Mercurial > repos > stef > falco

changeset 72:b8751995b54e draft

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Uploaded
author stef
date Fri, 27 Feb 2015 09:25:01 -0500
parents e913d39d9a2e
children 78f10251a484
files falco/bin/falco-filter-report falco/lib/perl/mkHtmlReportGalaxy.pl
diffstat 2 files changed, 5 insertions(+), 31 deletions(-) [+]
line wrap: on
line diff
--- 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" );
--- 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(
 <!DOCTYPE html>
 <html>
@@ -29,25 +29,7 @@
 </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");
@@ -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 (<QC>) {
 	chomp;
 	my @row = split(/\t/, $_);
@@ -215,18 +197,10 @@
 $excelBook->close();
 my @resCnt = map { $rescnt{$_} || 0 } qw/Falcosnp Falcoindel/;
 my $pctGood = sprintf("%.2f", $amp100 / scalar(keys(%QC)) * 100);
-#print INDEX "<tr><td><a href=$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;
 
-