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changeset 68:aaa240cf978b draft

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Uploaded
author stef
date Fri, 27 Feb 2015 08:56:16 -0500
parents 61c0e184e50d
children 2d757208b0c1
files mkHtmlReportGalaxy.pl
diffstat 1 files changed, 232 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mkHtmlReportGalaxy.pl	Fri Feb 27 08:56:16 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;
+
+