#!/usr/bin/perl
# repeatscan.perl
# cat $outblat | perl -n repeatscan.perl

## some of these are good looking genes (but maybe repeatetive protein struct...)
## tandy should probably just flag repeats not filter them.

my $MINREP=50;
my (%xrepeats, %grepeats);
while(<>){ 
  chomp; my @v=split"\t"; 
  my($qid,$ref,$pctid,$alen,$tb,$te,$eval,$bits)=@v[0,1,2,3,8,9,10,11]; 
  # if($eval > $MINEVAL) { next;  } # should filter MINEVAL or esp. MINALIGN

  $xrepeats{$qid}++;
  my($geneid,$exnum,$xloc)= split_exonid($qid, 1);
  $grepeats{$geneid}{$exnum}++;
}  
  
END{
  my @xids= sort{$xrepeats{$b} <=> $xrepeats{$a}} keys %xrepeats;
  foreach my $qid (@xids) {
    my $nrep= $xrepeats{$qid};
    next if ($nrep < $MINREP);
    my($geneid,$exnum,$xloc)= split_exonid($qid, 1);
    my @ex= sort keys %{$grepeats{$geneid}};
    my $minrep= $nrep;
    foreach my $ex (@ex) {
      my $xrep= $grepeats{$geneid}{$ex};
      $minrep= $xrep if($xrep < $minrep);
      }
    next if($minrep < $MINREP);
    my $nx= @ex;
    print "#Rep: $geneid nexon=$nx; nrep=$nrep; minrep=$minrep; \n";
    }
}

sub split_exonid {
  local $_= shift;
  my $dropnum= shift; $dropnum ||= 0;
  my ($exnum, $exloc, $exeq)=(0,"",-1);
  s/^[\+\*\@\%\#\&]*//; # drop marks  at ^front; or s/^\W+//;
  s/\=([\d\-]+)$// and  $exeq=$1; # added; testing
  s/\:([\d\-]+)$// and  $exloc=$1;
  if($dropnum && s/\.(\d+)$//) { $exnum= $1; };
  return (wantarray) ? ($_,$exnum,$exloc,$exeq) : $_;  
}