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: 11/10/2013 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 |
| 
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| ... |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 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 |
