#!/usr/bin/perl
$dir="D:/cagenome/consig/package"; #directory of the package
$genelist="Mitelman2008.all.id"; #fusion (Mitelman2008.all.id) or point mutation gene list (CGC_Mutation_2008-11-05.id)
$concept2gene="concepts2gene_v111808.delparent"; #concept2gene mapping
open (A,"$dir/$genelist");
while (<A>)
  {
  chomp;
  my @l=split(/\t/);
  if (exists $l[0] and $l[0]=~/\d+/)
    {
    $input{$l[0]}=1;
    }
  }
my $i=0;
foreach $gene (keys %input)
 {
 $i++;
 }
open (C,"$dir/$concept2gene");
while (<C>)
{
chomp;
my @l=split(/\t/);
$map{$l[0]}{$l[1]}=1;
$term{$l[0]}="$l[2]\t$l[3]\t$l[4]";
}
open (RE,">$dir/$genelist.concepts");
foreach $concept (keys %map)
{
my ($t,$n)=(0,0);
foreach $geneid(keys %{$map{$concept}})
 {
 if (exists $input{$geneid})
  {
  $t++;
  }
 $n++;
 }
print RE "$concept\t$term{$concept}\t$t\t$n\t$i\n";
}
print "done";