# HG changeset patch # User stef # Date 1425047101 18000 # Node ID b8751995b54e8ee853a7585496d3059b874ebcff # Parent e913d39d9a2e969e19fafc05693b27caca4c00f9 Uploaded diff -r e913d39d9a2e -r b8751995b54e falco/bin/falco-filter-report --- a/falco/bin/falco-filter-report Fri Feb 27 09:13:55 2015 -0500 +++ b/falco/bin/falco-filter-report Fri Feb 27 09:25:01 2015 -0500 @@ -91,4 +91,4 @@ ## REPORTING print STDOUT localtime() . " [$$] Creating HTML report\n"; -system( "perl $mkReport $base" ); +system( "perl $mkReport $base $qc_targets_txt" ); diff -r e913d39d9a2e -r b8751995b54e falco/lib/perl/mkHtmlReportGalaxy.pl --- a/falco/lib/perl/mkHtmlReportGalaxy.pl Fri Feb 27 09:13:55 2015 -0500 +++ b/falco/lib/perl/mkHtmlReportGalaxy.pl Fri Feb 27 09:25:01 2015 -0500 @@ -5,7 +5,8 @@ use Spreadsheet::WriteExcel; $| = 1; -my $sample = shift || die "No input\n"; +my $sample = shift || die "Missing input\n"; +my $qc_targets_txt = shift || die "Missing input\n"; my $dir = shift || "./"; my $outdir = shift || "./"; my $pat = shift || ""; @@ -15,7 +16,6 @@ # QC # Results my @samples = (); -#open INDEX, ">$outdir/index.html"; my $htmlHead = qq( @@ -29,25 +29,7 @@ ); -#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 ""; -#print INDEX ""; -#print INDEX "\n"; -#foreach my $sam (sort @samples) { -# print INDEX "\n"; -#} my %link = (); my $excelBook0 = Spreadsheet::WriteExcel->new("$outdir/runQC.xls"); my $excel0 = $excelBook0->add_worksheet("table1"); @@ -67,9 +49,9 @@ my $excel2 = $excelBook->add_worksheet("table2"); print OUT $htmlHead; my %QC = (); -open QC, "<$dir/$sample.qc.targets.txt"; +open QC, "<$qc_targets_txt" or die "Unable to open qc_targets_txt\n"; readline QC; -print STDERR "Reading in $sample.qc.targets.txt\n"; +print STDERR "Reading in $qc_targets_txt\n"; while () { chomp; my @row = split(/\t/, $_); @@ -215,18 +197,10 @@ $excelBook->close(); my @resCnt = map { $rescnt{$_} || 0 } qw/Falcosnp Falcoindel/; my $pctGood = sprintf("%.2f", $amp100 / scalar(keys(%QC)) * 100); -#print INDEX "\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 "
Download:runQC.xls
SampleBAMsnpindelreadCntAmp > 100
$samBAMBAI
$sampleBAM$resCnt[0]$resCnt[1]$readCnt$pctGood
"; -#print INDEX ""; -#print INDEX ""; -#print INDEX ""; -#print INDEX ""; -#close INDEX; -