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changeset 70:1c28c5e4e4da draft

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Deleted selected files
author stef
date Fri, 27 Feb 2015 09:13:14 -0500
parents 2d757208b0c1
children e913d39d9a2e
files mkHtmlReportGalaxy.pl
diffstat 1 files changed, 0 insertions(+), 232 deletions(-) [+]
line wrap: on
line diff
--- a/mkHtmlReportGalaxy.pl	Fri Feb 27 08:58:35 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,232 +0,0 @@
-#!/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;
-
-