--- /dev/null
+#!/usr/bin/env perl
+#
+# Author: petr.danecek@sanger
+#
+
+use strict;
+use warnings;
+use Carp;
+
+my $opts = parse_params();
+parse_bamcheck($opts);
+plot_qualities($opts);
+plot_acgt_cycles($opts);
+plot_gc($opts);
+plot_gc_depth($opts);
+plot_isize($opts);
+plot_coverage($opts);
+plot_mismatches_per_cycle($opts);
+plot_indel_dist($opts);
+plot_indel_cycles($opts);
+
+exit;
+
+#--------------------------------
+
+sub error
+{
+ my (@msg) = @_;
+ if ( scalar @msg ) { confess @msg; }
+ die
+ "Usage: plot-bamcheck [OPTIONS] file.bam.bc\n",
+ " plot-bamcheck -p outdir/ file.bam.bc\n",
+ "Options:\n",
+ " -k, --keep-files Do not remove temporary files.\n",
+ " -p, --prefix <path> The output files prefix, add a slash to create new directory.\n",
+ " -r, --ref-stats <file.fa.gc> Optional reference stats file with expected GC content (created with -s).\n",
+ " -s, --do-ref-stats <file.fa> Calculate reference sequence GC for later use with -r\n",
+ " -t, --targets <file.tab> Restrict -s to the listed regions (tab-delimited chr,from,to. 1-based, inclusive)\n",
+ " -h, -?, --help This help message.\n",
+ "\n";
+}
+
+
+sub parse_params
+{
+ $0 =~ s{^.+/}{};
+ my $opts = { args=>join(' ',$0,@ARGV) };
+ while (defined(my $arg=shift(@ARGV)))
+ {
+ if ( $arg eq '-k' || $arg eq '--keep-files' ) { $$opts{keep_files}=1; next; }
+ if ( $arg eq '-r' || $arg eq '--ref-stats' ) { $$opts{ref_stats}=shift(@ARGV); next; }
+ if ( $arg eq '-s' || $arg eq '--do-ref-stats' ) { $$opts{do_ref_stats}=shift(@ARGV); next; }
+ if ( $arg eq '-t' || $arg eq '--targets' ) { $$opts{targets}=shift(@ARGV); next; }
+ if ( $arg eq '-p' || $arg eq '--prefix' ) { $$opts{prefix}=shift(@ARGV); next; }
+ if ( $arg eq '-?' || $arg eq '-h' || $arg eq '--help' ) { error(); }
+ if ( -e $arg ) { $$opts{bamcheck}=$arg; next; }
+ error("Unknown parameter or non-existent file \"$arg\". Run -h for help.\n");
+ }
+ if ( exists($$opts{do_ref_stats }) ) { do_ref_stats($opts); exit; }
+ if ( !exists($$opts{bamcheck}) ) { error("No bamcheck file?\n") }
+ if ( !exists($$opts{prefix}) ) { error("Expected -p parameter.\n") }
+ if ( $$opts{prefix}=~m{/$} ) { `mkdir -p $$opts{prefix}`; }
+ elsif ( !($$opts{prefix}=~/-$/) ) { $$opts{prefix} .= '-'; }
+ return $opts;
+}
+
+
+# Creates GC stats for either the whole reference or only on target regions for exome QC
+sub do_ref_stats
+{
+ my ($opts) = @_;
+
+
+ my %targets = ();
+ if ( exists($$opts{targets}) )
+ {
+ my ($prev_chr,$prev_pos);
+ open(my $fh,'<',$$opts{targets}) or error("$$opts{targets}: $!");
+ while (my $line=<$fh>)
+ {
+ if ( $line=~/^#/ ) { next; }
+ my ($chr,$from,$to) = split(/\s+/,$line);
+ chomp($to);
+ push @{$targets{$chr}}, $from,$to;
+ if ( !defined $prev_chr or $chr ne $prev_chr ) { $prev_chr=$chr; $prev_pos=$from }
+ if ( $prev_pos > $from ) { error("The file must be sorted: $$opts{targets}\n"); }
+ $prev_pos = $from;
+ }
+ close($fh);
+ }
+
+ my $_len = 60; # for now do only standard fasta's with 60 bases per line
+ my %gc_counts = ();
+ my ($skip_chr,$pos,$ireg,$regions);
+ open(my $fh,'<',$$opts{do_ref_stats}) or error("$$opts{do_ref_stats}: $!");
+ while (my $line=<$fh>)
+ {
+ if ( $line=~/^>/ )
+ {
+ if ( !scalar %targets ) { next; }
+
+ if ( !($line=~/>(\S+)/) ) { error("FIXME: could not determine chromosome name: $line"); }
+ if ( !exists($targets{$1}) ) { $skip_chr=$1; next; }
+ undef $skip_chr;
+ $pos = 0;
+ $ireg = 0;
+ $regions = $targets{$1};
+ }
+ if ( defined $skip_chr ) { next; }
+
+ # Only $_len sized lines are considered and no chopping for target regions.
+ chomp($line);
+ my $len = length($line);
+ if ( $len ne $_len ) { next; }
+
+ if ( scalar %targets )
+ {
+ while ( $ireg<@$regions && $$regions[$ireg+1]<=$pos ) { $ireg += 2; }
+ $pos += $len;
+ if ( $ireg==@$regions ) { next; }
+ if ( $pos < $$regions[$ireg] ) { next; }
+ }
+
+ my $gc_count = 0;
+ for (my $i=0; $i<$len; $i++)
+ {
+ my $base = substr($line,$i,1);
+ if ( $base eq 'g' || $base eq 'G' || $base eq 'c' || $base eq 'C' ) { $gc_count++; }
+ }
+ $gc_counts{$gc_count}++;
+ }
+
+ print "# Generated by $$opts{args}\n";
+ print "# The columns are: GC content bin, normalized frequency\n";
+ my $max;
+ for my $count (values %gc_counts)
+ {
+ if ( !defined $max or $count>$max ) { $max=$count; }
+ }
+ for my $gc (sort {$a<=>$b} keys %gc_counts)
+ {
+ if ( $gc==0 ) { next; }
+ printf "%f\t%f\n", $gc*100./$_len, $gc_counts{$gc}/$max;
+ }
+}
+
+sub plot
+{
+ my ($cmdfile) = @_;
+ my $cmd = "gnuplot $cmdfile";
+ system($cmd);
+ if ( $? ) { error("The command exited with non-zero status $?:\n\t$cmd\n\n"); }
+}
+
+
+sub parse_bamcheck
+{
+ my ($opts) = @_;
+ open(my $fh,'<',$$opts{bamcheck}) or error("$$opts{bamcheck}: $!");
+ my $line = <$fh>;
+ if ( !($line=~/^# This file was produced by bamcheck (\S+)/) ) { error("Sanity check failed: was this file generated by bamcheck?"); }
+ $$opts{dat}{version} = $1;
+ while ($line=<$fh>)
+ {
+ if ( $line=~/^#/ ) { next; }
+ my @items = split(/\t/,$line);
+ chomp($items[-1]);
+ if ( $items[0] eq 'SN' )
+ {
+ $$opts{dat}{$items[1]} = splice(@items,2);
+ next;
+ }
+ push @{$$opts{dat}{$items[0]}}, [splice(@items,1)];
+ }
+ close($fh);
+
+ # Check sanity
+ if ( !exists($$opts{dat}{'sequences:'}) or !$$opts{dat}{'sequences:'} )
+ {
+ error("Sanity check failed: no sequences found by bamcheck??\n");
+ }
+}
+
+sub older_than
+{
+ my ($opts,$version) = @_;
+ my ($year,$month,$day) = split(/-/,$version);
+ $version = $$opts{dat}{version};
+ if ( !($version=~/\((\d+)-(\d+)-(\d+)\)$/) ) { return 1; }
+ if ( $1<$year ) { return 1; }
+ elsif ( $1>$year ) { return 0; }
+ if ( $2<$month ) { return 1; }
+ elsif ( $2>$month ) { return 0; }
+ if ( $3<$day ) { return 1; }
+ return 0;
+}
+
+sub get_defaults
+{
+ my ($opts,$img_fname,%args) = @_;
+
+ if ( !($img_fname=~/\.png$/i) ) { error("FIXME: currently only PNG supported. (Easy to extend.)\n"); }
+
+ # Determine the gnuplot script file name
+ my $gp_file = $img_fname;
+ $gp_file =~ s{\.[^.]+$}{.gp};
+ if ( !($gp_file=~/.gp$/) ) { $gp_file .= '.gp'; }
+
+ # Determine the default title:
+ # 5446_6/5446_6.bam.bc.gp -> 5446_6
+ # test.aaa.png -> test.aaa
+ if ( !($$opts{bamcheck}=~m{([^/]+?)(?:\.bam)?(?:\.bc)?$}i) ) { error("FIXME: Could not determine the title from [$img_fname]\n"); }
+ my $title = $1;
+
+ my $dir = $gp_file;
+ $dir =~ s{/[^/]+$}{};
+ if ( $dir && $dir ne $gp_file ) { `mkdir -p $dir`; }
+
+ my $wh = exists($args{wh}) ? $args{wh} : '600,400';
+
+ open(my $fh,'>',$gp_file) or error("$gp_file: $!");
+ return {
+ title => $title,
+ gp => $gp_file,
+ img => $img_fname,
+ fh => $fh,
+ terminal => qq[set terminal png size $wh truecolor],
+ grid => 'set grid xtics ytics y2tics back lc rgb "#cccccc"',
+ };
+}
+
+sub percentile
+{
+ my ($p,@vals) = @_;
+ my $N = 0;
+ for my $val (@vals) { $N += $val; }
+ my $n = $p*($N+1)/100.;
+ my $k = int($n);
+ my $d = $n-$k;
+ if ( $k<=0 ) { return 0; }
+ if ( $k>=$N ) { return scalar @vals-1; }
+ my $cnt;
+ for (my $i=0; $i<@vals; $i++)
+ {
+ $cnt += $vals[$i];
+ if ( $cnt>=$k ) { return $i; }
+ }
+ error("FIXME: this should not happen [percentile]\n");
+}
+
+sub plot_qualities
+{
+ my ($opts) = @_;
+
+ if ( !exists($$opts{dat}{FFQ}) or !@{$$opts{dat}{FFQ}} ) { return; }
+
+ my $yrange = @{$$opts{dat}{FFQ}[0]} > 50 ? @{$$opts{dat}{FFQ}[0]} : 50;
+ my $is_paired = $$opts{dat}{'is paired:'};
+
+ # Average quality per cycle, forward and reverse reads in one plot
+ my $args = get_defaults($opts,"$$opts{prefix}quals.png");
+ my $fh = $$args{fh};
+ print $fh qq[
+ $$args{terminal}
+ set output "$$args{img}"
+ $$args{grid}
+ set ylabel "Average Quality"
+ set xlabel "Cycle"
+ set yrange [0:$yrange]
+ set title "$$args{title}"
+ plot '-' using 1:2 with lines title 'Forward reads' ] . ($is_paired ? q[, '-' using 1:2 with lines title 'Reverse reads'] : '') . q[
+ ];
+ my (@fp75,@fp50,@fmean);
+ my (@lp75,@lp50,@lmean);
+ my ($fmax,$fmax_qual,$fmax_cycle);
+ my ($lmax,$lmax_qual,$lmax_cycle);
+ for my $cycle (@{$$opts{dat}{FFQ}})
+ {
+ my $sum=0; my $n=0;
+ for (my $iqual=1; $iqual<@$cycle; $iqual++)
+ {
+ $sum += $$cycle[$iqual]*$iqual;
+ $n += $$cycle[$iqual];
+ if ( !defined $fmax or $fmax<$$cycle[$iqual] ) { $fmax=$$cycle[$iqual]; $fmax_qual=$iqual; $fmax_cycle=$$cycle[0]; }
+ }
+ my $p25 = percentile(25,(@$cycle)[1..$#$cycle]);
+ my $p50 = percentile(50,(@$cycle)[1..$#$cycle]);
+ my $p75 = percentile(75,(@$cycle)[1..$#$cycle]);
+ if ( !$n ) { next; }
+ push @fp75, "$$cycle[0]\t$p25\t$p75\n";
+ push @fp50, "$$cycle[0]\t$p50\n";
+ push @fmean, sprintf "%d\t%.2f\n", $$cycle[0],$sum/$n;
+ printf $fh $fmean[-1];
+ }
+ print $fh "end\n";
+ if ( $is_paired )
+ {
+ for my $cycle (@{$$opts{dat}{LFQ}})
+ {
+ my $sum=0; my $n=0;
+ for (my $iqual=1; $iqual<@$cycle; $iqual++)
+ {
+ $sum += $$cycle[$iqual]*$iqual;
+ $n += $$cycle[$iqual];
+ if ( !defined $lmax or $lmax<$$cycle[$iqual] ) { $lmax=$$cycle[$iqual]; $lmax_qual=$iqual; $lmax_cycle=$$cycle[0]; }
+ }
+ my $p25 = percentile(25,(@$cycle)[1..$#$cycle]);
+ my $p50 = percentile(50,(@$cycle)[1..$#$cycle]);
+ my $p75 = percentile(75,(@$cycle)[1..$#$cycle]);
+ if ( !$n ) { next; }
+ push @lp75, "$$cycle[0]\t$p25\t$p75\n";
+ push @lp50, "$$cycle[0]\t$p50\n";
+ push @lmean, sprintf "%d\t%.2f\n", $$cycle[0],$sum/$n;
+ printf $fh $lmean[-1];
+ }
+ print $fh "end\n";
+ }
+ close($fh);
+ plot($$args{gp});
+
+
+
+ # Average, mean and quality percentiles per cycle, forward and reverse reads in separate plots
+ $args = get_defaults($opts,"$$opts{prefix}quals2.png",wh=>'700,500');
+ $fh = $$args{fh};
+ print $fh qq[
+ $$args{terminal}
+ set output "$$args{img}"
+ $$args{grid}
+ set multiplot
+ set rmargin 0
+ set lmargin 0
+ set tmargin 0
+ set bmargin 0
+ set origin 0.1,0.1
+ set size 0.4,0.8
+ set yrange [0:$yrange]
+ set ylabel "Quality"
+ set xlabel "Cycle (fwd reads)"
+ plot '-' using 1:2:3 with filledcurve lt 1 lc rgb "#cccccc" t '25-75th percentile' , '-' using 1:2 with lines lc rgb "#000000" t 'Median', '-' using 1:2 with lines lt 1 t 'Mean'
+ ];
+ print $fh join('',@fp75),"end\n";
+ print $fh join('',@fp50),"end\n";
+ print $fh join('',@fmean),"end\n";
+ if ( $is_paired )
+ {
+ print $fh qq[
+ set origin 0.55,0.1
+ set size 0.4,0.8
+ unset ytics
+ set y2tics mirror
+ set yrange [0:$yrange]
+ unset ylabel
+ set xlabel "Cycle (rev reads)"
+ set label "$$args{title}" at screen 0.5,0.95 center
+ plot '-' using 1:2:3 with filledcurve lt 1 lc rgb "#cccccc" t '25-75th percentile' , '-' using 1:2 with lines lc rgb "#000000" t 'Median', '-' using 1:2 with lines lt 2 t 'Mean'
+ ];
+ print $fh join('',@lp75),"end\n";
+ print $fh join('',@lp50),"end\n";
+ print $fh join('',@lmean),"end\n";
+ }
+ close($fh);
+ plot($$args{gp});
+
+
+
+ # Quality distribution per cycle, the distribution is for each cycle plotted as a separate curve
+ $args = get_defaults($opts,"$$opts{prefix}quals3.png",wh=>'600,600');
+ $fh = $$args{fh};
+ my $nquals = @{$$opts{dat}{FFQ}[0]}-1;
+ my $ncycles = @{$$opts{dat}{FFQ}};
+ print $fh qq[
+ $$args{terminal}
+ set output "$$args{img}"
+ $$args{grid}
+ set multiplot
+ set rmargin 0
+ set lmargin 0
+ set tmargin 0
+ set bmargin 0
+ set origin 0.15,0.52
+ set size 0.8,0.4
+ set title "$$args{title}"
+ set ylabel "Frequency (fwd reads)"
+ set label "Cycle $fmax_cycle" at $fmax_qual+1,$fmax
+ unset xlabel
+ set xrange [0:$nquals]
+ set format x ""
+ ];
+ my @plots;
+ for (my $i=0; $i<$ncycles; $i++) { push @plots, q['-' using 1:2 with lines t ''] }
+ print $fh "plot ", join(",", @plots), "\n";
+ for my $cycle (@{$$opts{dat}{FFQ}})
+ {
+ for (my $iqual=1; $iqual<$nquals; $iqual++) { print $fh "$iqual\t$$cycle[$iqual]\n"; }
+ print $fh "end\n";
+ }
+ if ( $is_paired )
+ {
+ print $fh qq[
+ set origin 0.15,0.1
+ set size 0.8,0.4
+ unset title
+ unset format
+ set xtics
+ set xlabel "Quality"
+ unset label
+ set label "Cycle $lmax_cycle" at $lmax_qual+1,$lmax
+ set ylabel "Frequency (rev reads)"
+ ];
+ print $fh "plot ", join(",", @plots), "\n";
+ for my $cycle (@{$$opts{dat}{LFQ}})
+ {
+ for (my $iqual=1; $iqual<$nquals; $iqual++)
+ {
+ print $fh "$iqual\t$$cycle[$iqual]\n";
+ }
+ print $fh "end\n";
+ }
+ }
+ close($fh);
+ plot($$args{gp});
+
+
+ # Heatmap qualitites
+ $args = get_defaults($opts,"$$opts{prefix}quals-hm.png", wh=>'600,500');
+ $fh = $$args{fh};
+ my $max = defined $lmax && $lmax > $fmax ? $lmax : $fmax;
+ my @ytics;
+ for my $cycle (@{$$opts{dat}{FFQ}}) { if ( $$cycle[0]%10==0 ) { push @ytics,qq["$$cycle[0]" $$cycle[0]]; } }
+ my $ytics = join(',', @ytics);
+ print $fh qq[
+ $$args{terminal}
+ set output "$$args{img}"
+ unset key
+ unset colorbox
+ set palette defined (0 0 0 0, 1 0 0 1, 3 0 1 0, 4 1 0 0, 6 1 1 1)
+ set cbrange [0:$max]
+ set yrange [0:$ncycles]
+ set xrange [0:$nquals]
+ set view map
+ set multiplot
+ set rmargin 0
+ set lmargin 0
+ set tmargin 0
+ set bmargin 0
+ set origin 0,0.46
+ set size 0.95,0.6
+ set obj 1 rectangle behind from first 0,0 to first $nquals,$ncycles
+ set obj 1 fillstyle solid 1.0 fillcolor rgbcolor "black"
+ set ylabel "Cycle (fwd reads)" offset character -1,0
+ unset ytics
+ set ytics ($ytics)
+ unset xtics
+ set title "$$args{title}"
+ splot '-' matrix with image
+ ];
+ for my $cycle (@{$$opts{dat}{FFQ}})
+ {
+ for (my $iqual=1; $iqual<@$cycle; $iqual++) { print $fh "\t$$cycle[$iqual]"; }
+ print $fh "\n";
+ }
+ print $fh "end\nend\n";
+ @ytics = ();
+ for my $cycle (@{$$opts{dat}{LFQ}}) { if ( $$cycle[0]%10==0 ) { push @ytics,qq["$$cycle[0]" $$cycle[0]]; } }
+ $ytics = join(',', @ytics);
+ print $fh qq[
+ set origin 0,0.03
+ set size 0.95,0.6
+ set ylabel "Cycle (rev reads)" offset character -1,0
+ set xlabel "Base Quality"
+ unset title
+ unset ytics
+ set ytics ($ytics)
+ set xrange [0:$nquals]
+ set xtics
+ set colorbox vertical user origin first ($nquals+1),0 size screen 0.025,0.812
+ set cblabel "Number of bases"
+ splot '-' matrix with image
+ ];
+ for my $cycle (@{$$opts{dat}{LFQ}})
+ {
+ for (my $iqual=1; $iqual<@$cycle; $iqual++) { print $fh "\t$$cycle[$iqual]"; }
+ print $fh "\n";
+ }
+ print $fh "end\nend\n";
+ close($fh);
+ plot($$args{gp});
+}
+
+
+sub plot_acgt_cycles
+{
+ my ($opts) = @_;
+
+ if ( !exists($$opts{dat}{GCC}) or !@{$$opts{dat}{GCC}} ) { return; }
+
+ my $args = get_defaults($opts,"$$opts{prefix}acgt-cycles.png");
+ my $fh = $$args{fh};
+ print $fh qq[
+ $$args{terminal}
+ set output "$$args{img}"
+ $$args{grid}
+ set style line 1 linecolor rgb "green"
+ set style line 2 linecolor rgb "red"
+ set style line 3 linecolor rgb "black"
+ set style line 4 linecolor rgb "blue"
+ set style increment user
+ set ylabel "Base content [%]"
+ set xlabel "Read Cycle"
+ set yrange [0:100]
+ set title "$$args{title}"
+ plot '-' w l ti 'A', '-' w l ti 'C', '-' w l ti 'G', '-' w l ti 'T'
+ ];
+ for my $base (1..4)
+ {
+ for my $cycle (@{$$opts{dat}{GCC}})
+ {
+ print $fh $$cycle[0]+1,"\t",$$cycle[$base],"\n";
+ }
+ print $fh "end\n";
+ }
+ close($fh);
+ plot($$args{gp});
+}
+
+
+sub plot_gc
+{
+ my ($opts) = @_;
+
+ my $is_paired = $$opts{dat}{'is paired:'};
+ my $args = get_defaults($opts,"$$opts{prefix}gc-content.png");
+ my $fh = $$args{fh};
+ my ($gcl_max,$gcf_max,$lmax,$fmax);
+ for my $gc (@{$$opts{dat}{GCF}}) { if ( !defined $gcf_max or $gcf_max<$$gc[1] ) { $gcf_max=$$gc[1]; $fmax=$$gc[0]; } }
+ for my $gc (@{$$opts{dat}{GCL}}) { if ( !defined $gcl_max or $gcl_max<$$gc[1] ) { $gcl_max=$$gc[1]; $lmax=$$gc[0]; } }
+ my $gcmax = $is_paired && $gcl_max > $gcf_max ? $lmax : $fmax;
+ print $fh qq[
+ $$args{terminal}
+ set output "$$args{img}"
+ $$args{grid}
+ set title "$$args{title}"
+ set ylabel "Normalized Frequency"
+ set xlabel "GC Content [%]"
+ set yrange [0:1.1]
+ set label sprintf("%.1f",$gcmax) at $gcmax,1 front offset 1,0
+ plot ]
+ . (exists($$opts{ref_stats}) ? q['-' smooth csplines with lines lt 0 title 'Reference', ] : '')
+ . q['-' smooth csplines with lines lc 1 title 'First fragments' ]
+ . ($is_paired ? q[, '-' smooth csplines with lines lc 2 title 'Last fragments'] : '')
+ . q[
+ ];
+ if ( exists($$opts{ref_stats}) )
+ {
+ open(my $ref,'<',$$opts{ref_stats}) or error("$$opts{ref_stats}: $!");
+ while (my $line=<$ref>) { print $fh $line }
+ close($ref);
+ print $fh "end\n";
+ }
+ for my $cycle (@{$$opts{dat}{GCF}}) { printf $fh "%d\t%f\n", $$cycle[0],$$cycle[1]/$gcf_max; }
+ print $fh "end\n";
+ if ( $is_paired )
+ {
+ for my $cycle (@{$$opts{dat}{GCL}}) { printf $fh "%d\t%f\n", $$cycle[0],$$cycle[1]/$gcl_max; }
+ print $fh "end\n";
+ }
+ close($fh);
+ plot($$args{gp});
+}
+
+
+sub plot_gc_depth
+{
+ my ($opts) = @_;
+
+ if ( !exists($$opts{dat}{GCD}) or !@{$$opts{dat}{GCD}} ) { return; }
+
+ # Find unique sequence percentiles for 30,40, and 50% GC content, just to draw x2tics.
+ my @tics = ( {gc=>30},{gc=>40},{gc=>50} );
+ for my $gc (@{$$opts{dat}{GCD}})
+ {
+ for my $tic (@tics)
+ {
+ my $diff = abs($$gc[0]-$$tic{gc});
+ if ( !exists($$tic{pr}) or $diff<$$tic{diff} ) { $$tic{pr}=$$gc[1]; $$tic{diff}=$diff; }
+ }
+ }
+
+ my @x2tics;
+ for my $tic (@tics) { push @x2tics, qq["$$tic{gc}" $$tic{pr}]; }
+ my $x2tics = join(',',@x2tics);
+
+ my $args = get_defaults($opts,"$$opts{prefix}gc-depth.png", wh=>'600,500');
+ my $fh = $$args{fh};
+ print $fh qq[
+ $$args{terminal}
+ set output "$$args{img}"
+ $$args{grid}
+ set ylabel "Mapped depth"
+ set xlabel "Percentile of mapped sequence ordered by GC content"
+ set x2label "GC Content [%]"
+ set title "$$args{title}"
+ set x2tics ($x2tics)
+ set xtics nomirror
+ set xrange [0.1:99.9]
+
+ plot '-' using 1:2:3 with filledcurve lt 1 lc rgb "#dedede" t '10-90th percentile' , \\
+ '-' using 1:2:3 with filledcurve lt 1 lc rgb "#bbdeff" t '25-75th percentile' , \\
+ '-' using 1:2 with lines lc rgb "#0084ff" t 'Median'
+ ];
+ for my $gc (@{$$opts{dat}{GCD}}) { print $fh "$$gc[1]\t$$gc[2]\t$$gc[6]\n"; } print $fh "end\n";
+ for my $gc (@{$$opts{dat}{GCD}}) { print $fh "$$gc[1]\t$$gc[3]\t$$gc[5]\n"; } print $fh "end\n";
+ for my $gc (@{$$opts{dat}{GCD}}) { print $fh "$$gc[1]\t$$gc[4]\n"; } print $fh "end\n";
+ close($fh);
+ plot($$args{gp});
+}
+
+
+sub plot_isize
+{
+ my ($opts) = @_;
+
+ if ( !$$opts{dat}{'is paired:'} or !exists($$opts{dat}{IS}) or !@{$$opts{dat}{IS}} ) { return; }
+
+ my ($isize_max,$isize_cnt);
+ for my $isize (@{$$opts{dat}{IS}})
+ {
+ if ( !defined $isize_max or $isize_cnt<$$isize[1] ) { $isize_cnt=$$isize[1]; $isize_max=$$isize[0]; }
+ }
+
+ my $args = get_defaults($opts,"$$opts{prefix}insert-size.png");
+ my $fh = $$args{fh};
+ print $fh qq[
+ $$args{terminal}
+ set output "$$args{img}"
+ $$args{grid}
+ set rmargin 5
+ set label sprintf("%d",$isize_max) at $isize_max+10,$isize_cnt
+ set ylabel "Number of pairs"
+ set xlabel "Insert Size"
+ set title "$$args{title}"
+ plot \\
+ '-' with lines lc rgb 'black' title 'All pairs', \\
+ '-' with lines title 'Inward', \\
+ '-' with lines title 'Outward', \\
+ '-' with lines title 'Other'
+ ];
+ for my $isize (@{$$opts{dat}{IS}}) { print $fh "$$isize[0]\t$$isize[1]\n"; } print $fh "end\n";
+ for my $isize (@{$$opts{dat}{IS}}) { print $fh "$$isize[0]\t$$isize[2]\n"; } print $fh "end\n";
+ for my $isize (@{$$opts{dat}{IS}}) { print $fh "$$isize[0]\t$$isize[3]\n"; } print $fh "end\n";
+ for my $isize (@{$$opts{dat}{IS}}) { print $fh "$$isize[0]\t$$isize[4]\n"; } print $fh "end\n";
+ close($fh);
+ plot($$args{gp});
+}
+
+
+sub plot_coverage
+{
+ my ($opts) = @_;
+
+ if ( !exists($$opts{dat}{COV}) or !@{$$opts{dat}{COV}} ) { return; }
+
+ my @vals;
+ for my $cov (@{$$opts{dat}{COV}}) { push @vals,$$cov[2]; }
+ my $i = percentile(99.8,@vals);
+ my $p99 = $$opts{dat}{COV}[$i][1];
+
+ my $args = get_defaults($opts,"$$opts{prefix}coverage.png");
+ my $fh = $$args{fh};
+ print $fh qq[
+ $$args{terminal}
+ set output "$$args{img}"
+ $$args{grid}
+ set ylabel "Number of mapped bases"
+ set xlabel "Coverage"
+ set style fill solid border -1
+ set title "$$args{title}"
+ set xrange [:$p99]
+ plot '-' with lines notitle
+ ];
+ for my $cov (@{$$opts{dat}{COV}})
+ {
+ if ( $$cov[2]==0 ) { next; }
+ print $fh "$$cov[1]\t$$cov[2]\n";
+ }
+ print $fh "end\n";
+ close($fh);
+ plot($$args{gp});
+}
+
+
+sub plot_mismatches_per_cycle
+{
+ my ($opts) = @_;
+
+ if ( !exists($$opts{dat}{MPC}) or !@{$$opts{dat}{MPC}} ) { return; }
+ if ( older_than($opts,'2012-02-06') ) { plot_mismatches_per_cycle_old($opts); }
+
+ my $nquals = @{$$opts{dat}{MPC}[0]} - 2;
+ my $ncycles = @{$$opts{dat}{MPC}};
+ my ($style,$with);
+ if ( $ncycles>100 ) { $style = ''; $with = 'w l'; }
+ else { $style = 'set style data histogram; set style histogram rowstacked'; $with = ''; }
+
+ my $args = get_defaults($opts,"$$opts{prefix}mism-per-cycle.png");
+ my $fh = $$args{fh};
+ print $fh qq[
+ $$args{terminal}
+ set output "$$args{img}"
+ $$args{grid}
+ set style line 1 linecolor rgb "#e40000"
+ set style line 2 linecolor rgb "#ff9f00"
+ set style line 3 linecolor rgb "#eeee00"
+ set style line 4 linecolor rgb "#4ebd68"
+ set style line 5 linecolor rgb "#0061ff"
+ set style increment user
+ set key left top
+ $style
+ set ylabel "Number of mismatches"
+ set xlabel "Read Cycle"
+ set style fill solid border -1
+ set title "$$args{title}"
+ set xrange [-1:$ncycles]
+ plot '-' $with ti 'Base Quality>30', \\
+ '-' $with ti '30>=Q>20', \\
+ '-' $with ti '20>=Q>10', \\
+ '-' $with ti '10>=Q', \\
+ '-' $with ti "N's"
+ ];
+ for my $cycle (@{$$opts{dat}{MPC}})
+ {
+ my $sum; for my $idx (31..$#$cycle) { $sum += $$cycle[$idx]; }
+ print $fh "$sum\n";
+ }
+ print $fh "end\n";
+ for my $cycle (@{$$opts{dat}{MPC}})
+ {
+ my $sum; for my $idx (22..31) { $sum += $$cycle[$idx]; }
+ print $fh "$sum\n";
+ }
+ print $fh "end\n";
+ for my $cycle (@{$$opts{dat}{MPC}})
+ {
+ my $sum; for my $idx (12..21) { $sum += $$cycle[$idx]; }
+ print $fh "$sum\n";
+ }
+ print $fh "end\n";
+ for my $cycle (@{$$opts{dat}{MPC}})
+ {
+ my $sum; for my $idx (2..11) { $sum += $$cycle[$idx]; }
+ print $fh "$sum\n";
+ }
+ print $fh "end\n";
+ for my $cycle (@{$$opts{dat}{MPC}}) { print $fh "$$cycle[1]\n"; }
+ print $fh "end\n";
+ close($fh);
+ plot($$args{gp});
+}
+
+sub plot_indel_dist
+{
+ my ($opts) = @_;
+
+ if ( !exists($$opts{dat}{ID}) or !@{$$opts{dat}{ID}} ) { return; }
+
+ my $args = get_defaults($opts,"$$opts{prefix}indel-dist.png");
+ my $fh = $$args{fh};
+ print $fh qq[
+ $$args{terminal}
+ set output "$$args{img}"
+ $$args{grid}
+ set style line 1 linetype 1 linecolor rgb "red"
+ set style line 2 linetype 2 linecolor rgb "black"
+ set style line 3 linetype 3 linecolor rgb "green"
+ set style increment user
+ set ylabel "Indel count [log]"
+ set xlabel "Indel length"
+ set y2label "Insertions/Deletions ratio"
+ set log y
+ set y2tics nomirror
+ set ytics nomirror
+ set title "$$args{title}"
+ plot '-' w l ti 'Insertions', '-' w l ti 'Deletions', '-' axes x1y2 w l ti "Ins/Dels ratio"
+ ];
+ for my $len (@{$$opts{dat}{ID}}) { print $fh "$$len[0]\t$$len[1]\n"; } print $fh "end\n";
+ for my $len (@{$$opts{dat}{ID}}) { print $fh "$$len[0]\t$$len[2]\n"; } print $fh "end\n";
+ for my $len (@{$$opts{dat}{ID}}) { printf $fh "%d\t%f\n", $$len[0],$$len[2]?$$len[1]/$$len[2]:0; } print $fh "end\n";
+ close($fh);
+ plot($$args{gp});
+}
+
+sub plot_indel_cycles
+{
+ my ($opts) = @_;
+
+ if ( !exists($$opts{dat}{IC}) or !@{$$opts{dat}{IC}} ) { return; }
+
+ my $args = get_defaults($opts,"$$opts{prefix}indel-cycles.png");
+ my $fh = $$args{fh};
+ print $fh qq[
+ $$args{terminal}
+ set output "$$args{img}"
+ $$args{grid}
+ set style line 1 linetype 1 linecolor rgb "red"
+ set style line 2 linetype 2 linecolor rgb "black"
+ set style line 3 linetype 3 linecolor rgb "green"
+ set style line 4 linetype 4 linecolor rgb "blue"
+ set style increment user
+ set ylabel "Indel count"
+ set xlabel "Read Cycle"
+ set title "$$args{title}"
+ plot '-' w l ti 'Insertions (fwd)', '' w l ti 'Insertions (rev)', '' w l ti 'Deletions (fwd)', '' w l ti 'Deletions (rev)'
+ ];
+ for my $len (@{$$opts{dat}{IC}}) { print $fh "$$len[0]\t$$len[1]\n"; } print $fh "end\n";
+ for my $len (@{$$opts{dat}{IC}}) { print $fh "$$len[0]\t$$len[2]\n"; } print $fh "end\n";
+ for my $len (@{$$opts{dat}{IC}}) { print $fh "$$len[0]\t$$len[3]\n"; } print $fh "end\n";
+ for my $len (@{$$opts{dat}{IC}}) { print $fh "$$len[0]\t$$len[4]\n"; } print $fh "end\n";
+ close($fh);
+ plot($$args{gp});
+}
+
+
+
+
+
+
+
+sub has_values
+{
+ my ($opts,@tags) = @_;
+ for my $tag (@tags)
+ {
+ my (@lines) = `cat $$opts{bamcheck} | grep ^$tag | wc -l`;
+ chomp($lines[0]);
+ if ( $lines[0]<2 ) { return 0; }
+ }
+ return 1;
+}
+
+sub plot_mismatches_per_cycle_old
+{
+ my ($opts) = @_;
+
+ my $args = get_defaults($opts,"$$opts{prefix}mism-per-cycle.png");
+ my ($nquals) = `grep ^MPC $$opts{bamcheck} | awk '\$2==1' | sed 's,\\t,\\n,g' | wc -l`;
+ my ($ncycles) = `grep ^MPC $$opts{bamcheck} | wc -l`;
+ chomp($nquals);
+ chomp($ncycles);
+ $nquals--;
+ $ncycles--;
+ my @gr0_15 = (2..17);
+ my @gr16_30 = (18..32);
+ my @gr31_n = (33..$nquals);
+ my $gr0_15 = '$'. join('+$',@gr0_15);
+ my $gr16_30 = '$'. join('+$',@gr16_30);
+ my $gr31_n = '$'. join('+$',@gr31_n);
+
+ open(my $fh,'>',$$args{gp}) or error("$$args{gp}: $!");
+ print $fh q[
+ set terminal png size 600,400 truecolor font "DejaVuSansMono,9"
+ set output "] . $$args{img} . q["
+
+ set key left top
+ set style data histogram
+ set style histogram rowstacked
+
+ set grid back lc rgb "#aaaaaa"
+ set ylabel "Number of mismatches"
+ set xlabel "Read Cycle"
+ set style fill solid border -1
+ set title "] . $$args{title} . qq["
+ set xrange [-1:$ncycles]
+
+ plot '< grep ^MPC $$opts{bamcheck} | cut -f 2-' using ($gr31_n) ti 'Base Quality>30', '' using ($gr16_30) ti '30>=Q>15', '' using ($gr0_15) ti '15>=Q'
+ ];
+ close($fh);
+
+ plot($$args{gp});
+}
+
+
projects / rsem.git / blobdiff