#!/usr/bin/perl
# tdovermodel.perl
# input gff sorted by location with largest span above; need <10b slop for that?
# use: cat gnomon.genes gleanr.genes | sort -k1,1 -k4,4n -k5,5nr -k2,2 | perl tdovermodel.pl

my %predna=();
# overGnomonGleanr();
overallmodels();

END{ 
my @k=sort keys %od; my $p;
if(scalar %predna) {
print "pred key: "; map{ $p=$predna{$_}||$_; print "$_=$p, "; }@k; print"\n\n";
}
print "Overextended tandem models: "; map{ $p=$predna{$_}||$_; print "\t$p=",$od{$_} }@k; print"\n";
print "      Inside tandem models: "; map{ $p=$predna{$_}||$_; print "\t$p=",$dp{$_} }@k; print"\n";
}

#........

sub overGnomonGleanr {

while(<>){ # gff in sorted by location
  chomp; my($tr,$ts,$tt,$tb,$te,$tp,$to)=split;
  my($gr)=m/ID=(\D+)/; 

    # fixme: for all predictors; find largest group of inside/tandem genes from tandem regions
    # need really dmel.aa blastp scores
    
  $gr=($gr=~/NCBI/)?"NCBI":"GLNR"; 
  my $og=($gr=~/NCBI/)?"GLNR":"NCBI"; 
  
  $tb = int($tb/10); $te = int($te/10); # for slop  
  # _overlap not good enough; need _insideof 
  if( _inside([$tr,$tb,$te],$lg{$og}) and _inside($lg{$gr},$lg{$og}) ) { 
    $od{$og}++; $dp{$gr}+=2;
    print "O1-$og:",$lg{$og}->[3],"\n";
    print "D1-$gr:",$lg{$gr}->[3],"\n";
    print "D2-$gr:$_\n\n"; 
    }
    
  $lg{$gr}=[$tr,$tb,$te,$_];
}
}

sub overallmodels {

my $grnum=0;
while(<>){ # gff in sorted by location
  chomp; my($tr,$ts,$tt,$tb,$te,$tp,$to)=split;
  my($gr)=m/ID=(\D+)/; 

    # fixme: for all predictors; find largest group of inside/tandem genes from tandem regions
    # need really dmel.aa blastp scores
    
  unless( $grid= $preds{$gr} ) { $grid= $preds{$gr}= ++$grnum; $predna{$grid}= $gr; }  
  
  $gr= $grid;
  # my $og=($gr=~/NCBI/)?"GLNR":"NCBI"; 
  
  #$tb = int($tb/10); $te = int($te/10); # for slop  
  $tb = int($tb/4); $te = int($te/4); # for slop  

  foreach my $og (1 .. $grnum) {
    next if ($og == $grid);
    if( _inside([$tr,$tb,$te], $lg{$og}) and _inside( $lg{$gr}, $lg{$og}) ) { 
      $od{$og}++; 
      $dp{$gr} += 2;
      
      print "O-$og:",$lg{$og}->[3],"\n";
      print "D-$gr:",$lg{$gr}->[3],"\n";
      print "D-$gr:$_\n\n"; 
      }
  }
  
  $lg{$gr}=[$tr,$tb,$te,$_];
}

}


sub _overlap { 
  my($a,$b)=@_; 
  return ($a and $b and $a->[0] eq $b->[0] and $a->[1] < $b->[2] and $a->[2] > $b->[1]) ? 1 : 0; 
}

sub _inside { # a is inside b (touching one/both ends, with <10b slop? 
  my($a,$b)=@_; 
  return ($a and $b and $a->[0] eq $b->[0] and 
    $a->[1] >= $b->[1] and $a->[1] < $b->[2] and
    $a->[2] <= $b->[2] and $a->[2] > $b->[1]) ? 1 : 0; 
}