+}\n+\n+.affix {\n+ position: fixed;\n+}\n' |
| b |
| diff -r 11708af40030 -r 967512924317 lib/sRNAPipe/html.pm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/sRNAPipe/html.pm Mon Jan 28 11:57:15 2019 -0500 |
| [ |
| b'@@ -0,0 +1,926 @@\n+package sRNAPipe::html;\n+\n+use strict;\n+use warnings;\n+use File::Basename;\n+use File::Copy::Recursive qw( dircopy );\n+\n+use Exporter;\n+our @ISA = qw( Exporter );\n+our @EXPORT_OK = qw( &main_page &details_pages &menu_page &ppp_page ©_css ©_js );\n+\n+sub main_page\n+{\n+ my ( $dir, $file, $list_mainTabP, $current, $ma, $ma_uni, $dir_root ) = @_;\n+ my ( $futHashP, $uniqueTabP, $randTabP, $pngTabP ) = get_genome ( $dir, $dir_root );\n+\n+ open my $h, \'>\', $file || die "cannot create $file $!\\n";\n+ header ( $h );\n+ navbar ( $h, $list_mainTabP, $current );\n+ print $h "<div class=\\"container\\"><p><a class=\\"btn\\" href=\\"$current-sub.html\\">View details »</a></p></div>\\n";\n+ futurette( $h, $current, $pngTabP, $futHashP );\n+ print $h "<div class=\\"container\\"><h2>mappers #: $ma</h2><h2>unique mappers #: $ma_uni</h2> </div>\\n";\n+ carousel2( $h, $uniqueTabP, $randTabP, $dir_root );\n+ footer($h);\n+ close $h;\n+}\n+\n+sub menu_page\n+{\n+ my ( $dir, $file, $list_mainTabP, $current, $min, $max, $simin, $simax, $pimin, $pimax, $dir_root ) = @_;\n+ my $html_ref = $1 if $dir =~ /$dir_root(.*)/;\n+ open 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+ my ( $dir_details, $prefix, $list_mainTabP, $current, $misTE, $dir_root, $ppp ) = @_;\n+ my ($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 ( $prefix =~ /piRNAs$/ && $ppp eq \'true\' )\n+ {\n+ print $h " <div class=\\"container\\">";\n+ print $h " <p><a class=\\"btn\\" href=\\"$html_ref\\">Ping Pong Partners</a></p>\\n";\n+ print $h "</div>";\n+ }\n+ fut($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.\'-transcripts.html\' || die "cannot create $prefix-transcripts.html $!\\n";\n+ header($h);\n+ navbar ( $h, $list_mainTabP, $current );\n+ fut($h,\'transcripts\',$Hex);\n+ footer($h);\n+ close $h;\n+}\n+\n+sub ppp_page\n+{\n+ my ( $dir, $file, $list_mainTabP, $current, $ppp, $dir_root ) = @_;\n+\n+ my $ppp_file = $ppp.\'ppp.txt\';\n+ open my $h, \'>\', $file || die "cannot create $file $!\\n";\n+ header($h);\n+ navbar ( $h, $list_mainTabP, $current );\n+ print $h \'<div class="container"> <table class="wb-tables table table-striped table-hover">\'."\\n";\n+ print $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+ open my $f, \'<\', $ppp_file || die "cannot open $ppp_file $!\\n";\n+ while ( <$f> )\n+ {\n+ chomp;\n+ print $h \'<tr>\';\n+ my ( $id, $sum, $ten, $mean, $sd, $zscore, $prob) = split /\\t/, $_;\n+ if( -d "$ppp/$id" )\n+ {\n+ my $sub_html = $ppp.$id.\'.html\';\n+ my $sub_html_ref = $1.$id if $ppp =~ /$dir_root(.*)/;\n+ print $h "<td> <a href=\\"$sub_html_ref.html\\">$id</a> </td>";\n+\n+ open my $sub, \'>\', $sub_html || die "cannot create $sub_html\\n";\n+'..b'=~ /.*($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=\\"$v->[2]\\">sense reads with PPP</a></p>\n+ <p class=\\"featurette-p\\"><a href=\\"$v->[3]\\">reverse reads with PPP</a></p>\n+ <p class=\\"featurette-p\\"><a href=\\"$v->[0]\\">sense reads without PPP</a></p>\n+ <p class=\\"featurette-p\\"><a href=\\"$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+sub copy_css\n+{\n+ my $dir = shift;\n+ my $path = dirname(__FILE__);\n+ dircopy( $path.\'/css\', $dir.\'/css\' );\n+}\n+\n+\n+sub copy_js\n+{\n+ my $dir = shift;\n+ my $path = dirname(__FILE__);\n+ dircopy( $path.\'/js\', $dir.\'/js\' );\n+}\n+\n+1;\n' |
| b |
| diff -r 11708af40030 -r 967512924317 lib/sRNAPipe/js/bootstrap-table.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/sRNAPipe/js/bootstrap-table.js Mon Jan 28 11:57:15 2019 -0500 |
| [ |
| b"@@ -0,0 +1,3094 @@\n+/**\n+ * @author zhixin wen <wenzhixin2010@gmail.com>\n+ * version: 1.11.1\n+ * https://github.com/wenzhixin/bootstrap-table/\n+ */\n+\n+(function ($) {\n+ 'use strict';\n+\n+ // TOOLS DEFINITION\n+ // ======================\n+\n+ var cachedWidth = null;\n+\n+ // it only does '%s', and return '' when arguments are undefined\n+ var sprintf = function (str) {\n+ var args = arguments,\n+ flag = true,\n+ i = 1;\n+\n+ str = str.replace(/%s/g, function () {\n+ var arg = args[i++];\n+\n+ if (typeof arg === 'undefined') {\n+ flag = false;\n+ return '';\n+ }\n+ return arg;\n+ });\n+ return flag ? str : '';\n+ };\n+\n+ var getPropertyFromOther = function (list, from, to, value) {\n+ var result = '';\n+ $.each(list, function (i, item) {\n+ if (item[from] === value) {\n+ result = item[to];\n+ return false;\n+ }\n+ return true;\n+ });\n+ return result;\n+ };\n+\n+ var getFieldIndex = function (columns, field) {\n+ var index = -1;\n+\n+ $.each(columns, function (i, column) {\n+ if (column.field === field) {\n+ index = i;\n+ return false;\n+ }\n+ return true;\n+ });\n+ return index;\n+ };\n+\n+ // http://jsfiddle.net/wenyi/47nz7ez9/3/\n+ var setFieldIndex = function (columns) {\n+ var i, j, k,\n+ totalCol = 0,\n+ flag = [];\n+\n+ for (i = 0; i < columns[0].length; i++) {\n+ totalCol += columns[0][i].colspan || 1;\n+ }\n+\n+ for (i = 0; i < columns.length; i++) {\n+ flag[i] = [];\n+ for (j = 0; j < totalCol; j++) {\n+ flag[i][j] = false;\n+ }\n+ }\n+\n+ for (i = 0; i < columns.length; i++) {\n+ for (j = 0; j < columns[i].length; j++) {\n+ var r = columns[i][j],\n+ rowspan = r.rowspan || 1,\n+ colspan = r.colspan || 1,\n+ index = $.inArray(false, flag[i]);\n+\n+ if (colspan === 1) {\n+ r.fieldIndex = index;\n+ // when field is undefined, use index instead\n+ if (typeof r.field === 'undefined') {\n+ r.field = index;\n+ }\n+ }\n+\n+ for (k = 0; k < rowspan; k++) {\n+ flag[i + k][index] = true;\n+ }\n+ for (k = 0; k < colspan; k++) {\n+ flag[i][index + k] = true;\n+ }\n+ }\n+ }\n+ };\n+\n+ var getScrollBarWidth = function () {\n+ if (cachedWidth === null) {\n+ var inner = $('<p/>').addClass('fixed-table-scroll-inner'),\n+ outer = $('<div/>').addClass('fixed-table-scroll-outer'),\n+ w1, w2;\n+\n+ outer.append(inner);\n+ $('body').append(outer);\n+\n+ w1 = inner[0].offsetWidth;\n+ outer.css('overflow', 'scroll');\n+ w2 = inner[0].offsetWidth;\n+\n+ if (w1 === w2) {\n+ w2 = outer[0].clientWidth;\n+ }\n+\n+ outer.remove();\n+ cachedWidth = w1 - w2;\n+ }\n+ return cachedWidth;\n+ };\n+\n+ var calculateObjectValue = function (self, name, args, defaultValue) {\n+ var func = name;\n+\n+ if (typeof name === 'string') {\n+ // support obj.func1.func2\n+ var names = name.split('.');\n+\n+ if (names.length > 1) {\n+ func = window;\n+ $.each(names, function (i, f) {\n+ func = func[f];\n+ });\n+ } else {\n+ func = window[name];\n+ }\n+ }\n+ if (typeof func === 'object') {\n+ return func;\n+ }\n+ if (typeof func === 'function') {\n+"..b' i < trs.length; i++) {\n+ this.expandRow_(true, $(trs[i]).data("index"));\n+ }\n+ }\n+ };\n+\n+ BootstrapTable.prototype.collapseAllRows = function (isSubTable) {\n+ if (isSubTable) {\n+ this.expandRow_(false, 0);\n+ } else {\n+ var trs = this.$body.children();\n+ for (var i = 0; i < trs.length; i++) {\n+ this.expandRow_(false, $(trs[i]).data("index"));\n+ }\n+ }\n+ };\n+\n+ BootstrapTable.prototype.updateFormatText = function (name, text) {\n+ if (this.options[sprintf(\'format%s\', name)]) {\n+ if (typeof text === \'string\') {\n+ this.options[sprintf(\'format%s\', name)] = function () {\n+ return text;\n+ };\n+ } else if (typeof text === \'function\') {\n+ this.options[sprintf(\'format%s\', name)] = text;\n+ }\n+ }\n+ this.initToolbar();\n+ this.initPagination();\n+ this.initBody();\n+ };\n+\n+ // BOOTSTRAP TABLE PLUGIN DEFINITION\n+ // =======================\n+\n+ var allowedMethods = [\n+ \'getOptions\',\n+ \'getSelections\', \'getAllSelections\', \'getData\',\n+ \'load\', \'append\', \'prepend\', \'remove\', \'removeAll\',\n+ \'insertRow\', \'updateRow\', \'updateCell\', \'updateByUniqueId\', \'removeByUniqueId\',\n+ \'getRowByUniqueId\', \'showRow\', \'hideRow\', \'getHiddenRows\',\n+ \'mergeCells\',\n+ \'checkAll\', \'uncheckAll\', \'checkInvert\',\n+ \'check\', \'uncheck\',\n+ \'checkBy\', \'uncheckBy\',\n+ \'refresh\',\n+ \'resetView\',\n+ \'resetWidth\',\n+ \'destroy\',\n+ \'showLoading\', \'hideLoading\',\n+ \'showColumn\', \'hideColumn\', \'getHiddenColumns\', \'getVisibleColumns\',\n+ \'showAllColumns\', \'hideAllColumns\',\n+ \'filterBy\',\n+ \'scrollTo\',\n+ \'getScrollPosition\',\n+ \'selectPage\', \'prevPage\', \'nextPage\',\n+ \'togglePagination\',\n+ \'toggleView\',\n+ \'refreshOptions\',\n+ \'resetSearch\',\n+ \'expandRow\', \'collapseRow\', \'expandAllRows\', \'collapseAllRows\',\n+ \'updateFormatText\'\n+ ];\n+\n+ $.fn.bootstrapTable = function (option) {\n+ var value,\n+ args = Array.prototype.slice.call(arguments, 1);\n+\n+ this.each(function () {\n+ var $this = $(this),\n+ data = $this.data(\'bootstrap.table\'),\n+ options = $.extend({}, BootstrapTable.DEFAULTS, $this.data(),\n+ typeof option === \'object\' && option);\n+\n+ if (typeof option === \'string\') {\n+ if ($.inArray(option, allowedMethods) < 0) {\n+ throw new Error("Unknown method: " + option);\n+ }\n+\n+ if (!data) {\n+ return;\n+ }\n+\n+ value = data[option].apply(data, args);\n+\n+ if (option === \'destroy\') {\n+ $this.removeData(\'bootstrap.table\');\n+ }\n+ }\n+\n+ if (!data) {\n+ $this.data(\'bootstrap.table\', (data = new BootstrapTable(this, options)));\n+ }\n+ });\n+\n+ return typeof value === \'undefined\' ? this : value;\n+ };\n+\n+ $.fn.bootstrapTable.Constructor = BootstrapTable;\n+ $.fn.bootstrapTable.defaults = BootstrapTable.DEFAULTS;\n+ $.fn.bootstrapTable.columnDefaults = BootstrapTable.COLUMN_DEFAULTS;\n+ $.fn.bootstrapTable.locales = BootstrapTable.LOCALES;\n+ $.fn.bootstrapTable.methods = allowedMethods;\n+ $.fn.bootstrapTable.utils = {\n+ sprintf: sprintf,\n+ getFieldIndex: getFieldIndex,\n+ compareObjects: compareObjects,\n+ calculateObjectValue: calculateObjectValue,\n+ getItemField: getItemField,\n+ objectKeys: objectKeys,\n+ isIEBrowser: isIEBrowser\n+ };\n+\n+ // BOOTSTRAP TABLE INIT\n+ // =======================\n+\n+ $(function () {\n+ $(\'[data-toggle="table"]\').bootstrapTable();\n+ });\n+})(jQuery);\n' |
| b |
| diff -r 11708af40030 -r 967512924317 lib/sRNAPipe/js/bootstrap.min.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/sRNAPipe/js/bootstrap.min.js Mon Jan 28 11:57:15 2019 -0500 |
| [ |
| b'@@ -0,0 +1,6 @@\n+/**\n+* Bootstrap.js v2.3.2 by @fat & @mdo\n+* Copyright 2013 Twitter, Inc.\n+* http://www.apache.org/licenses/LICENSE-2.0.txt\n+*/\n+!function(e){"use strict";e(function(){e.support.transition=function(){var e=function(){var e=document.createElement("bootstrap"),t={WebkitTransition:"webkitTransitionEnd",MozTransition:"transitionend",OTransition:"oTransitionEnd otransitionend",transition:"transitionend"},n;for(n in t)if(e.style[n]!==undefined)return t[n]}();return e&&{end:e}}()})}(window.jQuery),!function(e){"use strict";var t=\'[data-dismiss="alert"]\',n=function(n){e(n).on("click",t,this.close)};n.prototype.close=function(t){function s(){i.trigger("closed").remove()}var n=e(this),r=n.attr("data-target"),i;r||(r=n.attr("href"),r=r&&r.replace(/.*(?=#[^\\s]*$)/,"")),i=e(r),t&&t.preventDefault(),i.length||(i=n.hasClass("alert")?n:n.parent()),i.trigger(t=e.Event("close"));if(t.isDefaultPrevented())return;i.removeClass("in"),e.support.transition&&i.hasClass("fade")?i.on(e.support.transition.end,s):s()};var r=e.fn.alert;e.fn.alert=function(t){return this.each(function(){var r=e(this),i=r.data("alert");i||r.data("alert",i=new n(this)),typeof t=="string"&&i[t].call(r)})},e.fn.alert.Constructor=n,e.fn.alert.noConflict=function(){return e.fn.alert=r,this},e(document).on("click.alert.data-api",t,n.prototype.close)}(window.jQuery),!function(e){"use strict";var t=function(t,n){this.$element=e(t),this.options=e.extend({},e.fn.button.defaults,n)};t.prototype.setState=function(e){var t="disabled",n=this.$element,r=n.data(),i=n.is("input")?"val":"html";e+="Text",r.resetText||n.data("resetText",n[i]()),n[i](r[e]||this.options[e]),setTimeout(function(){e=="loadingText"?n.addClass(t).attr(t,t):n.removeClass(t).removeAttr(t)},0)},t.prototype.toggle=function(){var e=this.$element.closest(\'[data-toggle="buttons-radio"]\');e&&e.find(".active").removeClass("active"),this.$element.toggleClass("active")};var n=e.fn.button;e.fn.button=function(n){return this.each(function(){var r=e(this),i=r.data("button"),s=typeof n=="object"&&n;i||r.data("button",i=new t(this,s)),n=="toggle"?i.toggle():n&&i.setState(n)})},e.fn.button.defaults={loadingText:"loading..."},e.fn.button.Constructor=t,e.fn.button.noConflict=function(){return e.fn.button=n,this},e(document).on("click.button.data-api","[data-toggle^=button]",function(t){var n=e(t.target);n.hasClass("btn")||(n=n.closest(".btn")),n.button("toggle")})}(window.jQuery),!function(e){"use strict";var t=function(t,n){this.$element=e(t),this.$indicators=this.$element.find(".carousel-indicators"),this.options=n,this.options.pause=="hover"&&this.$element.on("mouseenter",e.proxy(this.pause,this)).on("mouseleave",e.proxy(this.cycle,this))};t.prototype={cycle:function(t){return t||(this.paused=!1),this.interval&&clearInterval(this.interval),this.options.interval&&!this.paused&&(this.interval=setInterval(e.proxy(this.next,this),this.options.interval)),this},getActiveIndex:function(){return this.$active=this.$element.find(".item.active"),this.$items=this.$active.parent().children(),this.$items.index(this.$active)},to:function(t){var n=this.getActiveIndex(),r=this;if(t>this.$items.length-1||t<0)return;return this.sliding?this.$element.one("slid",function(){r.to(t)}):n==t?this.pause().cycle():this.slide(t>n?"next":"prev",e(this.$items[t]))},pause:function(t){return t||(this.paused=!0),this.$element.find(".next, .prev").length&&e.support.transition.end&&(this.$element.trigger(e.support.transition.end),this.cycle(!0)),clearInterval(this.interval),this.interval=null,this},next:function(){if(this.sliding)return;return this.slide("next")},prev:function(){if(this.sliding)return;return this.slide("prev")},slide:function(t,n){var r=this.$element.find(".item.active"),i=n||r[t](),s=this.interval,o=t=="next"?"left":"right",u=t=="next"?"first":"last",a=this,f;this.sliding=!0,s&&this.pause(),i=i.length?i:this.$element.find(".item")[u](),f=e.Event("slide",{relatedTarget:i[0],direction:o});if(i.hasClass("active"))return;this.$indicat'..b',next:function(t){var n=this.$menu.find(".active").removeClass("active"),r=n.next();r.length||(r=e(this.$menu.find("li")[0])),r.addClass("active")},prev:function(e){var t=this.$menu.find(".active").removeClass("active"),n=t.prev();n.length||(n=this.$menu.find("li").last()),n.addClass("active")},listen:function(){this.$element.on("focus",e.proxy(this.focus,this)).on("blur",e.proxy(this.blur,this)).on("keypress",e.proxy(this.keypress,this)).on("keyup",e.proxy(this.keyup,this)),this.eventSupported("keydown")&&this.$element.on("keydown",e.proxy(this.keydown,this)),this.$menu.on("click",e.proxy(this.click,this)).on("mouseenter","li",e.proxy(this.mouseenter,this)).on("mouseleave","li",e.proxy(this.mouseleave,this))},eventSupported:function(e){var t=e in this.$element;return t||(this.$element.setAttribute(e,"return;"),t=typeof this.$element[e]=="function"),t},move:function(e){if(!this.shown)return;switch(e.keyCode){case 9:case 13:case 27:e.preventDefault();break;case 38:e.preventDefault(),this.prev();break;case 40:e.preventDefault(),this.next()}e.stopPropagation()},keydown:function(t){this.suppressKeyPressRepeat=~e.inArray(t.keyCode,[40,38,9,13,27]),this.move(t)},keypress:function(e){if(this.suppressKeyPressRepeat)return;this.move(e)},keyup:function(e){switch(e.keyCode){case 40:case 38:case 16:case 17:case 18:break;case 9:case 13:if(!this.shown)return;this.select();break;case 27:if(!this.shown)return;this.hide();break;default:this.lookup()}e.stopPropagation(),e.preventDefault()},focus:function(e){this.focused=!0},blur:function(e){this.focused=!1,!this.mousedover&&this.shown&&this.hide()},click:function(e){e.stopPropagation(),e.preventDefault(),this.select(),this.$element.focus()},mouseenter:function(t){this.mousedover=!0,this.$menu.find(".active").removeClass("active"),e(t.currentTarget).addClass("active")},mouseleave:function(e){this.mousedover=!1,!this.focused&&this.shown&&this.hide()}};var n=e.fn.typeahead;e.fn.typeahead=function(n){return this.each(function(){var r=e(this),i=r.data("typeahead"),s=typeof n=="object"&&n;i||r.data("typeahead",i=new t(this,s)),typeof n=="string"&&i[n]()})},e.fn.typeahead.defaults={source:[],items:8,menu:\'<ul class="typeahead dropdown-menu"></ul>\',item:\'<li><a href="#"></a></li>\',minLength:1},e.fn.typeahead.Constructor=t,e.fn.typeahead.noConflict=function(){return e.fn.typeahead=n,this},e(document).on("focus.typeahead.data-api",\'[data-provide="typeahead"]\',function(t){var n=e(this);if(n.data("typeahead"))return;n.typeahead(n.data())})}(window.jQuery),!function(e){"use strict";var t=function(t,n){this.options=e.extend({},e.fn.affix.defaults,n),this.$window=e(window).on("scroll.affix.data-api",e.proxy(this.checkPosition,this)).on("click.affix.data-api",e.proxy(function(){setTimeout(e.proxy(this.checkPosition,this),1)},this)),this.$element=e(t),this.checkPosition()};t.prototype.checkPosition=function(){if(!this.$element.is(":visible"))return;var t=e(document).height(),n=this.$window.scrollTop(),r=this.$element.offset(),i=this.options.offset,s=i.bottom,o=i.top,u="affix affix-top affix-bottom",a;typeof i!="object"&&(s=o=i),typeof o=="function"&&(o=i.top()),typeof s=="function"&&(s=i.bottom()),a=this.unpin!=null&&n+this.unpin<=r.top?!1:s!=null&&r.top+this.$element.height()>=t-s?"bottom":o!=null&&n<=o?"top":!1;if(this.affixed===a)return;this.affixed=a,this.unpin=a=="bottom"?r.top-n:null,this.$element.removeClass(u).addClass("affix"+(a?"-"+a:""))};var n=e.fn.affix;e.fn.affix=function(n){return this.each(function(){var r=e(this),i=r.data("affix"),s=typeof n=="object"&&n;i||r.data("affix",i=new t(this,s)),typeof n=="string"&&i[n]()})},e.fn.affix.Constructor=t,e.fn.affix.defaults={offset:0},e.fn.affix.noConflict=function(){return e.fn.affix=n,this},e(window).on("load",function(){e(\'[data-spy="affix"]\').each(function(){var t=e(this),n=t.data();n.offset=n.offset||{},n.offsetBottom&&(n.offset.bottom=n.offsetBottom),n.offsetTop&&(n.offset.top=n.offsetTop),t.affix(n)})})}(window.jQuery);\n\\ No newline at end of file\n' |
| b |
| diff -r 11708af40030 -r 967512924317 lib/sRNAPipe/js/filter.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/sRNAPipe/js/filter.js Mon Jan 28 11:57:15 2019 -0500 |
| [ |
| @@ -0,0 +1,20 @@ +function search(input) { + // Declare variables + var elt, filter, uls, li, a, i; + elt = input.parentElement; + filter = input.value.toUpperCase(); + uls = elt.getElementsByClassName('thumbs'); + + // Loop through all list items, and hide those who don't match the search query + for (j = 0; j < uls.length; j++) { + li = uls[j].getElementsByTagName('li'); + for (i = 0; i < li.length; i++) { + a = li[i].getElementsByTagName("a")[0]; + if (a.innerHTML.toUpperCase().indexOf(filter) > -1) { + li[i].style.display = ""; + } else { + li[i].style.display = "none"; + } + } + } +} |
| b |
| diff -r 11708af40030 -r 967512924317 lib/sRNAPipe/js/jquery.galleriffic.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/sRNAPipe/js/jquery.galleriffic.js Mon Jan 28 11:57:15 2019 -0500 |
| [ |
| b"@@ -0,0 +1,979 @@\n+/**\r\n+ * jQuery Galleriffic plugin\r\n+ *\r\n+ * Copyright (c) 2008 Trent Foley (http://trentacular.com)\r\n+ * Licensed under the MIT License:\r\n+ * http://www.opensource.org/licenses/mit-license.php\r\n+ *\r\n+ * Much thanks to primary contributer Ponticlaro (http://www.ponticlaro.com)\r\n+ */\r\n+;(function($) {\r\n+\t// Globally keep track of all images by their unique hash. Each item is an image data object.\r\n+\tvar allImages = {};\r\n+\tvar imageCounter = 0;\r\n+\n+\t// Galleriffic static class\r\n+\t$.galleriffic = {\n+\t\tversion: '2.0.1',\n+\n+\t\t// Strips invalid characters and any leading # characters\n+\t\tnormalizeHash: function(hash) {\r\n+\t\t\treturn hash.replace(/^.*#/, '').replace(/\\?.*$/, '');\n+\t\t},\n+\n+\t\tgetImage: function(hash) {\n+\t\t\tif (!hash)\n+\t\t\t\treturn undefined;\n+\n+\t\t\thash = $.galleriffic.normalizeHash(hash);\r\n+\t\t\treturn allImages[hash];\n+\t\t},\n+\r\n+\t\t// Global function that looks up an image by its hash and displays the image.\n+\t\t// Returns false when an image is not found for the specified hash.\n+\t\t// @param {String} hash This is the unique hash value assigned to an image.\n+\t\tgotoImage: function(hash) {\r\n+\t\t\tvar imageData = $.galleriffic.getImage(hash);\r\n+\t\t\tif (!imageData)\n+\t\t\t\treturn false;\r\n+\n+\t\t\tvar gallery = imageData.gallery;\n+\t\t\tgallery.gotoImage(imageData);\n+\t\t\t\n+\t\t\treturn true;\r\n+\t\t},\n+\n+\t\t// Removes an image from its respective gallery by its hash.\n+\t\t// Returns false when an image is not found for the specified hash or the\n+\t\t// specified owner gallery does match the located images gallery.\n+\t\t// @param {String} hash This is the unique hash value assigned to an image.\n+\t\t// @param {Object} ownerGallery (Optional) When supplied, the located images\n+\t\t// gallery is verified to be the same as the specified owning gallery before\n+\t\t// performing the remove operation.\n+\t\tremoveImageByHash: function(hash, ownerGallery) {\n+\t\t\tvar imageData = $.galleriffic.getImage(hash);\n+\t\t\tif (!imageData)\n+\t\t\t\treturn false;\n+\n+\t\t\tvar gallery = imageData.gallery;\n+\t\t\tif (ownerGallery && ownerGallery != gallery)\n+\t\t\t\treturn false;\n+\n+\t\t\treturn gallery.removeImageByIndex(imageData.index);\n+\t\t}\r\n+\t};\n+\r\n+\tvar defaults = {\r\n+\t\tdelay: 3000,\r\n+\t\tnumThumbs: 20,\r\n+\t\tpreloadAhead: 40, // Set to -1 to preload all images\r\n+\t\tenableTopPager: false,\r\n+\t\tenableBottomPager: true,\r\n+\t\tmaxPagesToShow: 7,\r\n+\t\timageContainerSel: '',\r\n+\t\tcaptionContainerSel: '',\r\n+\t\tcontrolsContainerSel: '',\r\n+\t\tloadingContainerSel: '',\r\n+\t\trenderSSControls: true,\r\n+\t\trenderNavControls: true,\r\n+\t\tplayLinkText: 'Play',\r\n+\t\tpauseLinkText: 'Pause',\r\n+\t\tprevLinkText: 'Previous',\r\n+\t\tnextLinkText: 'Next',\r\n+\t\tnextPageLinkText: 'Next ›',\r\n+\t\tprevPageLinkText: '‹ Prev',\r\n+\t\tenableHistory: false,\n+\t\tenableKeyboardNavigation: true,\r\n+\t\tautoStart: false,\r\n+\t\tsyncTransitions: false,\r\n+\t\tdefaultTransitionDuration: 1000,\r\n+\t\tonSlideChange: undefined, // accepts a delegate like such: function(prevIndex, nextIndex) { ... }\r\n+\t\tonTransitionOut: undefined, // accepts a delegate like such: function(slide, caption, isSync, callback) { ... }\r\n+\t\tonTransitionIn: undefined, // accepts a delegate like such: function(slide, caption, isSync) { ... }\r\n+\t\tonPageTransitionOut: undefined, // accepts a delegate like such: function(callback) { ... }\r\n+\t\tonPageTransitionIn: undefined, // accepts a delegate like such: function() { ... }\n+\t\tonImageAdded: undefined, // accepts a delegate like such: function(imageData, $li) { ... }\n+\t\tonImageRemoved: undefined // accepts a delegate like such: function(imageData, $li) { ... }\r\n+\t};\r\n+\n+\t// Primary Galleriffic initialization function that should be called on the thumbnail container.\r\n+\t$.fn.galleriffic = function(settings) {\r\n+\t\t// Extend Gallery O"..b'display all thumbnails.\r\n+\t\t\tbuildPageLink: function(pager, pageNum, numPages) {\r\n+\t\t\t\tvar pageLabel = pageNum + 1;\r\n+\t\t\t\tvar currentPage = this.getCurrentPage();\r\n+\t\t\t\tif (pageNum == currentPage)\r\n+\t\t\t\t\tpager.append(\'<span class="current">\'+pageLabel+\'</span>\');\r\n+\t\t\t\telse if (pageNum < numPages) {\r\n+\t\t\t\t\tvar imageIndex = pageNum*this.numThumbs;\r\n+\t\t\t\t\tpager.append(\'<a rel="history" href="#\'+this.data[imageIndex].hash+\'" title="\'+pageLabel+\'">\'+pageLabel+\'</a>\');\r\n+\t\t\t\t}\n+\t\t\t\t\n+\t\t\t\treturn this;\r\n+\t\t\t}\r\n+\t\t});\r\n+\r\n+\t\t// Now initialize the gallery\r\n+\t\t$.extend(this, defaults, settings);\r\n+\t\t\r\n+\t\t// Verify the history plugin is available\r\n+\t\tif (this.enableHistory && !$.historyInit)\r\n+\t\t\tthis.enableHistory = false;\r\n+\t\t\r\n+\t\t// Select containers\r\n+\t\tif (this.imageContainerSel) this.$imageContainer = $(this.imageContainerSel);\r\n+\t\tif (this.captionContainerSel) this.$captionContainer = $(this.captionContainerSel);\r\n+\t\tif (this.loadingContainerSel) this.$loadingContainer = $(this.loadingContainerSel);\r\n+\n+\t\t// Initialize the thumbails\r\n+\t\tthis.initializeThumbs();\r\n+\t\t\r\n+\t\tif (this.maxPagesToShow < 3)\r\n+\t\t\tthis.maxPagesToShow = 3;\r\n+\r\n+\t\tthis.displayedPage = -1;\n+\t\tthis.currentImage = this.data[0];\r\n+\t\tvar gallery = this;\r\n+\r\n+\t\t// Hide the loadingContainer\r\n+\t\tif (this.$loadingContainer)\r\n+\t\t\tthis.$loadingContainer.hide();\r\n+\r\n+\t\t// Setup controls\r\n+\t\tif (this.controlsContainerSel) {\r\n+\t\t\tthis.$controlsContainer = $(this.controlsContainerSel).empty();\r\n+\t\t\t\r\n+\t\t\tif (this.renderSSControls) {\r\n+\t\t\t\tif (this.autoStart) {\r\n+\t\t\t\t\tthis.$controlsContainer\r\n+\t\t\t\t\t\t.append(\'<div class="ss-controls"><a href="#pause" class="pause" title="\'+this.pauseLinkText+\'">\'+this.pauseLinkText+\'</a></div>\');\r\n+\t\t\t\t} else {\r\n+\t\t\t\t\tthis.$controlsContainer\r\n+\t\t\t\t\t\t.append(\'<div class="ss-controls"><a href="#play" class="play" title="\'+this.playLinkText+\'">\'+this.playLinkText+\'</a></div>\');\r\n+\t\t\t\t}\r\n+\r\n+\t\t\t\tthis.$controlsContainer.find(\'div.ss-controls a\')\r\n+\t\t\t\t\t.click(function(e) {\r\n+\t\t\t\t\t\tgallery.toggleSlideshow();\r\n+\t\t\t\t\t\te.preventDefault();\r\n+\t\t\t\t\t\treturn false;\r\n+\t\t\t\t\t});\r\n+\t\t\t}\r\n+\t\t\r\n+\t\t\tif (this.renderNavControls) {\r\n+\t\t\t\tthis.$controlsContainer\r\n+\t\t\t\t\t.append(\'<div class="nav-controls"><a class="prev" rel="history" title="\'+this.prevLinkText+\'">\'+this.prevLinkText+\'</a><a class="next" rel="history" title="\'+this.nextLinkText+\'">\'+this.nextLinkText+\'</a></div>\')\r\n+\t\t\t\t\t.find(\'div.nav-controls a\')\r\n+\t\t\t\t\t.click(function(e) {\r\n+\t\t\t\t\t\tgallery.clickHandler(e, this);\r\n+\t\t\t\t\t});\r\n+\t\t\t}\r\n+\t\t}\r\n+\n+\t\tvar initFirstImage = !this.enableHistory || !location.hash;\n+\t\tif (this.enableHistory && location.hash) {\n+\t\t\tvar hash = $.galleriffic.normalizeHash(location.hash);\n+\t\t\tvar imageData = allImages[hash];\r\n+\t\t\tif (!imageData)\n+\t\t\t\tinitFirstImage = true;\n+\t\t}\n+\r\n+\t\t// Setup gallery to show the first image\n+\t\tif (initFirstImage)\r\n+\t\t\tthis.gotoIndex(0, false, true);\r\n+\n+\t\t// Setup Keyboard Navigation\n+\t\tif (this.enableKeyboardNavigation) {\n+\t\t\t$(document).keydown(function(e) {\n+\t\t\t\tvar key = e.charCode ? e.charCode : e.keyCode ? e.keyCode : 0;\n+\t\t\t\tswitch(key) {\n+\t\t\t\t\tcase 32: // space\n+\t\t\t\t\t\tgallery.next();\n+\t\t\t\t\t\te.preventDefault();\n+\t\t\t\t\t\tbreak;\n+\t\t\t\t\tcase 33: // Page Up\n+\t\t\t\t\t\tgallery.previousPage();\n+\t\t\t\t\t\te.preventDefault();\n+\t\t\t\t\t\tbreak;\n+\t\t\t\t\tcase 34: // Page Down\n+\t\t\t\t\t\tgallery.nextPage();\n+\t\t\t\t\t\te.preventDefault();\n+\t\t\t\t\t\tbreak;\n+\t\t\t\t\tcase 35: // End\n+\t\t\t\t\t\tgallery.gotoIndex(gallery.data.length-1);\n+\t\t\t\t\t\te.preventDefault();\n+\t\t\t\t\t\tbreak;\n+\t\t\t\t\tcase 36: // Home\n+\t\t\t\t\t\tgallery.gotoIndex(0);\n+\t\t\t\t\t\te.preventDefault();\n+\t\t\t\t\t\tbreak;\n+\t\t\t\t\tcase 37: // left arrow\n+\t\t\t\t\t\tgallery.previous();\n+\t\t\t\t\t\te.preventDefault();\n+\t\t\t\t\t\tbreak;\n+\t\t\t\t\tcase 39: // right arrow\n+\t\t\t\t\t\tgallery.next();\n+\t\t\t\t\t\te.preventDefault();\n+\t\t\t\t\t\tbreak;\n+\t\t\t\t}\n+\t\t\t});\n+\t\t}\n+\n+\t\t// Auto start the slideshow\r\n+\t\tif (this.autoStart)\r\n+\t\t\tthis.play();\r\n+\r\n+\t\t// Kickoff Image Preloader after 1 second\r\n+\t\tsetTimeout(function() { gallery.preloadInit(); }, 1000);\r\n+\r\n+\t\treturn this;\r\n+\t};\r\n+})(jQuery);\r\n' |
| b |
| diff -r 11708af40030 -r 967512924317 lib/sRNAPipe/js/jquery.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/sRNAPipe/js/jquery.js Mon Jan 28 11:57:15 2019 -0500 |
| [ |
| b'@@ -0,0 +1,5 @@\n+/*! jQuery v1.9.1 | (c) 2005, 2012 jQuery Foundation, Inc. | jquery.org/license\n+//@ sourceMappingURL=jquery.min.map\n+*/(function(e,t){var n,r,i=typeof t,o=e.document,a=e.location,s=e.jQuery,u=e.$,l={},c=[],p="1.9.1",f=c.concat,d=c.push,h=c.slice,g=c.indexOf,m=l.toString,y=l.hasOwnProperty,v=p.trim,b=function(e,t){return new b.fn.init(e,t,r)},x=/[+-]?(?:\\d*\\.|)\\d+(?:[eE][+-]?\\d+|)/.source,w=/\\S+/g,T=/^[\\s\\uFEFF\\xA0]+|[\\s\\uFEFF\\xA0]+$/g,N=/^(?:(<[\\w\\W]+>)[^>]*|#([\\w-]*))$/,C=/^<(\\w+)\\s*\\/?>(?:<\\/\\1>|)$/,k=/^[\\],:{}\\s]*$/,E=/(?:^|:|,)(?:\\s*\\[)+/g,S=/\\\\(?:["\\\\\\/bfnrt]|u[\\da-fA-F]{4})/g,A=/"[^"\\\\\\r\\n]*"|true|false|null|-?(?:\\d+\\.|)\\d+(?:[eE][+-]?\\d+|)/g,j=/^-ms-/,D=/-([\\da-z])/gi,L=function(e,t){return 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define&&define.amd&&define.amd.jQuery&&define("jquery",[],function(){return b})})(window);\n\\ No newline at end of file\n' |
| b |
| diff -r 11708af40030 -r 967512924317 lib/sRNAPipe/js/jquery.opacityrollover.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/sRNAPipe/js/jquery.opacityrollover.js Mon Jan 28 11:57:15 2019 -0500 |
| b |
| @@ -0,0 +1,42 @@ +/** + * jQuery Opacity Rollover plugin + * + * Copyright (c) 2009 Trent Foley (http://trentacular.com) + * Licensed under the MIT License: + * http://www.opensource.org/licenses/mit-license.php + */ +;(function($) { + var defaults = { + mouseOutOpacity: 0.67, + mouseOverOpacity: 1.0, + fadeSpeed: 'fast', + exemptionSelector: '.selected' + }; + + $.fn.opacityrollover = function(settings) { + // Initialize the effect + $.extend(this, defaults, settings); + + var config = this; + + function fadeTo(element, opacity) { + var $target = $(element); + + if (config.exemptionSelector) + $target = $target.not(config.exemptionSelector); + + $target.fadeTo(config.fadeSpeed, opacity); + } + + this.css('opacity', this.mouseOutOpacity) + .hover( + function () { + fadeTo(this, config.mouseOverOpacity); + }, + function () { + fadeTo(this, config.mouseOutOpacity); + }); + + return this; + }; +})(jQuery); |
| b |
| diff -r 11708af40030 -r 967512924317 lib/sRNAPipe/ppp.pm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/sRNAPipe/ppp.pm Mon Jan 28 11:57:15 2019 -0500 |
| [ |
| b'@@ -0,0 +1,230 @@\n+package sRNAPipe::ppp;\n+\n+use strict;\n+use warnings;\n+use FindBin;\n+use lib "$FindBin::Bin/../lib";\n+use sRNAPipe::Rcall qw ( histogram );\n+use Math::CDF;\n+\n+use Exporter;\n+our @ISA = qw( Exporter );\n+our @EXPORT_OK = qw( &ping_pong_partners );\n+\n+sub ping_pong_partners\n+{\n+ my ( $TE_fai, $sam, $dir, $max ) = @_;\n+ my ( $hashRef, $dupRef, $hasPpp ) = count_mapped ( $TE_fai, $sam );\n+ my ( %num_per_overlap_size, $overlap_number, $reverseR, $begRev, $endRev, $sensR, $begSens, $endSens, $snum, $rnum, $overlap );\n+ my ( $SP, $AP, $SN, $AN, $txt );\n+ my $flag = 0;\n+ my @distri_overlap = (); my @overlaps_names = ();\n+\n+ open my $ppp_f, \'>\', $dir."ppp.txt" || die "cannot create ppp.txt $!\\n";\n+ foreach my $k ( sort keys %{$hashRef} )\n+ {\n+ my $v = $hashRef->{$k};\n+ my $TE_dir = $dir.$k.\'/\';\n+\n+ %num_per_overlap_size = (); $overlap_number = 0;\n+ $flag = 0;\n+ for ( my $i = 0; $i <= $#{$v->[1]} ; $i++ )\n+ {\n+ $reverseR = ${$v->[1]}[$i] ;\n+ $begRev = $reverseR->[0];\n+ $endRev = $begRev + length($reverseR->[1]) - 1;\n+\n+ my $revR = reverse($reverseR->[1]);\n+ $revR =~ tr/atgcuATGCU/tacgaTACGA/;\n+\n+ for ( my $j = 0; $j <= $#{$v->[0]}; $j++ )\n+ {\n+ $sensR = ${$v->[0]}[$j];\n+ $begSens = $sensR->[0];\n+ $endSens = $begSens + length($sensR->[1]) - 1;\n+\n+ if ( $begSens <= $endRev && $endSens > $endRev )\n+ {\n+ $flag = 1;\n+ mkdir $TE_dir;\n+ open $txt, \'>\', $TE_dir.\'overlap_size.txt\' || die "cannot open repartition\\n";\n+\n+ $overlap = $endRev - $begSens + 1;\n+ $snum = $dupRef->{$sensR->[0].$sensR->[1].$sensR->[2].$sensR->[3]};\n+ $rnum = $dupRef->{$reverseR->[0].$reverseR->[1].$reverseR->[2].$reverseR->[3]};\n+\n+ if ( $overlap == 10 )\n+ {\n+ $hasPpp->{ $sensR->[0].$sensR->[1].$sensR->[2].$sensR->[3] } = 1;\n+ $hasPpp->{ $reverseR->[0].$reverseR->[1].$reverseR->[2].$reverseR->[3] } = 1;\n+ }\n+ next if $overlap > $max;\n+ if ( $snum < $rnum )\n+ {\n+ $num_per_overlap_size{$overlap} += $snum;\n+ $overlap_number += $snum;\n+ }\n+ else\n+ {\n+ $num_per_overlap_size{$overlap} += $rnum ;\n+ $overlap_number += $rnum ;\n+ }\n+ }\n+ }\n+ }\n+ if ( $max != 0 )\n+ {\n+ my @overlaps = ();\n+ push @overlaps_names, $k;\n+ for my $i (1..$max)\n+ {\n+ $num_per_overlap_size{$i} = 0 unless exists( $num_per_overlap_size{$i} );\n+ push @overlaps, $num_per_overlap_size{$i};\n+ }\n+ push @distri_overlap, \\@overlaps;\n+ }\n+\n+ if ( $flag == 1 )\n+ {\n+ open $AP, \'>\', $TE_dir."antisensPPP.txt" || die "cannot create antisensPPP\\n";\n+ open $AN, \'>\', $TE_dir."antisens.txt" || die "cannot create antisens\\n";\n+ for ( my $i = 0; $i <= $#{$v->[1]} ; $i++ )\n+ {\n+ $reverseR = ${$v->[1]}[$i] ;\n+ my $revR = reverse($reverseR->[1]);\n+ $revR =~ tr/atgcuATGCU/tacgaTACGA/;\n+ $rnum = $dupRef->{$reverseR->[0].$reverseR->[1].$reverseR->[2].$reverseR->[3]};\n+ if ( $hasPpp->{ $reverseR->[0].$reverseR->[1].$reverseR->[2].$reverseR->[3] } == 1 )\n+ {\n+ print $AP ">$reverseR->[0]|$reverseR->[2]|$reverseR->[3]|$rnum\\n$revR\\n";\n+ }\n+ else\n+ {\n+ print $AN ">$reverseR->[0]|$re'..b' open $SP, \'>\', $TE_dir."sensPPP.txt" || die "cannot create sensPPP\\n";\n+ open $SN, \'>\', $TE_dir."sens.txt" || die "cannot create sens\\n";\n+ for ( my $j = 0; $j <= $#{$v->[0]}; $j++ )\n+ {\n+ $sensR = ${$v->[0]}[$j];\n+ $snum = $dupRef->{$sensR->[0].$sensR->[1].$sensR->[2].$sensR->[3]};\n+ if ( $hasPpp->{ $sensR->[0].$sensR->[1].$sensR->[2].$sensR->[3] } == 1 )\n+ {\n+ print $SP ">$sensR->[0]|$sensR->[2]|$sensR->[3]|$snum\\n$sensR->[1]\\n";\n+ }\n+ else\n+ {\n+ print $SN ">$sensR->[0]|$sensR->[2]|$sensR->[3]|$snum\\n$sensR->[1]\\n";\n+ }\n+ }\n+ close $SP; close $SN;\n+\n+ my $histo_png = $TE_dir.\'histogram.png\';\n+ histogram( \\%num_per_overlap_size, $histo_png, $overlap_number );\n+ print $txt "size\\tnumber\\tpercentage of the total overlap number\\n";\n+ foreach my $k ( sort {$a <=> $b} keys %num_per_overlap_size )\n+ {\n+ my $percentage = 0;\n+ $percentage = $num_per_overlap_size{$k} * 100 / $overlap_number unless $overlap_number == 0;\n+ print $txt "$k\\t$num_per_overlap_size{$k}\\t"; printf $txt "%.2f\\n",$percentage;\n+ }\n+ close $txt;\n+ }\n+ }\n+\n+ foreach my $tabP ( @distri_overlap )\n+ {\n+ my $sum = sum($tabP);\n+ my $ten = $tabP->[9];\n+ my $mean = mean($tabP);\n+ my $std = standard_deviation($tabP, $mean);\n+ my $zsc = z_significance($ten, $mean, $std);\n+ my $name = shift @overlaps_names;\n+ my $prob = \'NA\';\n+ $prob = 1 - &Math::CDF::pnorm( $zsc ) if $zsc ne \'NA\';\n+ print $ppp_f (join ("\\t", $name, $sum, $ten, $mean, $std, $zsc, $prob ),"\\n" );\n+ }\n+ close $ppp_f;\n+}\n+\n+sub count_mapped\n+{\n+ my ( $fai, $in_file ) = @_;\n+ my ( %mapped, %dup, %has_ppp );\n+\n+ open my $f, \'<\', $fai || die "cannot open $fai $! \\n";\n+ while(<$f>)\n+ {\n+ if ($_ =~ /(.*)\\t(\\d+)\\n/)\n+ {\n+ $mapped{$1} = [];\n+ $mapped{$1}->[0] = []; $mapped{$1}->[1] = [];\n+ }\n+ }\n+ close $f;\n+\n+ open my $infile, "samtools view \'$in_file\' |"|| die "cannot open input file $! \\n";\n+ while(<$infile>)\n+ {\n+ unless ($_ =~ /^\\@[A-Za-z][A-Za-z](\\t[A-Za-z][A-Za-z0-9]:[ -~]+)+$/ || $_ =~ /^\\@CO\\t.*/ )\n+ {\n+ my @line = split (/\\t/,$_);\n+ if ($line[1] == 0)\n+ {\n+ unless ( exists ($dup{$line[3].$line[9].$line[1].$line[2]}) )\n+ {\n+ push @{$mapped{$line[2]}->[0]} , [$line[3], $line[9], $line[1], $line[2]];\n+ $has_ppp {$line[3].$line[9].$line[1].$line[2]} = 0;\n+ }\n+ $dup{$line[3].$line[9].$line[1].$line[2]}+=1;\n+ }\n+ elsif ($line[1] == 16)\n+ {\n+ unless ( exists ($dup{$line[3].$line[9].$line[1].$line[2]}) )\n+ {\n+ push @{$mapped{$line[2]}->[1]} , [$line[3], $line[9], $line[1], $line[2]];\n+ $has_ppp{$line[3].$line[9].$line[1].$line[2]} = 0;\n+ }\n+ $dup{$line[3].$line[9].$line[1].$line[2]}+=1\n+ }\n+ }\n+ }\n+ close $infile;\n+ return (\\%mapped, \\%dup, \\%has_ppp );\n+}\n+\n+sub sum\n+{\n+ my $arrayref = shift;\n+ my $result = 0;\n+ foreach (@$arrayref) {$result += $_}\n+ return $result;\n+}\n+\n+sub mean\n+{\n+ my $arrayref = shift;\n+ my $result;\n+ foreach (@$arrayref) {$result += $_}\n+ return $result / scalar(@$arrayref);\n+}\n+\n+sub standard_deviation\n+{\n+ my ($arrayref, $mean) = @_;\n+ return sqrt ( mean ( [map $_**2 , @$arrayref ]) - ($mean**2));\n+}\n+\n+sub z_significance\n+{\n+ my ($ten, $mean, $std) = @_;\n+ my $z = \'NA\';\n+ $z = (($ten - $mean) / $std) if $std != 0;\n+ return $z;\n+}\n+\n+1;\n+\n' |
| b |
| diff -r 11708af40030 -r 967512924317 lib/sRNAPipe/resize.pm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/sRNAPipe/resize.pm Mon Jan 28 11:57:15 2019 -0500 |
| [ |
| @@ -0,0 +1,101 @@ +package sRNAPipe::resize; + +use strict; +use warnings; + +use FindBin; +use lib "$FindBin::Bin/../lib"; +use sRNAPipe::Rcall qw ( histogram ); + +use Exporter; +our @ISA = qw( Exporter ); +our @EXPORT_OK = qw( &size_distribution ); + +sub size_distribution +{ + my ( $fastq, $fastq_out, $dir, $min, $max ) = @_; + + my ( %fragments_size, %duplicates ) ; + my $num = size($min, $max, $fastq, $fastq_out, \%fragments_size, \%duplicates); + + my $png = $dir.'histogram.png'; + histogram(\%fragments_size, $png, $num); + + my $size = $dir.'reads_size.txt'; + + + my $pourcentage; + open my $o, '>', $size || die "cannot open $size $!\n"; + print $o "size\tnumber\tpercentage\n"; + foreach my $k (sort { $a <=> $b } keys %fragments_size ) + { + $pourcentage = $fragments_size{$k} / $num * 100; + + print $o "$k\t$fragments_size{$k}\t"; + printf $o "%.2f\n",$pourcentage; + } + close $o; + + my $dup = $dir.'duplicates.txt' ; + open $o, '>', $dup || die "cannot open $size $!\n"; + print $o "size\tnumber\n"; + foreach my $k (sort { $duplicates{$b} <=> $duplicates{$a} } keys %duplicates ) + { + print $o "$k\t$duplicates{$k}\n"; + } + close $o; +} + +sub size +{ + my ($min, $max, $in_file, $out_file, $sizeHashR, $duplicateHashR) = @_; + my ($numreads, $size, $cmp, $ok, $line) = (0, 0, 0, 0); + my @fastq; + open (my $in, $in_file) || die "cannot open $in_file $!\n"; + open (my $out, ">".$out_file) || die "cannot create $out_file $!\n"; + while(<$in>) + { + chomp $_; + $cmp++; $line++; + if ($cmp == 1) + { + die "file do not contain a @ at line $line\n" unless ($_ =~ /^\@/ ); + $ok = 0; @fastq = (); + push(@fastq,$_); + } + elsif ($cmp == 2) + { + #die "unrecognized symbol at line $line\n" unless ($_ =~ /[atcgATCGnN]+/ || $_ =~ /^$/ ); + push(@fastq,$_); + $size = length($_); + if ($size >= $min && $size <= $max) + { + $numreads++; + ${$sizeHashR}{$size}+=1; + ${$duplicateHashR}{$_}+=1 if (defined($duplicateHashR)); + $ok = 1; + } + } + elsif ($cmp == 3 ) + { + die "file do not contain a + at line $line\n" unless $_ =~ /^\+/; + push(@fastq,$_); + } + elsif ($cmp == 4 ) + { + push(@fastq,$_); + $cmp = 0; + if ($ok == 1) + { + foreach my $t (@fastq) + { + print $out $t."\n"; + } + } + } + } + close $in; close $out; + return $numreads; +} + +1; |
| b |
| diff -r 11708af40030 -r 967512924317 lib/sRNAPipe/subgroups.pm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/sRNAPipe/subgroups.pm Mon Jan 28 11:57:15 2019 -0500 |
| [ |
| @@ -0,0 +1,174 @@ +package sRNAPipe::subgroups; + +use strict; +use warnings; +use Exporter; +our @ISA = qw( Exporter ); +our @EXPORT_OK = qw( &subgroups ); + +use POSIX; +use File::Copy; +use FindBin; +use lib "$FindBin::Bin/../lib"; +use sRNAPipe::align qw ( get_hash_alignment ); + +sub subgroups +{ + my ($fin, $dir, $mis, $mis_TE, $proc, $tRNAs, $rRNAs, $snRNAs, $miRNAs, $transcripts, $TE, $min_si, $max_si, $min_pi, $max_pi, $report ) = @_; + my (@files, $sum, $pie, $repar, %ismapped, %isjunk, %repartition, @junk_ref, @all_ref ); + + srand(); + print $report "----------------------------\n"; + print $report "Create subgroups:\nfastq_in: $fin\ndirectory_out: $dir\nmismatches: $mis\nmismatches TE: $mis_TE\n"; + + mkdir $dir; + $dir = $dir.'/' unless $dir =~ /(.*)\/$/; + + my $accept_miRNas = $dir.'miRNAs.fastq'; + my $reject_miRNAs = $dir.'miRNAs_rejected.fastq'; + my $sam_miRNAs = $dir.'miRNAs.sam'; + my @tmp = get_hash_alignment($miRNAs, $mis, 1, 1, $accept_miRNas, $reject_miRNAs, $fin, $proc, 'miRNAs',$sam_miRNAs, $report); + my $mi = $tmp[0]; my $sam = ''; + $repartition{'miRNAs'} = $mi; + + + my $reject_rRNAs = $dir.'rRNAs_rejected.fastq'; + if ( $rRNAs eq 'None') + { + move($reject_miRNAs,$reject_rRNAs); + } + else + { + $sam = new String::Random; + $sam = $sam->randpattern("CCcccccc"); + @tmp = get_hash_alignment($rRNAs, $mis, 0, 1, 'NA', $reject_rRNAs, $reject_miRNAs, $proc, 'rRNAs', $sam, $report); + $repartition{'rRNAs'} = $tmp[0]; + unlink $sam, $sam.'_aln.err', $sam.'_samse.err'; + } + + my $reject_tRNAs = $dir.'rRNAs_rejected.fastq'; + if ( $rRNAs eq 'None') + { + move($reject_rRNAs,$reject_tRNAs); + } + else + { + $sam = new String::Random; + $sam = $sam->randpattern("CCcccccc"); + @tmp = get_hash_alignment($tRNAs, $mis, 0, 1, 'NA', $reject_tRNAs, $reject_rRNAs, $proc, 'tRNAs', $sam, $report); + $repartition{'tRNAs'} = $tmp[0]; + unlink $sam, $sam.'_aln.err', $sam.'_samse.err'; + } + + + my $bonafide = $dir.'bonafide_reads.fastq'; + if ( $rRNAs eq 'None') + { + move($reject_tRNAs,$bonafide); + } + else + { + $sam = new String::Random; + $sam = $sam->randpattern("CCcccccc"); + @tmp = get_hash_alignment($snRNAs, $mis, 0, 1, 'NA', $bonafide, $reject_tRNAs, $proc, 'snRNAs', $sam, $report); + $repartition{'snRNAs'} = $tmp[0]; + + unlink $sam, $sam.'_aln.err', $sam.'_samse.err'; + } + my $bo = $tmp[1]; + + my $sam_transcripts = $dir.'transcripts.sam'; + my $reject_transcripts = $dir.'rejected_transcripts.fastq'; + @tmp = get_hash_alignment($transcripts, $mis, 0, 1, 'NA', $reject_transcripts, $bonafide, $proc, 'transcripts', $sam_transcripts, $report, $dir.'transcripts.fai'); + $repartition{'transcripts'} = $tmp[0]; + + + my $sam_TEs = $dir.'TEs.sam'; + my $reject_TEs = $dir.'rejected.fastq'; + @tmp = get_hash_alignment($TE, $mis_TE, 0, 1, 'NA', $reject_TEs, $reject_transcripts, $proc, 'TEs', $sam_TEs, $report, $dir.'TEs.fai' ); + $repartition{'TEs'} = $tmp[0] ; $repartition{'others'} = $tmp[1]; + unlink $sam, $sam.'_aln.err', $sam.'_samse.err'; + unlink $reject_transcripts; + unlink $reject_rRNAs; + unlink $reject_miRNAs; + unlink $reject_tRNAs; + + #create repartition + my $pi = fastqSubgroups($bonafide, $dir, $min_si, $max_si, $min_pi, $max_pi ); + + open (my $re, '>'.$dir.'repartition.txt') || die "cannot open $dir repartition.txt $!\n"; + print $re "type\tnumber\tpercentage\n"; + $sum += $_ foreach values %repartition; + foreach my $k ( sort keys %repartition ) + { + my $prct = 0; + $prct = $repartition{$k} / $sum * 100 if $sum != 0; + print $re "$k\t$repartition{$k}\t"; printf $re "%.2f\n",$prct; + } + return ( $bo, $mi, $pi); +} + +sub fastqSubgroups +{ + my ( $fastq, $output_directory, $min_si, $max_si, $min_pi, $max_pi ) = @_; + my $fastq_siRNA = $output_directory."siRNAs.fastq"; + my $fastq_piRNA = $output_directory."piRNAs.fastq"; + + open my $fic, '<', $fastq || die "cannot open input file $! \n"; + open my $si, '>', $fastq_siRNA || die "cannot open siRNA.fastq $! \n"; + open my $pi, '>', $fastq_piRNA || die "cannot open piRNA.fastq $! \n"; + + my ($length, $cmp, $type, $siRNA_number, $miRNA_h_number, $piRNA_number, $not_pi_number) = (0,0,0,0,0,0,0); + my (@fastq) =(); my $seq_name; + my $out; + while(<$fic>) + { + chomp $_; + $cmp++; + if ($cmp == 1) + { + die "file do not contain a @ at line $cmp\n" unless ($_ =~ /^\@/ ); + $type = 0; @fastq = (); + if ($_ =~ /^\@(.*)\s.*/) { $seq_name = $1;} + elsif ($_ =~ /^\@(.*)/) {$seq_name = $1;} + push(@fastq,$_); + } + elsif ($cmp == 2) + { + #die "unrecognized symbol at line $cmp\n" unless $_ =~ /[atcgATCGnN]+/; + push(@fastq,$_); + $length = length($_); + $type = 0; + if ( $length >= $min_si && $length <= $max_si ) + { + $type = 2; + $siRNA_number++; + } + if ($length >= $min_pi && $length <= $max_pi ) + { + $type += 4; + $piRNA_number++; + } + } + elsif ($cmp == 3 ) + { + die "file do not contain a + at line $cmp\n" unless $_ =~ /^\+/; + push(@fastq,$_); + } + elsif ($cmp == 4 ) + { + push(@fastq,$_); + $cmp = 0; + if ($type != 0) + { + if ($type & 4 ) { foreach my $t (@fastq) { print $pi $t."\n";} } + if ($type & 2 ) { foreach my $t (@fastq) { print $si $t."\n";} } + } + } + } + close $fic; + close $si; close $pi; + return ($piRNA_number); +} + +1; |
| b |
| diff -r 11708af40030 -r 967512924317 sRNAPipe.xml --- a/sRNAPipe.xml Thu Jan 24 13:09:46 2019 -0500 +++ b/sRNAPipe.xml Mon Jan 28 11:57:15 2019 -0500 |
| [ |
| @@ -36,7 +36,7 @@ <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement> <requirement type="package" version="2.2.1">r-ggplot2</requirement> </requirements> - <version_command>perl '$__tool_directory__/bin/sRNAPipe.pl'</version_command> + <version_command>perl '$__tool_directory__/bin/sRNAPipe.pl' | grep 'version' | grep "version" | cut -d ' ' -f 3</version_command> <command detect_errors="aggressive"><![CDATA[ perl '$__tool_directory__/bin/sRNAPipe.pl' |