Mercurial > repos > stef > falco
changeset 71:e913d39d9a2e draft
Uploaded
| author | stef |
|---|---|
| date | Fri, 27 Feb 2015 09:13:55 -0500 |
| parents | 1c28c5e4e4da |
| children | b8751995b54e |
| files | falco-filter-report falco/bin/falco-filter-report falco/lib/perl/mkHtmlReportGalaxy.pl |
| diffstat | 3 files changed, 234 insertions(+), 96 deletions(-) [+] |
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--- a/falco-filter-report Fri Feb 27 09:13:14 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,94 +0,0 @@ -#!/usr/bin/perl -use strict; -use Cwd 'abs_path'; -use Getopt::Long; -use File::Basename; - -my $absPath = abs_path($0); -my $dir = dirname($absPath); -my $lib = "$dir/../lib/"; - -my $vcf2tsv = "$lib/perl/vcf2tsv.pl"; -my $spliteff = "$lib/perl/splitEff.pl"; -my $filter = "$lib/perl/filter.pl"; -my $plotPng = "$lib/R/plotsPng.R"; -my $mkReport = "$lib/perl/mkHtmlReportGalaxy.pl"; - -my $locifilt = "$dir/../ref/filters/filter.tsv"; -my $manifest = "$dir/../ref/TSACP/TruSeq_Amplicon_Cancer_Panel_Manifest_AFP1_PN15032433.txt"; - -my $canonicals = "$dir/../ref/TSACP/canonicals.tsv"; -my $clinvar = "$dir/../ref/filters/clinvar_00-latest.f.vcf"; -my $cosmic = "$dir/../ref/filters/CosmicCodingMuts_v64_26032013_noLimit_wgs.f.vcf"; -my $cosmicNC = "$dir/../ref/filters/CosmicNonCodingVariants_v64_26032013_noLimit_wgs.f.vcf"; - -my $base = undef; -my $vcf = undef; -my $vcfOther = undef; -my $noFilt = undef; -my $noPlot = undef; - -my $qc_ann_qual_txt = undef; -my $qc2_ann_txt = undef -my $qc_targets_txt = undef; - -GetOptions ( - "vcf=s" => \$vcf, - "vcfOther=s" => \$vcfOther, - "output=s" => \$base, - "canonicals=s" => \$canonicals, - "clinvar=s" => \$clinvar, - "cosmic=s" => \$cosmic, - "cosmicNC=s" => \$cosmicNC, - "noFilt" => \$noFilt, - "noPlot" => \$noPlot, - "qc_ann_qual_txt=s" => \$qc_ann_qual_txt, - "qc2_ann_txt=s" => \$qc2_ann_txt, - "qc_targets_txt=s" => \$qc_targets_txt, -) -or die("Error in command line arguments\n"); - -## sanity checks -die( "No base name provided [-output]\n" ) unless defined($base) and $base ne ''; -die( "No VCF file provided [-vcf]\n" ) unless defined($vcf) and -f $vcf; -die( "Missing input [-qc_ann_qual_txt]\n" ) unless defined($qc_ann_qual_txt) and -f $qc_ann_qual_txt; -die( "Missing input [-qc2_ann_txt]\n" ) unless defined($qc2_ann_txt) and -f $qc2_ann_txt; -die( "Missing input [-qc_targets_txt]\n" ) unless defined($qc_targets_txt) and -f $qc_targets_txt; -die( "Required file does not exists [$canonicals]\n" ) unless -f $canonicals; -die( "Required file does not exists [$clinvar]\n" ) unless -f $clinvar; -die( "Required file does not exists [$cosmic]\n" ) unless -f $cosmic; -die( "Required file does not exists [$cosmicNC]\n" ) unless -f $cosmicNC; - - -## Rscript check -my $rscript = `which Rscript`; -chomp $rscript; -if ($rscript !~ /Rscript$/) { - print STDERR "No Rscript present in PATH\n"; - exit 1; -} - -## FILTERING -print STDOUT localtime() . " [$$] converting vcf to tsv\n"; -system( "$vcf2tsv $vcf > $base\.tsv" ); - -print STDOUT localtime() . " [$$] splitting vcf columns\n"; -system( "$spliteff $base\.tsv Falco >> $base\.res\.tsv" ); - -if ( defined($vcfOther) ){ - print STDOUT localtime() . " [$$] converting vcf to tsv\n"; - system( "$vcf2tsv $vcf > $base\.Other\.tsv" ); - print STDOUT localtime() . " [$$] splitting vcf columns\n"; - system( "$spliteff $base\.Other\.tsv Other >> $base\.res\.tsv" ); -} - -print STDOUT localtime() . " [$$] filtering data\n"; -system( "$filter $base\.res\.tsv $canonicals $clinvar $cosmic $cosmicNC > $base\.res\.filtered\.tsv" ); - -## PLOTTING -print STDOUT localtime() . " [$$] Creating plots\n"; -system( "Rscript $plotPng $qc_ann_qual_txt $qc2_ann_txt $qc_targets_txt $base\.res\.filtered\.tsv $clinvar $locifilt $base" ); - -## REPORTING -print STDOUT localtime() . " [$$] Creating HTML report\n"; -system( "perl $mkReport $base" );
--- a/falco/bin/falco-filter-report Fri Feb 27 09:13:14 2015 -0500 +++ b/falco/bin/falco-filter-report Fri Feb 27 09:13:55 2015 -0500 @@ -12,7 +12,7 @@ my $spliteff = "$lib/perl/splitEff.pl"; my $filter = "$lib/perl/filter.pl"; my $plotPng = "$lib/R/plotsPng.R"; -my $mkReport = "$lib/perl/mkHtmlReport.pl"; +my $mkReport = "$lib/perl/mkHtmlReportGalaxy.pl"; my $locifilt = "$dir/../ref/filters/filter.tsv"; my $manifest = "$dir/../ref/TSACP/TruSeq_Amplicon_Cancer_Panel_Manifest_AFP1_PN15032433.txt"; @@ -91,4 +91,4 @@ ## REPORTING print STDOUT localtime() . " [$$] Creating HTML report\n"; -system( "perl $mkReport" ); +system( "perl $mkReport $base" );
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/falco/lib/perl/mkHtmlReportGalaxy.pl Fri Feb 27 09:13:55 2015 -0500 @@ -0,0 +1,232 @@ +#!/usr/bin/perl -w + +use strict; +use Cwd; +use Spreadsheet::WriteExcel; + +$| = 1; +my $sample = shift || die "No input\n"; +my $dir = shift || "./"; +my $outdir = shift || "./"; +my $pat = shift || ""; +my $cwd = cwd(); +(my $runName = $cwd) =~ s/^.*\/(.*?)$/$1/; + +# QC +# Results +my @samples = (); +#open INDEX, ">$outdir/index.html"; +my $htmlHead = qq( +<!DOCTYPE html> +<html> +<head> +<style type="text/css"> +body {font-family:arial;} +table {font-family:arial;border-collapse: collapse; font-size: smaller;} +th {border: 1px solid gray; padding: 5px;} +td {border: 1px solid gray; padding: 5px; text-align: right;} +</style> +</head> +<body> +); +#print INDEX $htmlHead; +# opendir DIR, "$dir"; +# while (my $cd = readdir DIR) { +# if ($cd =~ /(.*$pat)\.qc\.targets\.txt$/) { +# my $sam = $1; +# # next if ($sam =~ /R[12]/); +# print STDERR $1 . "\n"; +# push @samples, $1; +# } +# } +# close DIR; + +#print INDEX "<table>"; +#print INDEX "<tr><th>Download:</th><th><a href=\"runQC.xls\">runQC.xls</a></th>"; +#print INDEX "<tr><th>Sample</th><th>BAM</th><th>snp</th><th>indel</th><th>readCnt</th><th>Amp > 100</th>\n"; +#foreach my $sam (sort @samples) { +# print INDEX "<tr><td><a href=$sam.html>$sam</a></td><td><a href=$sam.bam>BAM</a></td><td><a href=$sam.bam.bai>BAI</a></td></tr>\n"; + +#} +my %link = (); +my $excelBook0 = Spreadsheet::WriteExcel->new("$outdir/runQC.xls"); +my $excel0 = $excelBook0->add_worksheet("table1"); +my $excel0Ref = [[qw/sampleName runName totalReads pct100 ntbGenes/]]; + +print STDERR "Processing $sample\n"; +# next if ($sample =~ /R[12]/); + +my $readCnt = 0; +my $amp100 = 0; +my %ntbGenes = (); + +open OUT, ">$outdir/$sample.html"; +open OUT2, ">$outdir/$sample.tsv"; +my $excelBook = Spreadsheet::WriteExcel->new("$outdir/$sample.xls"); +my $excel1 = $excelBook->add_worksheet("table1"); +my $excel2 = $excelBook->add_worksheet("table2"); +print OUT $htmlHead; +my %QC = (); +open QC, "<$dir/$sample.qc.targets.txt"; +readline QC; +print STDERR "Reading in $sample.qc.targets.txt\n"; +while (<QC>) { + chomp; + my @row = split(/\t/, $_); + my @id = split(/[\_\.\-:]/, $row[0]); + $row[-1] = 0 if ($row[-1] eq "NA"); + $readCnt += $row[-1]; # DP + if ($#id != 10) { + $id[0] =~ /(\D+)(\d+)/; + $id[0] = $2; + unshift @id, $1; + } + + if ($row[-1] >= 100) { + $amp100++ + } + else { + $ntbGenes{$row[0]}{dp} = $row[-1]; + $ntbGenes{$row[0]}{id} = [@id]; + } + + $QC{$row[0]}{QC} = [@id, @row];# if ($id[0]); + foreach my $c ($row[4] .. $row[5]) { + $link{$id[-3] . ":" . $c}{$row[0]} = "Assay"; + } + foreach my $c ($row[2] .. $row[4], $row[5] .. $row[3]) { + $link{$id[-3] . ":" . $c}{$row[0]} = "LSO"; + } +} +close QC; + +open RES, "<$dir/$sample.res.filtered.tsv" or die "Unable to open $dir/$sample\n"; +my %uniq = (); +my $colCnt = 0; +my $resHead = readline(RES); +chomp $resHead; +$resHead =~ s/^#//; +$resHead =~ s/\s+$//; +my %resCol = map { $_ => $colCnt++ } split(/\t/, $resHead); +my @keyColsN = qw/QUAL Gene_Name Codon_Change Amino_Acid_change vaf DP AD Tag CHROM POS ID REF ALT Context Effect_Impact Functional_Class Amino_Acid_length Gene_Coding Transcript_ID Exon_Rank/; +# my @keyColsN = qw/CHROM POS ID REF ALT QUAL DP AD vaf Context Effect_Impact Functional_Class Codon_Change Amino_Acid_change Amino_Acid_length Gene_Name Coding Transcript Exon Tag/; +my @keyColsI = map { $resCol{$_} } @keyColsN; +foreach my $i (0 .. $#keyColsN) { + print STDERR join(":", $i, $keyColsN[$i], $keyColsI[$i]) . "\n"; +} + +print STDERR "Processing results\n"; +while (<RES>) { + chomp; + my @row = split(/\t/, $_); + my $cpos = join(":", @row[0, 1]); + if (exists $link{$cpos}) { +# my $key = join(":", @row[0 .. 4,6, 9,10,11,12,14 .. 21]); + my $key = join(":", @row[@keyColsI]); + #print STDERR join(":", @keyColsI) . "\n"; +# print STDERR join(":", @row) . "\n"; sleep 1; + if (not exists($uniq{$key})) { + foreach my $locus (keys(%{$link{$cpos}})) { + next if ($link{$cpos}{$locus} eq "LSO"); + push @{$QC{$locus}{RES}}, [@row, $link{$cpos}{$locus}]; + # print STDERR "Adding $key to $locus\n\n"; #sleep 1; + } + $uniq{$key} = 0; + } + else { + # print STDERR $key . " : Exists\n\n"; #sleep 1; + } + } +} +close RES; + +## Rplots that are not self-explanatory enough +#print OUT "<img src=\"$sample/$sample.vaf.png\">"; +#print OUT "<img src=\"$sample/$sample.raf.png\">"; +#print OUT "<img src=\"$sample/$sample.snv-q.png\">"; +#print OUT "<img src=\"$sample/$sample.snv-q-zoom.png\">"; +#print OUT "<img src=\"$sample/$sample.ins-q.png\">"; +#print OUT "<img src=\"$sample/$sample.del-q.png\">"; + +print OUT "<img src=\"$sample/$sample.amp-dp.png\">"; +#print OUT "<img src=\"$sample/$sample.heat.png\">"; +#print OUT "<img src=\"$sample/$sample.bias.png\">"; +#print OUT "<img src=\"$sample/$sample.biasheat.png\">"; +#print OUT "<img src=\"$sample/$sample.vafcut.png\">"; +print OUT "<table border=1><tr><th>Download:</th><th><a href=\"$sample.tsv\">TSV</a></th>"; +print OUT "<th><a href=\"$sample.xls\">XLS</a></th></table>"; +print OUT "<table border=1>\n"; +# my @colnames = qw/depth chr pos id ref var qual DP AD vaf context impact effectClass codonChange AAChange RefSeqLength geneName RefSeqClass RefSeqID Exon Tag/; +my @colnames = ("depth", @keyColsN); +print OUT "<tr>" . join("", map { "<th>$_</th>" } ("Amplicon", "c","c2", "b", @colnames)) . "</tr>"; +print OUT2 join("\t", "Amplicon", @colnames) . "\n"; +my $excelAref = [["Amplicon", @colnames]]; +my $excelAref2 = [[qw/gene exon protein vaf func depth /]]; +my %rescnt = (); +foreach my $locus (sort keys(%QC)) { +# my @targets = keys(%{$QC{$locus}{QC}}); +# print OUT "</td>"; + my $nres = 1; + $nres = scalar(@{$QC{$locus}{RES}}) if ($QC{$locus}{RES}); + + print OUT "<tr><td rowspan=\"$nres\">$locus</td>\n"; + print OUT "<td rowspan=\"$nres\"><a href=\"$sample/$sample.$locus.cov.png\">c</a></td>\n"; + print OUT "<td rowspan=\"$nres\"><a href=\"$sample/$sample.$locus.cov2.png\">c2</a></td>\n"; + print OUT "<td rowspan=\"$nres\"><a href=\"$sample/$sample.$locus.bias.png\">b</a></td>\n"; + print OUT "<td rowspan=\"$nres\">$QC{$locus}{QC}->[-1]</td>\n"; #<td rowspan=\"$nres\">"; + + foreach my $res (@{$QC{$locus}{RES}}) { + $res = [map {$_ || ""} @$res]; + print OUT "<td>\n"; + print OUT join("</td><td>\n", @{$res}[@keyColsI]); + print OUT "</td></tr><tr>\n"; + print OUT2 join("\t", $locus, $QC{$locus}{QC}->[-1], @{$res}[@keyColsI]) . "\n"; + push @$excelAref, [$locus, $QC{$locus}{QC}->[-1], @{$res}[@keyColsI]]; + +# qw/QUAL Gene_Name Codon_Change Amino_Acid_change vaf DP AD Tag CHROM POS ID REF ALT Context Effect_Impact Functional_Class Amino_Acid_length Coding Transcript Exon/; + push @$excelAref2, [map {$_ || "NA"} @{$res}[map { $resCol{$_} } (qw/Gene_Name Exon_Rank Amino_Acid_change vaf Functional_Class/)], $QC{$locus}{QC}->[-1]]; +# push @$excelAref2, [map {$_ || "NA"} @{$res}[[qw/Gene_Name Exon_Rank Cdna_change Amino_Acid_change vaf Functional_Class/]], $QC{$locus}{QC}->[-1]]; + my $pl = $res->[$keyColsI[7]]; + my $ref = $res->[$keyColsI[11]]; + my $var = $res->[$keyColsI[12]]; +# print STDERR "$pl $ref $var\n"; sleep 1; + if (length($ref) == length($var)) { + $rescnt{$pl . "snp"}++; + } + else { + $rescnt{$pl . "indel"}++; + } +# $rescnt++; + } + print STDERR $locus . ":" . $nres . "\n"; + print STDERR $locus . ":" . join("-", @{$QC{$locus}{RES}}) . "\n"; + if (scalar(@{$QC{$locus}{RES}}) == 0) { #$nres == 0) { + print OUT2 join("\t", $locus, $QC{$locus}{QC}->[-1], ("-") x scalar(@keyColsI)) . "\n"; + push @$excelAref, [$locus, $QC{$locus}{QC}->[-1], ("-") x scalar(@keyColsI)]; + } + print OUT "</tr>\n"; +} +print OUT "</table>\n"; +print OUT "</body></html>\n"; +close OUT; +close OUT2; +$excel1->write_col(0,0, $excelAref); +$excel2->write_col(0,0, $excelAref2); +$excelBook->close(); +my @resCnt = map { $rescnt{$_} || 0 } qw/Falcosnp Falcoindel/; +my $pctGood = sprintf("%.2f", $amp100 / scalar(keys(%QC)) * 100); +#print INDEX "<tr><td><a href=$sample.html>$sample</a></td><td><a href=$sample.bam>BAM</a></td><td>$resCnt[0]</td><td>$resCnt[1]</td><td>$readCnt</td><td>$pctGood</td></tr>\n"; +my $ntbsAmps = join(",", map { s/^(.*?)\.chr.*$/$1/; $_; } keys(%ntbGenes)); +push @{$excel0Ref}, [$sample, $runName, $readCnt, $pctGood, $ntbsAmps]; + +$excel0->write_col(0,0, $excel0Ref); +$excelBook0->close(); + +#print INDEX "</table>"; +#print INDEX "<img src=\"alnStats.png\">"; +#print INDEX "<img src=\"errStats.png\">"; +#print INDEX "<img src=\"qualStats.png\">"; +#print INDEX "</html>"; +#close INDEX; + +