InterProScan result summary page
- ' )
+
+for filename in [f for f in os.listdir( sys.argv[2] ) if os.path.isfile( os.path.join( sys.argv[2], f) )]:
+ o.write( '
- %s ' % ( filename, os.path.splitext( filename )[0] ) ) + +o.write( '
PRINSEQ-'.$WHAT.' v'.$VERSION.' HTML Report
[Generated: '.$time.']'; + $html .= '
';
+
+ #input info
+ if(exists $data->{numseqs}) {
+ $html .= '
'; + } + + #length plot + if(exists $data->{counts}->{length} && keys %{$data->{counts}->{length}}) { + $html .= '
File 2
'; + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts2}->{length},1),$data->{stats2}->{length},'Length Distribution','Read Length in bp','# Sequences','',0,' bp'); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + $html .= '';
+ } else {
+ $html .= '
'; + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts}->{length},1),$data->{stats}->{length},'Length Distribution','Read Length in bp','# Sequences','',0,' bp'); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + $html .= '';
+ }
+ $html .= '
'; + } + + #GC content + if(exists $data->{counts}->{gc} && keys %{$data->{counts}->{gc}}) { + $html .= '
File 2
'; + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts2}->{gc},0),$data->{stats2}->{gc},'GC Content Distribution','GC Content (0-100%)','Number of Sequences','',1); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + $html .= '';
+ } else {
+ $html .= '
'; + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts}->{gc},0),$data->{stats}->{gc},'GC Content Distribution','GC Content (0-100%)','Number of Sequences','',1); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + $html .= '';
+ }
+ $html .= '
'; + } + + #Base quality + if(exists $data->{quals} || exists $data->{qualsmean} || exists $data->{qualsbin}) { + $html .= '
'; + } + + #Ns + if((exists $data->{counts}->{ns} && keys %{$data->{counts}->{ns}}) || (exists $data->{counts2} && exists $data->{counts2}->{ns} && keys %{$data->{counts2}->{ns}})) { + $html .= '
'; + } + + #tails + if(exists $data->{tail} || exists $data->{tail2}) { + $html .= '
'; + } + + + #tag sequence check + if(exists $data->{freqs} || exists $data->{freqs2}) { + $html .= '
'; + } + + #Sequence duplicates + if(exists $data->{dubslength} || exists $data->{dubscounts}) { + $html .= '
';
+ }
+ if(exists $dubs{all} && $dubs{all}) {
+ if(exists $data->{dubslength} && keys %{$data->{dubslength}}) {
+ $surface = &createStackBarPlot(&convertOdToStackBinMatrix($data->{dubslength},5,1),'Sequence duplication level','Read Length in bp','Number of duplicates','',0,' bp');
+ $png = '';
+ $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; });
+ $html .= '
'.&insert_image($png); + } + if(exists $data->{dubscounts} && keys %{$data->{dubscounts}}) { + $surface = &createStackBarPlot(&convertOdToStackBinMatrix($data->{dubscounts},5,1,100),'Sequence duplication level','Number of duplicates','Number of sequences','',0); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
' if(exists $data->{dubslength}); + $html .= &insert_image($png); + my %dubsmax; + my $count = 1; + foreach my $n (sort {$b <=> $a} keys %{$data->{dubscounts}}) { + foreach my $s (keys %{$data->{dubscounts}->{$n}}) { + foreach my $i (1..$data->{dubscounts}->{$n}->{$s}) { + $dubsmax{$count++}->{$s} = $n; + last unless($count <= 100); + } + last unless($count <= 100); + } + last unless($count <= 100); + } + $surface = &createStackBarPlot(&convertOdToStackBinMatrix(\%dubsmax,5,1,100),'Sequence duplication level','Sequence','Number of duplicates','',0); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
' if(exists $data->{dubslength}); + $html .= &insert_image($png); + } + } + if(exists $data->{dubslength} || exists $data->{dubscounts}) { + $html .= '
'; + } + + #Sequence complexity + if(exists $data->{compldust} || exists $data->{complentropy}) { + $html .= '
/g; + $data->{complvals}->{$d}->{$m} = $complseq; + } + } + } + $html .= '
'; + } + if(exists $data->{compldust}) { + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{compldust},0),undef,'Sequence complexity distribution','Mean sequence complexity (DUST scores)','Number of sequences','',1); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + } + if(exists $data->{complentropy}) { + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{complentropy},0),undef,'Sequence complexity distribution','Mean sequence complexity (Entropy values)','Number of sequences','',1); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
' if(exists $data->{compldust}); + $html .= &insert_image($png); + } + if(exists $data->{compldust} || exists $data->{complentropy}) { + $html .= '
'; + } + + #Dinucleotide odd ratio PCA - microbial/viral + if(exists $data->{dinucodds} && keys %{$data->{dinucodds}}) { + $html .= '
'; + my @new = map {$data->{dinucodds}->{$_}} sort keys %{$data->{dinucodds}}; + $surface = &createOddsRatioPlot($data->{dinucodds},'Odds ratios','Dinucleotide','Odds ratio',''); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + #$surface = &createPCAPlot(&convertToPCAValues(\@new,'m'),'PCA','1st Principal Component Score','2nd Principal Component Score',''); + #$png = ''; + #$surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + #$html .= '
'; + #$html .= &insert_image($png); + #$surface = &createPCAPlot(&convertToPCAValues(\@new,'v'),'PCA','1st Principal Component Score','2nd Principal Component Score',''); + #$png = ''; + #$surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + #$html .= '
'; + #$html .= &insert_image($png); + $html .= '';
+ }
+
+ $html .= '
';
+ $html .= &footer();
+
+ #write html to file
+ $file = &getFileName('.html');
+ open(FH, ">$file") or &printError("Can't open file ".$file.": $!");
+ print FH $html;
+ close(FH);
+ &printLog("Done with HTML data");
+}
+
+sub insert_image {
+ my ($data, $height, $width, $noencode) = @_;
+ my $content .= 'Input Information
';
+ $html .= '| Input file(s): | '.($data->{filename1} ? &convertIntToString($data->{filename1}) : '-').($data->{filename2} ? ' and '.&convertIntToString($data->{filename2}) : '').' |
| Input format(s): | '.($data->{format1} ? uc($data->{format1}) : '-').($data->{format2} ? ' and '.uc($data->{format2}) : '').' |
| # Sequences (file 1): | '.&addCommas($data->{numseqs}||'-').' |
| Total bases (file 1): | '.&addCommas($data->{numbases}||'-').' |
| # Sequences (file 2): | '.&addCommas($data->{numseqs2}||'-').' |
| Total bases (file 2): | '.&addCommas($data->{numbases2}||'-').' |
| # Pairs: | '.&addCommas($data->{pairs}||'-').($data->{pairs} ? ' ('.sprintf("%.2f",(100*(2*$data->{pairs})/(($data->{numseqs}||0)+($data->{numseqs2}||0)))).'% of sequences)' : '').' |
| # Singletons (file 1): | '.&addCommas($singletons1).($singletons1 ? ' ('.sprintf("%.2f",(100*$singletons1/$data->{numseqs})).'%)' : '').' |
| # Singletons (file 2): | '.&addCommas($singletons2).($singletons2 ? ' ('.sprintf("%.2f",(100*$singletons2/$data->{numseqs2})).'%)' : '').' |
| # Sequences: | '.&addCommas($data->{numseqs}||'-').' |
| Total bases: | '.&addCommas($data->{numbases}||'-').' |
'; + } + + #length plot + if(exists $data->{counts}->{length} && keys %{$data->{counts}->{length}}) { + $html .= '
Length Distribution
';
+ if(exists $data->{pairedend} && $data->{pairedend}) {
+ $html .= 'File 1
'; + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts}->{length},1),$data->{stats}->{length},'Length Distribution','Read Length in bp','# Sequences','',0,' bp'); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + $html .= '
';
+ $html .= '| Mean sequence length: | '.(exists $data->{stats}->{length}->{mean} ? sprintf("%.2f",$data->{stats}->{length}->{mean}) : '-').' ± '.(exists $data->{stats}->{length}->{std} ? sprintf("%.2f",$data->{stats}->{length}->{std}) : '-').' bp |
| Minimum length: | '.(exists $data->{stats}->{length}->{min} ? &addCommas($data->{stats}->{length}->{min}) : '-').' bp |
| Maximum length: | '.(exists $data->{stats}->{length}->{max} ? &addCommas($data->{stats}->{length}->{max}) : '-').' bp |
| Length range: | '.(exists $data->{stats}->{length}->{range} ? &addCommas($data->{stats}->{length}->{range}) : '-').' bp |
| Mode length: | '.(exists $data->{stats}->{length}->{mode} ? &addCommas($data->{stats}->{length}->{mode}) : '-').' bp with '.(exists $data->{stats}->{length}->{modeval} ? &addCommas($data->{stats}->{length}->{modeval}) : '-').' sequences |
'; + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts}->{length},1),$data->{stats}->{length},'Length Distribution','Read Length in bp','# Sequences','',0,' bp'); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + $html .= '
File 2
| Mean sequence length: | '.(exists $data->{stats2}->{length}->{mean} ? sprintf("%.2f",$data->{stats2}->{length}->{mean}) : '-').' ± '.(exists $data->{stats2}->{length}->{std} ? sprintf("%.2f",$data->{stats2}->{length}->{std}) : '-').' bp |
| Minimum length: | '.(exists $data->{stats2}->{length}->{min} ? &addCommas($data->{stats2}->{length}->{min}) : '-').' bp |
| Maximum length: | '.(exists $data->{stats2}->{length}->{max} ? &addCommas($data->{stats2}->{length}->{max}) : '-').' bp |
| Length range: | '.(exists $data->{stats2}->{length}->{range} ? &addCommas($data->{stats2}->{length}->{range}) : '-').' bp |
| Mode length: | '.(exists $data->{stats2}->{length}->{mode} ? &addCommas($data->{stats2}->{length}->{mode}) : '-').' bp with '.(exists $data->{stats2}->{length}->{modeval} ? &addCommas($data->{stats2}->{length}->{modeval}) : '-').' sequences |
'; + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts2}->{length},1),$data->{stats2}->{length},'Length Distribution','Read Length in bp','# Sequences','',0,' bp'); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + $html .= '
| Mean sequence length: | '.(exists $data->{stats}->{length}->{mean} ? sprintf("%.2f",$data->{stats}->{length}->{mean}) : '-').' ± '.(exists $data->{stats}->{length}->{std} ? sprintf("%.2f",$data->{stats}->{length}->{std}) : '-').' bp |
| Minimum length: | '.(exists $data->{stats}->{length}->{min} ? &addCommas($data->{stats}->{length}->{min}) : '-').' bp |
| Maximum length: | '.(exists $data->{stats}->{length}->{max} ? &addCommas($data->{stats}->{length}->{max}) : '-').' bp |
| Length range: | '.(exists $data->{stats}->{length}->{range} ? &addCommas($data->{stats}->{length}->{range}) : '-').' bp |
| Mode length: | '.(exists $data->{stats}->{length}->{mode} ? &addCommas($data->{stats}->{length}->{mode}) : '-').' bp with '.(exists $data->{stats}->{length}->{modeval} ? &addCommas($data->{stats}->{length}->{modeval}) : '-').' sequences |
'; + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts}->{length},1),$data->{stats}->{length},'Length Distribution','Read Length in bp','# Sequences','',0,' bp'); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + $html .= '
'; + } + + #GC content + if(exists $data->{counts}->{gc} && keys %{$data->{counts}->{gc}}) { + $html .= '
GC Content Distribution
';
+ if(exists $data->{pairedend} && $data->{pairedend}) {
+ $html .= 'File 1
'; + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts}->{gc},0),$data->{stats}->{gc},'GC Content Distribution','GC Content (0-100%)','Number of Sequences','',1); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + $html .= '
';
+ $html .= '| Mean GC content: | '.(exists $data->{stats}->{gc}->{mean} ? sprintf("%.2f",$data->{stats}->{gc}->{mean}) : '-').' ± '.(exists $data->{stats}->{gc}->{std} ? sprintf("%.2f",$data->{stats}->{gc}->{std}) : '-').' % |
| Minimum GC content: | '.(exists $data->{stats}->{gc}->{min} ? $data->{stats}->{gc}->{min} : '-').' % |
| Maximum GC content: | '.(exists $data->{stats}->{gc}->{max} ? $data->{stats}->{gc}->{max} : '-').' % |
| GC content range: | '.(exists $data->{stats}->{gc}->{range} ? $data->{stats}->{gc}->{range} : '-').' % |
| Mode GC content: | '.(exists $data->{stats}->{gc}->{mode} ? $data->{stats}->{gc}->{mode} : '-').' % with '.(exists $data->{stats}->{gc}->{modeval} ? &addCommas($data->{stats}->{gc}->{modeval}) : '-').' sequences |
'; + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts}->{gc},0),$data->{stats}->{gc},'GC Content Distribution','GC Content (0-100%)','Number of Sequences','',1); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + $html .= '
File 2
| Mean GC content: | '.(exists $data->{stats2}->{gc}->{mean} ? sprintf("%.2f",$data->{stats2}->{gc}->{mean}) : '-').' ± '.(exists $data->{stats2}->{gc}->{std} ? sprintf("%.2f",$data->{stats2}->{gc}->{std}) : '-').' % |
| Minimum GC content: | '.(exists $data->{stats2}->{gc}->{min} ? $data->{stats2}->{gc}->{min} : '-').' % |
| Maximum GC content: | '.(exists $data->{stats2}->{gc}->{max} ? $data->{stats2}->{gc}->{max} : '-').' % |
| GC content range: | '.(exists $data->{stats2}->{gc}->{range} ? $data->{stats2}->{gc}->{range} : '-').' % |
| Mode GC content: | '.(exists $data->{stats2}->{gc}->{mode} ? $data->{stats2}->{gc}->{mode} : '-').' % with '.(exists $data->{stats2}->{gc}->{modeval} ? &addCommas($data->{stats2}->{gc}->{modeval}) : '-').' sequences |
'; + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts2}->{gc},0),$data->{stats2}->{gc},'GC Content Distribution','GC Content (0-100%)','Number of Sequences','',1); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + $html .= '
| Mean GC content: | '.(exists $data->{stats}->{gc}->{mean} ? sprintf("%.2f",$data->{stats}->{gc}->{mean}) : '-').' ± '.(exists $data->{stats}->{gc}->{std} ? sprintf("%.2f",$data->{stats}->{gc}->{std}) : '-').' % |
| Minimum GC content: | '.(exists $data->{stats}->{gc}->{min} ? $data->{stats}->{gc}->{min} : '-').' % |
| Maximum GC content: | '.(exists $data->{stats}->{gc}->{max} ? $data->{stats}->{gc}->{max} : '-').' % |
| GC content range: | '.(exists $data->{stats}->{gc}->{range} ? $data->{stats}->{gc}->{range} : '-').' % |
| Mode GC content: | '.(exists $data->{stats}->{gc}->{mode} ? $data->{stats}->{gc}->{mode} : '-').' % with '.(exists $data->{stats}->{gc}->{modeval} ? &addCommas($data->{stats}->{gc}->{modeval}) : '-').' sequences |
'; + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts}->{gc},0),$data->{stats}->{gc},'GC Content Distribution','GC Content (0-100%)','Number of Sequences','',1); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + $html .= '
'; + } + + #Base quality + if(exists $data->{quals} || exists $data->{qualsmean} || exists $data->{qualsbin}) { + $html .= '
Base Quality Distribution
';
+ if(exists $data->{pairedend} && $data->{pairedend}) {
+ $html .= 'File 1
'; + } + } + if(exists $data->{quals} && keys %{$data->{quals}}) { + $surface = &createBoxPlot(&convertToBoxValues($data->{quals},4),'Base Quality Distribution','Read position in %','Quality score',''); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + } + if(exists $data->{qualsbin} && keys %{$data->{qualsbin}}) { + $surface = &createBoxPlot(&convertToBoxValues($data->{qualsbin},4),'Base Quality Distribution','Read position in bp','Quality score','',0,'bp',$data->{binval}); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
' if(exists $data->{quals}); + $html .= &insert_image($png); + } + if(exists $data->{qualsmean} && keys %{$data->{qualsmean}}) { + $surface = &createBarPlot(&convertToBarValues($data->{qualsmean},5,1),'Sequence Quality Distribution','Mean of quality scores per sequence','Number of sequences','',0); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
' if(exists $data->{qualsbin}); + $html .= &insert_image($png); + } + if(exists $data->{pairedend} && $data->{pairedend}) { + if(exists $data->{quals} || exists $data->{qualsmean} || exists $data->{qualsbin}) { + $html .= '
File 2
'; + } + if(exists $data->{quals2} && keys %{$data->{quals2}}) { + $surface = &createBoxPlot(&convertToBoxValues($data->{quals2},4),'Base Quality Distribution','Read position in %','Quality score',''); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + } + if(exists $data->{qualsbin2} && keys %{$data->{qualsbin2}}) { + $surface = &createBoxPlot(&convertToBoxValues($data->{qualsbin2},4),'Base Quality Distribution','Read position in bp','Quality score','',0,'bp',$data->{binval}); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
' if(exists $data->{quals2}); + $html .= &insert_image($png); + } + if(exists $data->{qualsmean2} && keys %{$data->{qualsmean2}}) { + $surface = &createBarPlot(&convertToBarValues($data->{qualsmean2},5,1),'Sequence Quality Distribution','Mean of quality scores per sequence','Number of sequences','',0); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
' if(exists $data->{qualsbin2}); + $html .= &insert_image($png); + } + } + if(exists $data->{quals} || exists $data->{qualsmean} || exists $data->{qualsbin}) { + $html .= '
'; + } + } + if(exists $data->{quals} && keys %{$data->{quals}}) { + $surface = &createBoxPlot(&convertToBoxValues($data->{quals},4),'Base Quality Distribution','Read position in %','Quality score',''); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + } + if(exists $data->{qualsbin} && keys %{$data->{qualsbin}}) { + $surface = &createBoxPlot(&convertToBoxValues($data->{qualsbin},4),'Base Quality Distribution','Read position in bp','Quality score','',0,'bp',$data->{binval}); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
' if(exists $data->{quals}); + $html .= &insert_image($png); + } + if(exists $data->{qualsmean} && keys %{$data->{qualsmean}}) { + $surface = &createBarPlot(&convertToBarValues($data->{qualsmean},5,1),'Sequence Quality Distribution','Mean of quality scores per sequence','Number of sequences','',0); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
' if(exists $data->{qualsbin}); + $html .= &insert_image($png); + } + if(exists $data->{pairedend} && $data->{pairedend}) { + if(exists $data->{quals} || exists $data->{qualsmean} || exists $data->{qualsbin}) { + $html .= '
File 2
'; + } + if(exists $data->{quals2} && keys %{$data->{quals2}}) { + $surface = &createBoxPlot(&convertToBoxValues($data->{quals2},4),'Base Quality Distribution','Read position in %','Quality score',''); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + } + if(exists $data->{qualsbin2} && keys %{$data->{qualsbin2}}) { + $surface = &createBoxPlot(&convertToBoxValues($data->{qualsbin2},4),'Base Quality Distribution','Read position in bp','Quality score','',0,'bp',$data->{binval}); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
' if(exists $data->{quals2}); + $html .= &insert_image($png); + } + if(exists $data->{qualsmean2} && keys %{$data->{qualsmean2}}) { + $surface = &createBarPlot(&convertToBarValues($data->{qualsmean2},5,1),'Sequence Quality Distribution','Mean of quality scores per sequence','Number of sequences','',0); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
' if(exists $data->{qualsbin2}); + $html .= &insert_image($png); + } + } + if(exists $data->{quals} || exists $data->{qualsmean} || exists $data->{qualsbin}) { + $html .= '
'; + } + + #Ns + if((exists $data->{counts}->{ns} && keys %{$data->{counts}->{ns}}) || (exists $data->{counts2} && exists $data->{counts2}->{ns} && keys %{$data->{counts2}->{ns}})) { + $html .= '
Occurence of N
';
+ if(exists $data->{pairedend} && $data->{pairedend}) {
+ $html .= 'File 1
'; + } + } + if(exists $data->{counts}->{ns} && keys %{$data->{counts}->{ns}}) { + my $nscount = 0; + foreach my $n (values %{$data->{counts}->{ns}}) { + $nscount += $n; + } + $html .= '
';
+ if($nscount) {
+ $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts}->{ns},1),undef,'Percentage of N\'s (> 0%)','Percentage of N\'s per Read (1-100%)','# Sequences','',0);
+ $png = '';
+ $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; });
+ $html .= '
'.&insert_image($png); + } + } + if(exists $data->{pairedend} && $data->{pairedend} && exists $data->{counts2}->{ns} && keys %{$data->{counts2}->{ns}}) { + $html .= '
File 2
'; + my $nscount = 0; + foreach my $n (values %{$data->{counts2}->{ns}}) { + $nscount += $n; + } + $html .= '
';
+ if($nscount) {
+ $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts2}->{ns},1),undef,'Percentage of N\'s (> 0%)','Percentage of N\'s per Read (1-100%)','# Sequences','',0);
+ $png = '';
+ $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; });
+ $html .= '
'.&insert_image($png); + } + } + if((exists $data->{counts}->{ns} && keys %{$data->{counts}->{ns}}) || (exists $data->{counts2} && exists $data->{counts2}->{ns} && keys %{$data->{counts2}->{ns}})) { + $html .= '
'; + } + } + if(exists $data->{counts}->{ns} && keys %{$data->{counts}->{ns}}) { + my $nscount = 0; + foreach my $n (values %{$data->{counts}->{ns}}) { + $nscount += $n; + } + $html .= '
| Sequences with N: | '.($nscount ? &addCommas($nscount).' ('.sprintf("%.2f",100/$data->{numseqs}*$nscount).' %)' : 0).' |
| Max percentage of Ns per sequence: | '.(exists $data->{stats}->{ns}->{max} ? $data->{stats}->{ns}->{max} : 0).' % |
'.&insert_image($png); + } + } + if(exists $data->{pairedend} && $data->{pairedend} && exists $data->{counts2}->{ns} && keys %{$data->{counts2}->{ns}}) { + $html .= '
File 2
'; + my $nscount = 0; + foreach my $n (values %{$data->{counts2}->{ns}}) { + $nscount += $n; + } + $html .= '
| Sequences with N: | '.($nscount ? &addCommas($nscount).' ('.sprintf("%.2f",100/$data->{numseqs2}*$nscount).' %)' : 0).' |
| Max percentage of Ns per sequence: | '.(exists $data->{stats2}->{ns}->{max} ? $data->{stats2}->{ns}->{max} : 0).' % |
'.&insert_image($png); + } + } + if((exists $data->{counts}->{ns} && keys %{$data->{counts}->{ns}}) || (exists $data->{counts2} && exists $data->{counts2}->{ns} && keys %{$data->{counts2}->{ns}})) { + $html .= '
'; + } + + #tails + if(exists $data->{tail} || exists $data->{tail2}) { + $html .= '
Poly-A/T Tails
';
+ }
+ if(exists $data->{tail}) {
+ my $tail5count = 0;
+ foreach my $n (values %{$data->{counts}->{tail5}}) {
+ $tail5count += $n;
+ }
+ my $tail3count = 0;
+ foreach my $n (values %{$data->{counts}->{tail3}}) {
+ $tail3count += $n;
+ }
+ if(exists $data->{pairedend} && $data->{pairedend}) {
+ $html .= 'File 1
'; + } + $html .= '
';
+ if($tail5count) {
+ $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts}->{tail5},1),undef,'Poly-A/T Tail Distribution (> 4bp)','5\' Tail Length in bp','# Sequences','',0,' bp');
+ $png = '';
+ $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; });
+ $html .= '
'.&insert_image($png); + if($tail3count) { + $html .= '
'; + } + } + if($tail3count) { + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts}->{tail3},1),undef,'Poly-A/T Tail Distribution (> 4bp)','3\' Tail Length in bp','# Sequences','',0,' bp'); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
'.&insert_image($png); + } + } + if(exists $data->{pairedend} && $data->{pairedend} && exists $data->{tail2}) { + my $tail5count = 0; + foreach my $n (values %{$data->{counts2}->{tail5}}) { + $tail5count += $n; + } + my $tail3count = 0; + foreach my $n (values %{$data->{counts2}->{tail3}}) { + $tail3count += $n; + } + $html .= '
File 2
'; + $html .= '
';
+ if($tail5count) {
+ $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts2}->{tail5},1),undef,'Poly-A/T Tail Distribution (> 4bp)','5\' Tail Length in bp','# Sequences','',0,' bp');
+ $png = '';
+ $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; });
+ $html .= '
'.&insert_image($png); + if($tail3count) { + $html .= '
'; + } + } + if($tail3count) { + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts2}->{tail3},1),undef,'Poly-A/T Tail Distribution (> 4bp)','3\' Tail Length in bp','# Sequences','',0,' bp'); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
'.&insert_image($png); + } + } + if(exists $data->{tail} || exists $data->{tail2}) { + $html .= '
'; + } + $html .= '
| 5\'-end | 3\'-end | |
| Sequences with tail: | '.($tail5count ? &addCommas($tail5count).' ('.sprintf("%.2f",100/$data->{numseqs}*$tail5count).' %)' : 0).' | '.($tail3count ? &addCommas($tail3count).' ('.sprintf("%.2f",100/$data->{numseqs}*$tail3count).' %)' : 0).' |
| Maximum tail length: | '.(exists $data->{stats}->{tail5}->{max} ? $data->{stats}->{tail5}->{max} : 0).' | '.(exists $data->{stats}->{tail3}->{max} ? $data->{stats}->{tail3}->{max} : 0).' |
'.&insert_image($png); + if($tail3count) { + $html .= '
'; + } + } + if($tail3count) { + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts}->{tail3},1),undef,'Poly-A/T Tail Distribution (> 4bp)','3\' Tail Length in bp','# Sequences','',0,' bp'); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
'.&insert_image($png); + } + } + if(exists $data->{pairedend} && $data->{pairedend} && exists $data->{tail2}) { + my $tail5count = 0; + foreach my $n (values %{$data->{counts2}->{tail5}}) { + $tail5count += $n; + } + my $tail3count = 0; + foreach my $n (values %{$data->{counts2}->{tail3}}) { + $tail3count += $n; + } + $html .= '
File 2
'; + $html .= '
| 5\'-end | 3\'-end | |
| Sequences with tail: | '.($tail5count ? &addCommas($tail5count).' ('.sprintf("%.2f",100/$data->{numseqs2}*$tail5count).' %)' : 0).' | '.($tail3count ? &addCommas($tail3count).' ('.sprintf("%.2f",100/$data->{numseqs2}*$tail3count).' %)' : 0).' |
| Maximum tail length: | '.(exists $data->{stats2}->{tail5}->{max} ? $data->{stats2}->{tail5}->{max} : 0).' | '.(exists $data->{stats2}->{tail3}->{max} ? $data->{stats2}->{tail3}->{max} : 0).' |
'.&insert_image($png); + if($tail3count) { + $html .= '
'; + } + } + if($tail3count) { + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts2}->{tail3},1),undef,'Poly-A/T Tail Distribution (> 4bp)','3\' Tail Length in bp','# Sequences','',0,' bp'); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
'.&insert_image($png); + } + } + if(exists $data->{tail} || exists $data->{tail2}) { + $html .= '
'; + } + + + #tag sequence check + if(exists $data->{freqs} || exists $data->{freqs2}) { + $html .= '
Tag Sequence Check
';
+ }
+ if(exists $data->{freqs}) {
+ my $tagmidseq;
+ if(exists $data->{tagmidseq}) {
+ $tagmidseq = $data->{tagmidseq};
+ $tagmidseq =~ s/\,/\
/g; + } + if(exists $data->{pairedend} && $data->{pairedend}) { + $html .= 'File 1
'; + } + $html .= '
'; + $html .= '
';
+ }
+ if(exists $data->{pairedend} && $data->{pairedend} && exists $data->{freqs2}) {
+ $html .= '
File 2
'; + $html .= '
'; + $html .= '
';
+ }
+ if(exists $data->{freqs} || exists $data->{freqs2}) {
+ $html .= '
/g; + } + if(exists $data->{pairedend} && $data->{pairedend}) { + $html .= 'File 1
'; + } + $html .= '
| 5\'-end | 3\'-end | |
| Probability of tag sequence: | '.(exists $data->{tagprob}->{5} ? $data->{tagprob}->{5}.' %' : '-').' | '.(exists $data->{tagprob}->{3} ? $data->{tagprob}->{3}.' %' : '-').' |
| GSMIDs or RLMIDs: | '.(exists $data->{tagmidnum} ? ($data->{tagmidnum} == 0 ? 'none' : ($tagmidseq ? $tagmidseq : $data->{tagmidnum})) : '-').' |
'; + $html .= '
| '.&insert_image($FREQCHART_L,undef,undef,1).' | '; + foreach my $pos (sort {$a <=> $b} keys %{$data->{freqs}->{5}}) { + $html .= '';
+ foreach my $base (qw(A C G T N)) {
+ if($data->{freqs}->{5}->{$pos}->{$base}) {
+ $html .= &insert_image($BASE64_BASES->{$base},$data->{freqs}->{5}->{$pos}->{$base},14,1).' '; + #' '; + } + } + $html .= &insert_image($MMCHART_B2,6,16,1).' | ';
+ }
+ $html .= '... | '; + foreach my $pos (sort {$a <=> $b} keys %{$data->{freqs}->{3}}) { + $html .= '';
+ foreach my $base (qw(A C G T N)) {
+ if($data->{freqs}->{3}->{$pos}->{$base}) {
+ $html .= &insert_image($BASE64_BASES->{$base},$data->{freqs}->{3}->{$pos}->{$base},14,1).' '; + } + } + $html .= &insert_image($MMCHART_B2,6,16,1).' | ';
+ }
+ $html .= '||||||||||||||||||||||||||||||||||||||
| '; + foreach my $num (1,0,0,0,5,0,0,0,0,10,0,0,0,0,15,0,0,0,0,20,0,20,0,0,0,0,15,0,0,0,0,10,0,0,0,0,5,0,0,0,1) { + $html .= ' | '.($num ? $num : '').' | '; + } + $html .= '||||||||||||||||||||||||||||||||||||||||
| Position from Sequence Ends | |||||||||||||||||||||||||||||||||||||||||
File 2
'; + $html .= '
| 5\'-end | 3\'-end | |
| Probability of tag sequence: | '.(exists $data->{tagprob2}->{5} ? $data->{tagprob2}->{5}.' %' : '-').' | '.(exists $data->{tagprob2}->{3} ? $data->{tagprob2}->{3}.' %' : '-').' |
'; + $html .= '
| '.&insert_image($FREQCHART_L,undef,undef,1).' | '; + foreach my $pos (sort {$a <=> $b} keys %{$data->{freqs2}->{5}}) { + $html .= '';
+ foreach my $base (qw(A C G T N)) {
+ if($data->{freqs2}->{5}->{$pos}->{$base}) {
+ $html .= &insert_image($BASE64_BASES->{$base},$data->{freqs2}->{5}->{$pos}->{$base},14,1).' '; + #' '; + } + } + $html .= &insert_image($MMCHART_B2,6,16,1).' | ';
+ }
+ $html .= '... | '; + foreach my $pos (sort {$a <=> $b} keys %{$data->{freqs2}->{3}}) { + $html .= '';
+ foreach my $base (qw(A C G T N)) {
+ if($data->{freqs2}->{3}->{$pos}->{$base}) {
+ $html .= &insert_image($BASE64_BASES->{$base},$data->{freqs2}->{3}->{$pos}->{$base},14,1).' '; + } + } + $html .= &insert_image($MMCHART_B2,6,16,1).' | ';
+ }
+ $html .= '||||||||||||||||||||||||||||||||||||||
| '; + foreach my $num (1,0,0,0,5,0,0,0,0,10,0,0,0,0,15,0,0,0,0,20,0,20,0,0,0,0,15,0,0,0,0,10,0,0,0,0,5,0,0,0,1) { + $html .= ' | '.($num ? $num : '').' | '; + } + $html .= '||||||||||||||||||||||||||||||||||||||||
| Position from Sequence Ends | |||||||||||||||||||||||||||||||||||||||||
'; + } + + #Sequence duplicates + if(exists $data->{dubslength} || exists $data->{dubscounts}) { + $html .= '
Sequence Duplication
';
+ }
+ my %dubs;
+ if(exists $data->{dubscounts} && keys %{$data->{dubscounts}}) {
+ my $exactonly = $data->{exactonly}||0;
+ foreach my $n (keys %{$data->{dubscounts}}) {
+ foreach my $s (keys %{$data->{dubscounts}->{$n}}) {
+ $dubs{$s}->{count} += $data->{dubscounts}->{$n}->{$s} * $n;
+ $dubs{$s}->{max} = $n unless(exists $dubs{$s}->{max} && $dubs{$s}->{max} > $n);
+ $dubs{all} += $data->{dubscounts}->{$n}->{$s} * $n;
+ }
+ }
+ $html .= '| # Sequences | Max duplicates | |
| Exact duplicates: | '.(exists $dubs{0}->{count} ? &addCommas($dubs{0}->{count}).' ('.sprintf("%.2f",100/$data->{numseqs}*$dubs{0}->{count}).' %)' : 0).' | '.($dubs{0}->{max}||0).' |
| Exact duplicates with reverse complements: | '.(exists $dubs{3}->{count} ? &addCommas($dubs{3}->{count}).' ('.sprintf("%.2f",100/$data->{numseqs}*$dubs{3}->{count}).' %)' : 0).' | '.($dubs{3}->{max}||0).' |
| 5\' duplicates | '.(exists $dubs{1}->{count} ? &addCommas($dubs{1}->{count}).' ('.sprintf("%.2f",100/$data->{numseqs}*$dubs{1}->{count}).' %)' : 0).' | '.($dubs{1}->{max}||0).' |
| 3\' duplicates | '.(exists $dubs{2}->{count} ? &addCommas($dubs{2}->{count}).' ('.sprintf("%.2f",100/$data->{numseqs}*$dubs{2}->{count}).' %)' : 0).' | '.($dubs{2}->{max}||0).' |
| 5\'/3\' duplicates with reverse complements | '.(exists $dubs{4}->{count} ? &addCommas($dubs{4}->{count}).' ('.sprintf("%.2f",100/$data->{numseqs}*$dubs{4}->{count}).' %)' : 0).' | '.($dubs{4}->{max}||0).' |
| Total: | '.(exists $dubs{all} ? &addCommas($dubs{all}).' ('.sprintf("%.2f",100/$data->{numseqs}*$dubs{all}).' %)' : 0).' | - |
'.&insert_image($png); + } + if(exists $data->{dubscounts} && keys %{$data->{dubscounts}}) { + $surface = &createStackBarPlot(&convertOdToStackBinMatrix($data->{dubscounts},5,1,100),'Sequence duplication level','Number of duplicates','Number of sequences','',0); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
' if(exists $data->{dubslength}); + $html .= &insert_image($png); + my %dubsmax; + my $count = 1; + foreach my $n (sort {$b <=> $a} keys %{$data->{dubscounts}}) { + foreach my $s (keys %{$data->{dubscounts}->{$n}}) { + foreach my $i (1..$data->{dubscounts}->{$n}->{$s}) { + $dubsmax{$count++}->{$s} = $n; + last unless($count <= 100); + } + last unless($count <= 100); + } + last unless($count <= 100); + } + $surface = &createStackBarPlot(&convertOdToStackBinMatrix(\%dubsmax,5,1,100),'Sequence duplication level','Sequence','Number of duplicates','',0); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
' if(exists $data->{dubslength}); + $html .= &insert_image($png); + } + } + if(exists $data->{dubslength} || exists $data->{dubscounts}) { + $html .= '
'; + } + + #Sequence complexity + if(exists $data->{compldust} || exists $data->{complentropy}) { + $html .= '
Sequence Complexity
';
+ if(exists $data->{complvals}) {
+ my $complseq;
+ foreach my $d (keys %{$data->{complvals}}) {
+ foreach my $m ('minseq','maxseq') {
+ $complseq = $data->{complvals}->{$d}->{$m};
+ $complseq = substr($complseq,0,797).'...' if(length($complseq) > 800);
+ $complseq =~ s/(.{60})/$1\/g; + $data->{complvals}->{$d}->{$m} = $complseq; + } + } + } + $html .= '
| Value | Sequence | |
| Minimum DUST score: | '.(exists $data->{complvals}->{dust}->{minval} ? $data->{complvals}->{dust}->{minval} : '-').' | '.(exists $data->{complvals}->{dust}->{minseq} ? $data->{complvals}->{dust}->{minseq} : '').' |
| Maximum DUST score: | '.(exists $data->{complvals}->{dust}->{maxval} ? $data->{complvals}->{dust}->{maxval} : '').' | '.(exists $data->{complvals}->{dust}->{maxseq} ? $data->{complvals}->{dust}->{maxseq} : '').' |
| Minimum Entropy value: | '.(exists $data->{complvals}->{entropy}->{minval} ? $data->{complvals}->{entropy}->{minval} : '').' | '.(exists $data->{complvals}->{entropy}->{minseq} ? $data->{complvals}->{entropy}->{minseq} : '').' |
| Maximum Entropy value: | '.(exists $data->{complvals}->{entropy}->{maxval} ? $data->{complvals}->{entropy}->{maxval} : '').' | '.(exists $data->{complvals}->{entropy}->{maxseq} ? $data->{complvals}->{entropy}->{maxseq} : '').' |
'; + } + if(exists $data->{compldust}) { + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{compldust},0),undef,'Sequence complexity distribution','Mean sequence complexity (DUST scores)','Number of sequences','',1); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + } + if(exists $data->{complentropy}) { + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{complentropy},0),undef,'Sequence complexity distribution','Mean sequence complexity (Entropy values)','Number of sequences','',1); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
' if(exists $data->{compldust}); + $html .= &insert_image($png); + } + if(exists $data->{compldust} || exists $data->{complentropy}) { + $html .= '
'; + } + + #Dinucleotide odd ratio PCA - microbial/viral + if(exists $data->{dinucodds} && keys %{$data->{dinucodds}}) { + $html .= '
Dinucleotide Odds Ratios
';
+ $html .= '| '; + foreach my $d (map {join("/",(m/../g ))} sort keys %{$data->{dinucodds}}) { + $html .= ' | '.$d.' | '; + } + $html .= '
| Odds ratio | '; + foreach my $d (map {sprintf("%.4f",$data->{dinucodds}->{$_})} sort keys %{$data->{dinucodds}}) { + $html .= ''.$d.' | '; + } + $html .= '
'; + my @new = map {$data->{dinucodds}->{$_}} sort keys %{$data->{dinucodds}}; + $surface = &createOddsRatioPlot($data->{dinucodds},'Odds ratios','Dinucleotide','Odds ratio',''); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + #$surface = &createPCAPlot(&convertToPCAValues(\@new,'m'),'PCA','1st Principal Component Score','2nd Principal Component Score',''); + #$png = ''; + #$surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + #$html .= '
'; + #$html .= &insert_image($png); + #$surface = &createPCAPlot(&convertToPCAValues(\@new,'v'),'PCA','1st Principal Component Score','2nd Principal Component Score',''); + #$png = ''; + #$surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + #$html .= '
'; + #$html .= &insert_image($png); + $html .= '
PRINSEQ-'.$WHAT.' v'.$VERSION.' HTML Report
[Generated: '.$time.']'; + $html .= '
';
+
+ #input info
+ if(exists $data->{numseqs}) {
+ $html .= '
'; + } + + #length plot + if(exists $data->{counts}->{length} && keys %{$data->{counts}->{length}}) { + $html .= '
File 2
'; + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts2}->{length},1),$data->{stats2}->{length},'Length Distribution','Read Length in bp','# Sequences','',0,' bp'); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + $html .= '';
+ } else {
+ $html .= '
'; + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts}->{length},1),$data->{stats}->{length},'Length Distribution','Read Length in bp','# Sequences','',0,' bp'); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + $html .= '';
+ }
+ $html .= '
'; + } + + #GC content + if(exists $data->{counts}->{gc} && keys %{$data->{counts}->{gc}}) { + $html .= '
File 2
'; + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts2}->{gc},0),$data->{stats2}->{gc},'GC Content Distribution','GC Content (0-100%)','Number of Sequences','',1); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + $html .= '';
+ } else {
+ $html .= '
'; + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts}->{gc},0),$data->{stats}->{gc},'GC Content Distribution','GC Content (0-100%)','Number of Sequences','',1); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + $html .= '';
+ }
+ $html .= '
'; + } + + #Base quality + if(exists $data->{quals} || exists $data->{qualsmean} || exists $data->{qualsbin}) { + $html .= '
'; + } + + #Ns + if((exists $data->{counts}->{ns} && keys %{$data->{counts}->{ns}}) || (exists $data->{counts2} && exists $data->{counts2}->{ns} && keys %{$data->{counts2}->{ns}})) { + $html .= '
'; + } + + #tails + if(exists $data->{tail} || exists $data->{tail2}) { + $html .= '
'; + } + + + #tag sequence check + if(exists $data->{freqs} || exists $data->{freqs2}) { + $html .= '
'; + } + + #Sequence duplicates + if(exists $data->{dubslength} || exists $data->{dubscounts}) { + $html .= '
';
+ }
+ if(exists $dubs{all} && $dubs{all}) {
+ if(exists $data->{dubslength} && keys %{$data->{dubslength}}) {
+ $surface = &createStackBarPlot(&convertOdToStackBinMatrix($data->{dubslength},5,1),'Sequence duplication level','Read Length in bp','Number of duplicates','',0,' bp');
+ $png = '';
+ $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; });
+ $html .= '
'.&insert_image($png); + } + if(exists $data->{dubscounts} && keys %{$data->{dubscounts}}) { + $surface = &createStackBarPlot(&convertOdToStackBinMatrix($data->{dubscounts},5,1,100),'Sequence duplication level','Number of duplicates','Number of sequences','',0); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
' if(exists $data->{dubslength}); + $html .= &insert_image($png); + my %dubsmax; + my $count = 1; + foreach my $n (sort {$b <=> $a} keys %{$data->{dubscounts}}) { + foreach my $s (keys %{$data->{dubscounts}->{$n}}) { + foreach my $i (1..$data->{dubscounts}->{$n}->{$s}) { + $dubsmax{$count++}->{$s} = $n; + last unless($count <= 100); + } + last unless($count <= 100); + } + last unless($count <= 100); + } + $surface = &createStackBarPlot(&convertOdToStackBinMatrix(\%dubsmax,5,1,100),'Sequence duplication level','Sequence','Number of duplicates','',0); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
' if(exists $data->{dubslength}); + $html .= &insert_image($png); + } + } + if(exists $data->{dubslength} || exists $data->{dubscounts}) { + $html .= '
'; + } + + #Sequence complexity + if(exists $data->{compldust} || exists $data->{complentropy}) { + $html .= '
/g; + $data->{complvals}->{$d}->{$m} = $complseq; + } + } + } + $html .= '
'; + } + if(exists $data->{compldust}) { + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{compldust},0),undef,'Sequence complexity distribution','Mean sequence complexity (DUST scores)','Number of sequences','',1); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + } + if(exists $data->{complentropy}) { + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{complentropy},0),undef,'Sequence complexity distribution','Mean sequence complexity (Entropy values)','Number of sequences','',1); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
' if(exists $data->{compldust}); + $html .= &insert_image($png); + } + if(exists $data->{compldust} || exists $data->{complentropy}) { + $html .= '
'; + } + + #Dinucleotide odd ratio PCA - microbial/viral + if(exists $data->{dinucodds} && keys %{$data->{dinucodds}}) { + $html .= '
'; + my @new = map {$data->{dinucodds}->{$_}} sort keys %{$data->{dinucodds}}; + $surface = &createOddsRatioPlot($data->{dinucodds},'Odds ratios','Dinucleotide','Odds ratio',''); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + $surface = &createPCAPlot(&convertToPCAValues(\@new,'m'),'PCA','1st Principal Component Score','2nd Principal Component Score',''); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
'; + $html .= &insert_image($png); + $surface = &createPCAPlot(&convertToPCAValues(\@new,'v'),'PCA','1st Principal Component Score','2nd Principal Component Score',''); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
'; + $html .= &insert_image($png); + $html .= '';
+ }
+
+ $html .= '
';
+ $html .= &footer();
+
+ #write html to file
+ $file = &getFileName('.html');
+ open(FH, ">$file") or &printError("Can't open file ".$file.": $!");
+ print FH $html;
+ close(FH);
+ &printLog("Done with HTML data");
+}
+
+sub insert_image {
+ my ($data, $height, $width, $noencode) = @_;
+ my $content .= 'Input Information
';
+ $html .= '| Input file(s): | '.($data->{filename1} ? &convertIntToString($data->{filename1}) : '-').($data->{filename2} ? ' and '.&convertIntToString($data->{filename2}) : '').' |
| Input format(s): | '.($data->{format1} ? uc($data->{format1}) : '-').($data->{format2} ? ' and '.uc($data->{format2}) : '').' |
| # Sequences (file 1): | '.&addCommas($data->{numseqs}||'-').' |
| Total bases (file 1): | '.&addCommas($data->{numbases}||'-').' |
| # Sequences (file 2): | '.&addCommas($data->{numseqs2}||'-').' |
| Total bases (file 2): | '.&addCommas($data->{numbases2}||'-').' |
| # Pairs: | '.&addCommas($data->{pairs}||'-').($data->{pairs} ? ' ('.sprintf("%.2f",(100*(2*$data->{pairs})/(($data->{numseqs}||0)+($data->{numseqs2}||0)))).'% of sequences)' : '').' |
| # Singletons (file 1): | '.&addCommas($singletons1).($singletons1 ? ' ('.sprintf("%.2f",(100*$singletons1/$data->{numseqs})).'%)' : '').' |
| # Singletons (file 2): | '.&addCommas($singletons2).($singletons2 ? ' ('.sprintf("%.2f",(100*$singletons2/$data->{numseqs2})).'%)' : '').' |
| # Sequences: | '.&addCommas($data->{numseqs}||'-').' |
| Total bases: | '.&addCommas($data->{numbases}||'-').' |
'; + } + + #length plot + if(exists $data->{counts}->{length} && keys %{$data->{counts}->{length}}) { + $html .= '
Length Distribution
';
+ if(exists $data->{pairedend} && $data->{pairedend}) {
+ $html .= 'File 1
'; + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts}->{length},1),$data->{stats}->{length},'Length Distribution','Read Length in bp','# Sequences','',0,' bp'); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + $html .= '
';
+ $html .= '| Mean sequence length: | '.(exists $data->{stats}->{length}->{mean} ? sprintf("%.2f",$data->{stats}->{length}->{mean}) : '-').' ± '.(exists $data->{stats}->{length}->{std} ? sprintf("%.2f",$data->{stats}->{length}->{std}) : '-').' bp |
| Minimum length: | '.(exists $data->{stats}->{length}->{min} ? &addCommas($data->{stats}->{length}->{min}) : '-').' bp |
| Maximum length: | '.(exists $data->{stats}->{length}->{max} ? &addCommas($data->{stats}->{length}->{max}) : '-').' bp |
| Length range: | '.(exists $data->{stats}->{length}->{range} ? &addCommas($data->{stats}->{length}->{range}) : '-').' bp |
| Mode length: | '.(exists $data->{stats}->{length}->{mode} ? &addCommas($data->{stats}->{length}->{mode}) : '-').' bp with '.(exists $data->{stats}->{length}->{modeval} ? &addCommas($data->{stats}->{length}->{modeval}) : '-').' sequences |
'; + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts}->{length},1),$data->{stats}->{length},'Length Distribution','Read Length in bp','# Sequences','',0,' bp'); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + $html .= '
File 2
| Mean sequence length: | '.(exists $data->{stats2}->{length}->{mean} ? sprintf("%.2f",$data->{stats2}->{length}->{mean}) : '-').' ± '.(exists $data->{stats2}->{length}->{std} ? sprintf("%.2f",$data->{stats2}->{length}->{std}) : '-').' bp |
| Minimum length: | '.(exists $data->{stats2}->{length}->{min} ? &addCommas($data->{stats2}->{length}->{min}) : '-').' bp |
| Maximum length: | '.(exists $data->{stats2}->{length}->{max} ? &addCommas($data->{stats2}->{length}->{max}) : '-').' bp |
| Length range: | '.(exists $data->{stats2}->{length}->{range} ? &addCommas($data->{stats2}->{length}->{range}) : '-').' bp |
| Mode length: | '.(exists $data->{stats2}->{length}->{mode} ? &addCommas($data->{stats2}->{length}->{mode}) : '-').' bp with '.(exists $data->{stats2}->{length}->{modeval} ? &addCommas($data->{stats2}->{length}->{modeval}) : '-').' sequences |
'; + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts2}->{length},1),$data->{stats2}->{length},'Length Distribution','Read Length in bp','# Sequences','',0,' bp'); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + $html .= '
| Mean sequence length: | '.(exists $data->{stats}->{length}->{mean} ? sprintf("%.2f",$data->{stats}->{length}->{mean}) : '-').' ± '.(exists $data->{stats}->{length}->{std} ? sprintf("%.2f",$data->{stats}->{length}->{std}) : '-').' bp |
| Minimum length: | '.(exists $data->{stats}->{length}->{min} ? &addCommas($data->{stats}->{length}->{min}) : '-').' bp |
| Maximum length: | '.(exists $data->{stats}->{length}->{max} ? &addCommas($data->{stats}->{length}->{max}) : '-').' bp |
| Length range: | '.(exists $data->{stats}->{length}->{range} ? &addCommas($data->{stats}->{length}->{range}) : '-').' bp |
| Mode length: | '.(exists $data->{stats}->{length}->{mode} ? &addCommas($data->{stats}->{length}->{mode}) : '-').' bp with '.(exists $data->{stats}->{length}->{modeval} ? &addCommas($data->{stats}->{length}->{modeval}) : '-').' sequences |
'; + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts}->{length},1),$data->{stats}->{length},'Length Distribution','Read Length in bp','# Sequences','',0,' bp'); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + $html .= '
'; + } + + #GC content + if(exists $data->{counts}->{gc} && keys %{$data->{counts}->{gc}}) { + $html .= '
GC Content Distribution
';
+ if(exists $data->{pairedend} && $data->{pairedend}) {
+ $html .= 'File 1
'; + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts}->{gc},0),$data->{stats}->{gc},'GC Content Distribution','GC Content (0-100%)','Number of Sequences','',1); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + $html .= '
';
+ $html .= '| Mean GC content: | '.(exists $data->{stats}->{gc}->{mean} ? sprintf("%.2f",$data->{stats}->{gc}->{mean}) : '-').' ± '.(exists $data->{stats}->{gc}->{std} ? sprintf("%.2f",$data->{stats}->{gc}->{std}) : '-').' % |
| Minimum GC content: | '.(exists $data->{stats}->{gc}->{min} ? $data->{stats}->{gc}->{min} : '-').' % |
| Maximum GC content: | '.(exists $data->{stats}->{gc}->{max} ? $data->{stats}->{gc}->{max} : '-').' % |
| GC content range: | '.(exists $data->{stats}->{gc}->{range} ? $data->{stats}->{gc}->{range} : '-').' % |
| Mode GC content: | '.(exists $data->{stats}->{gc}->{mode} ? $data->{stats}->{gc}->{mode} : '-').' % with '.(exists $data->{stats}->{gc}->{modeval} ? &addCommas($data->{stats}->{gc}->{modeval}) : '-').' sequences |
'; + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts}->{gc},0),$data->{stats}->{gc},'GC Content Distribution','GC Content (0-100%)','Number of Sequences','',1); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + $html .= '
File 2
| Mean GC content: | '.(exists $data->{stats2}->{gc}->{mean} ? sprintf("%.2f",$data->{stats2}->{gc}->{mean}) : '-').' ± '.(exists $data->{stats2}->{gc}->{std} ? sprintf("%.2f",$data->{stats2}->{gc}->{std}) : '-').' % |
| Minimum GC content: | '.(exists $data->{stats2}->{gc}->{min} ? $data->{stats2}->{gc}->{min} : '-').' % |
| Maximum GC content: | '.(exists $data->{stats2}->{gc}->{max} ? $data->{stats2}->{gc}->{max} : '-').' % |
| GC content range: | '.(exists $data->{stats2}->{gc}->{range} ? $data->{stats2}->{gc}->{range} : '-').' % |
| Mode GC content: | '.(exists $data->{stats2}->{gc}->{mode} ? $data->{stats2}->{gc}->{mode} : '-').' % with '.(exists $data->{stats2}->{gc}->{modeval} ? &addCommas($data->{stats2}->{gc}->{modeval}) : '-').' sequences |
'; + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts2}->{gc},0),$data->{stats2}->{gc},'GC Content Distribution','GC Content (0-100%)','Number of Sequences','',1); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + $html .= '
| Mean GC content: | '.(exists $data->{stats}->{gc}->{mean} ? sprintf("%.2f",$data->{stats}->{gc}->{mean}) : '-').' ± '.(exists $data->{stats}->{gc}->{std} ? sprintf("%.2f",$data->{stats}->{gc}->{std}) : '-').' % |
| Minimum GC content: | '.(exists $data->{stats}->{gc}->{min} ? $data->{stats}->{gc}->{min} : '-').' % |
| Maximum GC content: | '.(exists $data->{stats}->{gc}->{max} ? $data->{stats}->{gc}->{max} : '-').' % |
| GC content range: | '.(exists $data->{stats}->{gc}->{range} ? $data->{stats}->{gc}->{range} : '-').' % |
| Mode GC content: | '.(exists $data->{stats}->{gc}->{mode} ? $data->{stats}->{gc}->{mode} : '-').' % with '.(exists $data->{stats}->{gc}->{modeval} ? &addCommas($data->{stats}->{gc}->{modeval}) : '-').' sequences |
'; + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts}->{gc},0),$data->{stats}->{gc},'GC Content Distribution','GC Content (0-100%)','Number of Sequences','',1); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + $html .= '
'; + } + + #Base quality + if(exists $data->{quals} || exists $data->{qualsmean} || exists $data->{qualsbin}) { + $html .= '
Base Quality Distribution
';
+ if(exists $data->{pairedend} && $data->{pairedend}) {
+ $html .= 'File 1
'; + } + } + if(exists $data->{quals} && keys %{$data->{quals}}) { + $surface = &createBoxPlot(&convertToBoxValues($data->{quals},4),'Base Quality Distribution','Read position in %','Quality score',''); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + } + if(exists $data->{qualsbin} && keys %{$data->{qualsbin}}) { + $surface = &createBoxPlot(&convertToBoxValues($data->{qualsbin},4),'Base Quality Distribution','Read position in bp','Quality score','',0,'bp',$data->{binval}); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
' if(exists $data->{quals}); + $html .= &insert_image($png); + } + if(exists $data->{qualsmean} && keys %{$data->{qualsmean}}) { + $surface = &createBarPlot(&convertToBarValues($data->{qualsmean},5,1),'Sequence Quality Distribution','Mean of quality scores per sequence','Number of sequences','',0); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
' if(exists $data->{qualsbin}); + $html .= &insert_image($png); + } + if(exists $data->{pairedend} && $data->{pairedend}) { + if(exists $data->{quals} || exists $data->{qualsmean} || exists $data->{qualsbin}) { + $html .= '
File 2
'; + } + if(exists $data->{quals2} && keys %{$data->{quals2}}) { + $surface = &createBoxPlot(&convertToBoxValues($data->{quals2},4),'Base Quality Distribution','Read position in %','Quality score',''); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + } + if(exists $data->{qualsbin2} && keys %{$data->{qualsbin2}}) { + $surface = &createBoxPlot(&convertToBoxValues($data->{qualsbin2},4),'Base Quality Distribution','Read position in bp','Quality score','',0,'bp',$data->{binval}); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
' if(exists $data->{quals2}); + $html .= &insert_image($png); + } + if(exists $data->{qualsmean2} && keys %{$data->{qualsmean2}}) { + $surface = &createBarPlot(&convertToBarValues($data->{qualsmean2},5,1),'Sequence Quality Distribution','Mean of quality scores per sequence','Number of sequences','',0); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
' if(exists $data->{qualsbin2}); + $html .= &insert_image($png); + } + } + if(exists $data->{quals} || exists $data->{qualsmean} || exists $data->{qualsbin}) { + $html .= '
'; + } + } + if(exists $data->{quals} && keys %{$data->{quals}}) { + $surface = &createBoxPlot(&convertToBoxValues($data->{quals},4),'Base Quality Distribution','Read position in %','Quality score',''); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + } + if(exists $data->{qualsbin} && keys %{$data->{qualsbin}}) { + $surface = &createBoxPlot(&convertToBoxValues($data->{qualsbin},4),'Base Quality Distribution','Read position in bp','Quality score','',0,'bp',$data->{binval}); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
' if(exists $data->{quals}); + $html .= &insert_image($png); + } + if(exists $data->{qualsmean} && keys %{$data->{qualsmean}}) { + $surface = &createBarPlot(&convertToBarValues($data->{qualsmean},5,1),'Sequence Quality Distribution','Mean of quality scores per sequence','Number of sequences','',0); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
' if(exists $data->{qualsbin}); + $html .= &insert_image($png); + } + if(exists $data->{pairedend} && $data->{pairedend}) { + if(exists $data->{quals} || exists $data->{qualsmean} || exists $data->{qualsbin}) { + $html .= '
File 2
'; + } + if(exists $data->{quals2} && keys %{$data->{quals2}}) { + $surface = &createBoxPlot(&convertToBoxValues($data->{quals2},4),'Base Quality Distribution','Read position in %','Quality score',''); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + } + if(exists $data->{qualsbin2} && keys %{$data->{qualsbin2}}) { + $surface = &createBoxPlot(&convertToBoxValues($data->{qualsbin2},4),'Base Quality Distribution','Read position in bp','Quality score','',0,'bp',$data->{binval}); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
' if(exists $data->{quals2}); + $html .= &insert_image($png); + } + if(exists $data->{qualsmean2} && keys %{$data->{qualsmean2}}) { + $surface = &createBarPlot(&convertToBarValues($data->{qualsmean2},5,1),'Sequence Quality Distribution','Mean of quality scores per sequence','Number of sequences','',0); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
' if(exists $data->{qualsbin2}); + $html .= &insert_image($png); + } + } + if(exists $data->{quals} || exists $data->{qualsmean} || exists $data->{qualsbin}) { + $html .= '
'; + } + + #Ns + if((exists $data->{counts}->{ns} && keys %{$data->{counts}->{ns}}) || (exists $data->{counts2} && exists $data->{counts2}->{ns} && keys %{$data->{counts2}->{ns}})) { + $html .= '
Occurence of N
';
+ if(exists $data->{pairedend} && $data->{pairedend}) {
+ $html .= 'File 1
'; + } + } + if(exists $data->{counts}->{ns} && keys %{$data->{counts}->{ns}}) { + my $nscount = 0; + foreach my $n (values %{$data->{counts}->{ns}}) { + $nscount += $n; + } + $html .= '
';
+ if($nscount) {
+ $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts}->{ns},1),undef,'Percentage of N\'s (> 0%)','Percentage of N\'s per Read (1-100%)','# Sequences','',0);
+ $png = '';
+ $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; });
+ $html .= '
'.&insert_image($png); + } + } + if(exists $data->{pairedend} && $data->{pairedend} && exists $data->{counts2}->{ns} && keys %{$data->{counts2}->{ns}}) { + $html .= '
File 2
'; + my $nscount = 0; + foreach my $n (values %{$data->{counts2}->{ns}}) { + $nscount += $n; + } + $html .= '
';
+ if($nscount) {
+ $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts2}->{ns},1),undef,'Percentage of N\'s (> 0%)','Percentage of N\'s per Read (1-100%)','# Sequences','',0);
+ $png = '';
+ $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; });
+ $html .= '
'.&insert_image($png); + } + } + if((exists $data->{counts}->{ns} && keys %{$data->{counts}->{ns}}) || (exists $data->{counts2} && exists $data->{counts2}->{ns} && keys %{$data->{counts2}->{ns}})) { + $html .= '
'; + } + } + if(exists $data->{counts}->{ns} && keys %{$data->{counts}->{ns}}) { + my $nscount = 0; + foreach my $n (values %{$data->{counts}->{ns}}) { + $nscount += $n; + } + $html .= '
| Sequences with N: | '.($nscount ? &addCommas($nscount).' ('.sprintf("%.2f",100/$data->{numseqs}*$nscount).' %)' : 0).' |
| Max percentage of Ns per sequence: | '.(exists $data->{stats}->{ns}->{max} ? $data->{stats}->{ns}->{max} : 0).' % |
'.&insert_image($png); + } + } + if(exists $data->{pairedend} && $data->{pairedend} && exists $data->{counts2}->{ns} && keys %{$data->{counts2}->{ns}}) { + $html .= '
File 2
'; + my $nscount = 0; + foreach my $n (values %{$data->{counts2}->{ns}}) { + $nscount += $n; + } + $html .= '
| Sequences with N: | '.($nscount ? &addCommas($nscount).' ('.sprintf("%.2f",100/$data->{numseqs2}*$nscount).' %)' : 0).' |
| Max percentage of Ns per sequence: | '.(exists $data->{stats2}->{ns}->{max} ? $data->{stats2}->{ns}->{max} : 0).' % |
'.&insert_image($png); + } + } + if((exists $data->{counts}->{ns} && keys %{$data->{counts}->{ns}}) || (exists $data->{counts2} && exists $data->{counts2}->{ns} && keys %{$data->{counts2}->{ns}})) { + $html .= '
'; + } + + #tails + if(exists $data->{tail} || exists $data->{tail2}) { + $html .= '
Poly-A/T Tails
';
+ }
+ if(exists $data->{tail}) {
+ my $tail5count = 0;
+ foreach my $n (values %{$data->{counts}->{tail5}}) {
+ $tail5count += $n;
+ }
+ my $tail3count = 0;
+ foreach my $n (values %{$data->{counts}->{tail3}}) {
+ $tail3count += $n;
+ }
+ if(exists $data->{pairedend} && $data->{pairedend}) {
+ $html .= 'File 1
'; + } + $html .= '
';
+ if($tail5count) {
+ $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts}->{tail5},1),undef,'Poly-A/T Tail Distribution (> 4bp)','5\' Tail Length in bp','# Sequences','',0,' bp');
+ $png = '';
+ $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; });
+ $html .= '
'.&insert_image($png); + if($tail3count) { + $html .= '
'; + } + } + if($tail3count) { + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts}->{tail3},1),undef,'Poly-A/T Tail Distribution (> 4bp)','3\' Tail Length in bp','# Sequences','',0,' bp'); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
'.&insert_image($png); + } + } + if(exists $data->{pairedend} && $data->{pairedend} && exists $data->{tail2}) { + my $tail5count = 0; + foreach my $n (values %{$data->{counts2}->{tail5}}) { + $tail5count += $n; + } + my $tail3count = 0; + foreach my $n (values %{$data->{counts2}->{tail3}}) { + $tail3count += $n; + } + $html .= '
File 2
'; + $html .= '
';
+ if($tail5count) {
+ $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts2}->{tail5},1),undef,'Poly-A/T Tail Distribution (> 4bp)','5\' Tail Length in bp','# Sequences','',0,' bp');
+ $png = '';
+ $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; });
+ $html .= '
'.&insert_image($png); + if($tail3count) { + $html .= '
'; + } + } + if($tail3count) { + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts2}->{tail3},1),undef,'Poly-A/T Tail Distribution (> 4bp)','3\' Tail Length in bp','# Sequences','',0,' bp'); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
'.&insert_image($png); + } + } + if(exists $data->{tail} || exists $data->{tail2}) { + $html .= '
'; + } + $html .= '
| 5\'-end | 3\'-end | |
| Sequences with tail: | '.($tail5count ? &addCommas($tail5count).' ('.sprintf("%.2f",100/$data->{numseqs}*$tail5count).' %)' : 0).' | '.($tail3count ? &addCommas($tail3count).' ('.sprintf("%.2f",100/$data->{numseqs}*$tail3count).' %)' : 0).' |
| Maximum tail length: | '.(exists $data->{stats}->{tail5}->{max} ? $data->{stats}->{tail5}->{max} : 0).' | '.(exists $data->{stats}->{tail3}->{max} ? $data->{stats}->{tail3}->{max} : 0).' |
'.&insert_image($png); + if($tail3count) { + $html .= '
'; + } + } + if($tail3count) { + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts}->{tail3},1),undef,'Poly-A/T Tail Distribution (> 4bp)','3\' Tail Length in bp','# Sequences','',0,' bp'); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
'.&insert_image($png); + } + } + if(exists $data->{pairedend} && $data->{pairedend} && exists $data->{tail2}) { + my $tail5count = 0; + foreach my $n (values %{$data->{counts2}->{tail5}}) { + $tail5count += $n; + } + my $tail3count = 0; + foreach my $n (values %{$data->{counts2}->{tail3}}) { + $tail3count += $n; + } + $html .= '
File 2
'; + $html .= '
| 5\'-end | 3\'-end | |
| Sequences with tail: | '.($tail5count ? &addCommas($tail5count).' ('.sprintf("%.2f",100/$data->{numseqs2}*$tail5count).' %)' : 0).' | '.($tail3count ? &addCommas($tail3count).' ('.sprintf("%.2f",100/$data->{numseqs2}*$tail3count).' %)' : 0).' |
| Maximum tail length: | '.(exists $data->{stats2}->{tail5}->{max} ? $data->{stats2}->{tail5}->{max} : 0).' | '.(exists $data->{stats2}->{tail3}->{max} ? $data->{stats2}->{tail3}->{max} : 0).' |
'.&insert_image($png); + if($tail3count) { + $html .= '
'; + } + } + if($tail3count) { + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{counts2}->{tail3},1),undef,'Poly-A/T Tail Distribution (> 4bp)','3\' Tail Length in bp','# Sequences','',0,' bp'); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
'.&insert_image($png); + } + } + if(exists $data->{tail} || exists $data->{tail2}) { + $html .= '
'; + } + + + #tag sequence check + if(exists $data->{freqs} || exists $data->{freqs2}) { + $html .= '
Tag Sequence Check
';
+ }
+ if(exists $data->{freqs}) {
+ my $tagmidseq;
+ if(exists $data->{tagmidseq}) {
+ $tagmidseq = $data->{tagmidseq};
+ $tagmidseq =~ s/\,/\
/g; + } + if(exists $data->{pairedend} && $data->{pairedend}) { + $html .= 'File 1
'; + } + $html .= '
'; + $html .= '
';
+ }
+ if(exists $data->{pairedend} && $data->{pairedend} && exists $data->{freqs2}) {
+ $html .= '
File 2
'; + $html .= '
'; + $html .= '
';
+ }
+ if(exists $data->{freqs} || exists $data->{freqs2}) {
+ $html .= '
/g; + } + if(exists $data->{pairedend} && $data->{pairedend}) { + $html .= 'File 1
'; + } + $html .= '
| 5\'-end | 3\'-end | |
| Probability of tag sequence: | '.(exists $data->{tagprob}->{5} ? $data->{tagprob}->{5}.' %' : '-').' | '.(exists $data->{tagprob}->{3} ? $data->{tagprob}->{3}.' %' : '-').' |
| GSMIDs or RLMIDs: | '.(exists $data->{tagmidnum} ? ($data->{tagmidnum} == 0 ? 'none' : ($tagmidseq ? $tagmidseq : $data->{tagmidnum})) : '-').' |
'; + $html .= '
| '.&insert_image($FREQCHART_L,undef,undef,1).' | '; + foreach my $pos (sort {$a <=> $b} keys %{$data->{freqs}->{5}}) { + $html .= '';
+ foreach my $base (qw(A C G T N)) {
+ if($data->{freqs}->{5}->{$pos}->{$base}) {
+ $html .= &insert_image($BASE64_BASES->{$base},$data->{freqs}->{5}->{$pos}->{$base},14,1).' '; + #' '; + } + } + $html .= &insert_image($MMCHART_B2,6,16,1).' | ';
+ }
+ $html .= '... | '; + foreach my $pos (sort {$a <=> $b} keys %{$data->{freqs}->{3}}) { + $html .= '';
+ foreach my $base (qw(A C G T N)) {
+ if($data->{freqs}->{3}->{$pos}->{$base}) {
+ $html .= &insert_image($BASE64_BASES->{$base},$data->{freqs}->{3}->{$pos}->{$base},14,1).' '; + } + } + $html .= &insert_image($MMCHART_B2,6,16,1).' | ';
+ }
+ $html .= '||||||||||||||||||||||||||||||||||||||
| '; + foreach my $num (1,0,0,0,5,0,0,0,0,10,0,0,0,0,15,0,0,0,0,20,0,20,0,0,0,0,15,0,0,0,0,10,0,0,0,0,5,0,0,0,1) { + $html .= ' | '.($num ? $num : '').' | '; + } + $html .= '||||||||||||||||||||||||||||||||||||||||
| Position from Sequence Ends | |||||||||||||||||||||||||||||||||||||||||
File 2
'; + $html .= '
| 5\'-end | 3\'-end | |
| Probability of tag sequence: | '.(exists $data->{tagprob2}->{5} ? $data->{tagprob2}->{5}.' %' : '-').' | '.(exists $data->{tagprob2}->{3} ? $data->{tagprob2}->{3}.' %' : '-').' |
'; + $html .= '
| '.&insert_image($FREQCHART_L,undef,undef,1).' | '; + foreach my $pos (sort {$a <=> $b} keys %{$data->{freqs2}->{5}}) { + $html .= '';
+ foreach my $base (qw(A C G T N)) {
+ if($data->{freqs2}->{5}->{$pos}->{$base}) {
+ $html .= &insert_image($BASE64_BASES->{$base},$data->{freqs2}->{5}->{$pos}->{$base},14,1).' '; + #' '; + } + } + $html .= &insert_image($MMCHART_B2,6,16,1).' | ';
+ }
+ $html .= '... | '; + foreach my $pos (sort {$a <=> $b} keys %{$data->{freqs2}->{3}}) { + $html .= '';
+ foreach my $base (qw(A C G T N)) {
+ if($data->{freqs2}->{3}->{$pos}->{$base}) {
+ $html .= &insert_image($BASE64_BASES->{$base},$data->{freqs2}->{3}->{$pos}->{$base},14,1).' '; + } + } + $html .= &insert_image($MMCHART_B2,6,16,1).' | ';
+ }
+ $html .= '||||||||||||||||||||||||||||||||||||||
| '; + foreach my $num (1,0,0,0,5,0,0,0,0,10,0,0,0,0,15,0,0,0,0,20,0,20,0,0,0,0,15,0,0,0,0,10,0,0,0,0,5,0,0,0,1) { + $html .= ' | '.($num ? $num : '').' | '; + } + $html .= '||||||||||||||||||||||||||||||||||||||||
| Position from Sequence Ends | |||||||||||||||||||||||||||||||||||||||||
'; + } + + #Sequence duplicates + if(exists $data->{dubslength} || exists $data->{dubscounts}) { + $html .= '
Sequence Duplication
';
+ }
+ my %dubs;
+ if(exists $data->{dubscounts} && keys %{$data->{dubscounts}}) {
+ my $exactonly = $data->{exactonly}||0;
+ foreach my $n (keys %{$data->{dubscounts}}) {
+ foreach my $s (keys %{$data->{dubscounts}->{$n}}) {
+ $dubs{$s}->{count} += $data->{dubscounts}->{$n}->{$s} * $n;
+ $dubs{$s}->{max} = $n unless(exists $dubs{$s}->{max} && $dubs{$s}->{max} > $n);
+ $dubs{all} += $data->{dubscounts}->{$n}->{$s} * $n;
+ }
+ }
+ $html .= '| # Sequences | Max duplicates | |
| Exact duplicates: | '.(exists $dubs{0}->{count} ? &addCommas($dubs{0}->{count}).' ('.sprintf("%.2f",100/$data->{numseqs}*$dubs{0}->{count}).' %)' : 0).' | '.($dubs{0}->{max}||0).' |
| Exact duplicates with reverse complements: | '.(exists $dubs{3}->{count} ? &addCommas($dubs{3}->{count}).' ('.sprintf("%.2f",100/$data->{numseqs}*$dubs{3}->{count}).' %)' : 0).' | '.($dubs{3}->{max}||0).' |
| 5\' duplicates | '.(exists $dubs{1}->{count} ? &addCommas($dubs{1}->{count}).' ('.sprintf("%.2f",100/$data->{numseqs}*$dubs{1}->{count}).' %)' : 0).' | '.($dubs{1}->{max}||0).' |
| 3\' duplicates | '.(exists $dubs{2}->{count} ? &addCommas($dubs{2}->{count}).' ('.sprintf("%.2f",100/$data->{numseqs}*$dubs{2}->{count}).' %)' : 0).' | '.($dubs{2}->{max}||0).' |
| 5\'/3\' duplicates with reverse complements | '.(exists $dubs{4}->{count} ? &addCommas($dubs{4}->{count}).' ('.sprintf("%.2f",100/$data->{numseqs}*$dubs{4}->{count}).' %)' : 0).' | '.($dubs{4}->{max}||0).' |
| Total: | '.(exists $dubs{all} ? &addCommas($dubs{all}).' ('.sprintf("%.2f",100/$data->{numseqs}*$dubs{all}).' %)' : 0).' | - |
'.&insert_image($png); + } + if(exists $data->{dubscounts} && keys %{$data->{dubscounts}}) { + $surface = &createStackBarPlot(&convertOdToStackBinMatrix($data->{dubscounts},5,1,100),'Sequence duplication level','Number of duplicates','Number of sequences','',0); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
' if(exists $data->{dubslength}); + $html .= &insert_image($png); + my %dubsmax; + my $count = 1; + foreach my $n (sort {$b <=> $a} keys %{$data->{dubscounts}}) { + foreach my $s (keys %{$data->{dubscounts}->{$n}}) { + foreach my $i (1..$data->{dubscounts}->{$n}->{$s}) { + $dubsmax{$count++}->{$s} = $n; + last unless($count <= 100); + } + last unless($count <= 100); + } + last unless($count <= 100); + } + $surface = &createStackBarPlot(&convertOdToStackBinMatrix(\%dubsmax,5,1,100),'Sequence duplication level','Sequence','Number of duplicates','',0); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
' if(exists $data->{dubslength}); + $html .= &insert_image($png); + } + } + if(exists $data->{dubslength} || exists $data->{dubscounts}) { + $html .= '
'; + } + + #Sequence complexity + if(exists $data->{compldust} || exists $data->{complentropy}) { + $html .= '
Sequence Complexity
';
+ if(exists $data->{complvals}) {
+ my $complseq;
+ foreach my $d (keys %{$data->{complvals}}) {
+ foreach my $m ('minseq','maxseq') {
+ $complseq = $data->{complvals}->{$d}->{$m};
+ $complseq = substr($complseq,0,797).'...' if(length($complseq) > 800);
+ $complseq =~ s/(.{60})/$1\/g; + $data->{complvals}->{$d}->{$m} = $complseq; + } + } + } + $html .= '
| Value | Sequence | |
| Minimum DUST score: | '.(exists $data->{complvals}->{dust}->{minval} ? $data->{complvals}->{dust}->{minval} : '-').' | '.(exists $data->{complvals}->{dust}->{minseq} ? $data->{complvals}->{dust}->{minseq} : '').' |
| Maximum DUST score: | '.(exists $data->{complvals}->{dust}->{maxval} ? $data->{complvals}->{dust}->{maxval} : '').' | '.(exists $data->{complvals}->{dust}->{maxseq} ? $data->{complvals}->{dust}->{maxseq} : '').' |
| Minimum Entropy value: | '.(exists $data->{complvals}->{entropy}->{minval} ? $data->{complvals}->{entropy}->{minval} : '').' | '.(exists $data->{complvals}->{entropy}->{minseq} ? $data->{complvals}->{entropy}->{minseq} : '').' |
| Maximum Entropy value: | '.(exists $data->{complvals}->{entropy}->{maxval} ? $data->{complvals}->{entropy}->{maxval} : '').' | '.(exists $data->{complvals}->{entropy}->{maxseq} ? $data->{complvals}->{entropy}->{maxseq} : '').' |
'; + } + if(exists $data->{compldust}) { + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{compldust},0),undef,'Sequence complexity distribution','Mean sequence complexity (DUST scores)','Number of sequences','',1); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + } + if(exists $data->{complentropy}) { + $surface = &createAnnotBarPlot(&convertOdToBinMatrix($data->{complentropy},0),undef,'Sequence complexity distribution','Mean sequence complexity (Entropy values)','Number of sequences','',1); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
' if(exists $data->{compldust}); + $html .= &insert_image($png); + } + if(exists $data->{compldust} || exists $data->{complentropy}) { + $html .= '
'; + } + + #Dinucleotide odd ratio PCA - microbial/viral + if(exists $data->{dinucodds} && keys %{$data->{dinucodds}}) { + $html .= '
Dinucleotide Odds Ratios
';
+ $html .= '| '; + foreach my $d (map {join("/",(m/../g ))} sort keys %{$data->{dinucodds}}) { + $html .= ' | '.$d.' | '; + } + $html .= '
| Odds ratio | '; + foreach my $d (map {sprintf("%.4f",$data->{dinucodds}->{$_})} sort keys %{$data->{dinucodds}}) { + $html .= ''.$d.' | '; + } + $html .= '
'; + my @new = map {$data->{dinucodds}->{$_}} sort keys %{$data->{dinucodds}}; + $surface = &createOddsRatioPlot($data->{dinucodds},'Odds ratios','Dinucleotide','Odds ratio',''); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= &insert_image($png); + $surface = &createPCAPlot(&convertToPCAValues(\@new,'m'),'PCA','1st Principal Component Score','2nd Principal Component Score',''); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
'; + $html .= &insert_image($png); + $surface = &createPCAPlot(&convertToPCAValues(\@new,'v'),'PCA','1st Principal Component Score','2nd Principal Component Score',''); + $png = ''; + $surface->write_to_png_stream(sub { my ($closure, $data) = @_; $png .= $data; }); + $html .= '
'; + $html .= &insert_image($png); + $html .= '
PRINSEQ-graphs v0.6 HTML Report
[Generated: 03/13/2013 12:12:36]Input Information
| Input file(s): | example1.fastq |
| Input format(s): | FASTQ |
| # Sequences: | 12 |
| Total bases: | 1,150 |
Length Distribution
| Mean sequence length: | 95.83 ± 37.96 bp |
| Minimum length: | 50 bp |
| Maximum length: | 200 bp |
| Length range: | 151 bp |
| Mode length: | 100 bp with 8 sequences |
+GC Content Distribution
| Mean GC content: | 48.17 ± 14.83 % |
| Minimum GC content: | 0 % |
| Maximum GC content: | 57 % |
| GC content range: | 58 % |
| Mode GC content: | 50 % with 5 sequences |
+Base Quality Distribution
+
+
+Occurence of N
| Sequences with N: | 2 (16.67 %) |
| Max percentage of Ns per sequence: | 10 % |
+Poly-A/T Tails
| 5'-end | 3'-end | |
| Sequences with tail: | 1 (8.33 %) | 1 (8.33 %) |
| Maximum tail length: | 50 | 50 |
+
+Tag Sequence Check
| 5'-end | 3'-end | |
| Probability of tag sequence: | 33 % | 33 % |
| GSMIDs or RLMIDs: | none |
+ | 
+
+
+
+ |
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+ |
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+ | ... |
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| 1 | 5 | 10 | 15 | 20 | 20 | 15 | 10 | 5 | 1 | ||||||||||||||||||||||||||||||||
| Position from Sequence Ends | |||||||||||||||||||||||||||||||||||||||||
Sequence Duplication
| # Sequences | Max duplicates | |
| Exact duplicates: | 4 (33.33 %) | 3 |
| Exact duplicates with reverse complements: | 0 | 0 |
| 5' duplicates | 0 | 0 |
| 3' duplicates | 0 | 0 |
| 5'/3' duplicates with reverse complements | 0 | 0 |
| Total: | 4 (33.33 %) | - |
+
+
+Sequence Complexity
| Value | Sequence | |
| Minimum DUST score: | 2 | NNNNNNNNNNTACACCAGAGGTGTCTCTGTGTGGGGCCTGTGTGCCAAAAGTGAGAGTTG AGAAGAGGCGTGGAGGAGATGACACACCCCGTGTGTTCTC |
| Maximum DUST score: | 100 | AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
| Minimum Entropy value: | 0 | AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
| Maximum Entropy value: | 81 | NNNNNNNNNNTACACCAGAGGTGTCTCTGTGTGGGGCCTGTGTGCCAAAAGTGAGAGTTG AGAAGAGGCGTGGAGGAGATGACACACCCCGTGTGTTCTC |
+
+Dinucleotide Odds Ratios
| AA/TT | AC/GT | AG/CT | AT | CA/TG | CC/GG | CG | GA/TC | GC | TA | |
| Odds ratio | 0.3954 | 2.4378 | 0.4858 | 0.3623 | 1.0736 | 0.3006 | 1.9166 | 0.4338 | 0.5829 | 1.8332 |
+
+
+