UNIX for Dummies Questions & Answers

#!/usr/bin/perl
print "Enter minimum coverage: ";
chomp($min_cov=<STDIN>);
print "Enter minimum novel_Allele_Starts: ";
chomp($min_nas=<STDIN>);
open I, "$ARGV[0]";
while (<I>){
  @F=split;
  $F[8]=~/coverage=([^;]+)/;
  $cov=$1;
  $F[8]=~/novelAlleleStarts=([^;]+)/;
  $nas=$1;
  if ($cov>=$min_cov && $nas>=$min_nas){
    $cov{$F[0]}{$F[3]}+=$cov;
    $nas{$F[0]}{$F[3]}+=$nas;
  }
  $n{$F[0]}{$F[3]}++;
  $h{$F[0]}++;
}
END{
  @sorted_cov=sort {$a cmp $b} keys %cov;
  for $i (@sorted_cov){
    for $j (keys %{$cov{$i}}){
      print "$i\t$j\t";
      printf "%.1f\t", ($cov{$i}{$j}/$n{$i}{$j});
      printf "%.1f\n", ($nas{$i}{$j}/$n{$i}{$j});
    }
  }
  @sorted_h=sort {$a cmp $b} keys %h;
  for $i (@sorted_h){
    print "$i\t$h{$i}\n";
    $t+=$h{$i};
  }
}

  if ($cov>=$min_cov && $nas>=$min_nas){
    $cov{$F[0]}{$F[3]}+=$cov;
    $nas{$F[0]}{$F[3]}+=$nas;
    $n{$F[0]}{$F[3]}++;
    $h{$F[0]}++;
  }
}

$lines=join ("", $_);

$lines=$_++;

if ($cov>=$min_cov && $nas>=$min_nas){
    $cov{$F[0]}{$F[3]}+=$cov;
    $nas{$F[0]}{$F[3]}+=$nas;
    $n{$F[0]}{$F[3]}++;
    $h{$F[0]}++;
    $lines.=$_;
  }