remove parse_cnvkit_table.pl

variants/parse_cnvkit_table.pl

-#!/usr/bin/perl -w
-#parse_cnvkit_table.pl
-
-my @keep = ("AKT2","ATM","AURKA","BAP1","BCL2L1","BCL6","BIRC3","BRCA2","CCND1","CCNE1","CD79B","CDK8","CDKN2A","CDKN2B","CEBPA","EGFR","ERBB2","FGF10","FGF14","FGF19","FGF3","FGF4","FLT1","FLT3","FOXP1","GATA6","GNA13","GNAS","IKZF1","IL7R","IRS2","KDM4C","KLHL6","KMT2A","KRAS","LYN","MCL1","MITF","MYC","NOTCH2","PIK3CA","PRKAR1A","PRKDC","PTEN","RB1","RICTOR","RUNX1T1","SDHA","TFDP1","TP53","ZNF217");
-
-my %keep = map {$_ => 1} @keep;
-
-
-my @cvncalls = @ARGV;
-foreach my $file (@ARGV) {
-    open IN, "<$file" or die $!;
-    my $out = $file;
-    $out =~ s/call.cns/cnvcalls.txt/;
-    open OUT, ">$out" or die $!;
-    print OUT join("\t","CHROM","START","END","LEN","CN","DEPTH",
-		   "Probes","Weight","GeneIDs"),"\n";
-    my $header = <IN>;
-    while (my $line = <IN>) {
-	chomp($line);
-	my ($chr,$start,$end,$geneids,$log2,$cn,$depth,
-	    $probes,$weight) = split(/\t/,$line);
-	my %genes;
-	my @ids = split(/;|,/,$geneids);
-	foreach my $gid (@ids) {
-	    my ($key,$value) = split(/=/,$gid);
-	    if ($key eq 'ensembl_gn' || $key eq 'identifier') {
-		$genes{$value} = 1 if $keep{$value};
-	    }
-	}
-	my $newgeneids = join(";", keys %genes);
-	my $len = sprintf("%.1f",($end-$start)/1000000);
-	next if ($cn == 2) || scalar(keys %genes) < 1;
-	print OUT join("\t",$chr,$start,$end,$len,$cn,$depth,
-		       $probes,$weight,$newgeneids),"\n";
-    }
-    close IN;
-    close OUT;
-}