PA5098  PA5100  PA5092  PA3175

##</code><code>##

PA5098  PA5100  1
PA5098  PA5092  2
PA5098  PA3175  3
PA5100  PA5092  1
PA5100  PA3175  2
PA5092  PA3175  1

##</code><code>##

PA5098	 PA5100	1
PA5098	 PA5092	2
PA5098	 PA3175	3
PA5100	 PA5092	2
PA5100	 PA3175	3
PA5092	 PA3175 3

##</code><code>##

############# open pathways output list with PA01 locus IDs
my $in=$ARGV[1] || "pathways.col";
open (IN,$in) or die "cannot open $in\n";
##
my $out="$in.$org.stepSize.tab";
open(OUT,">",$out);
#
my %HoCplx2ID; my %HoPwyPair;my %HoPairs;
while (my $lines=<IN>){
        next if ($lines =~/^#/);
        next if ($lines =~/^UNIQUE-ID/);
        chomp $lines;
        my @cols=split(/\t/,$lines);
        my $cmplxID=$cols[0];
        my $cmplxNm=$cols[1];
        my @restCols=@cols[2..$#cols];
        my @cycIDs=grep(/^GCXG-/, @restCols);
        @cycIDs=grep($_ ne '',@cycIDs);
        my $pwySize=scalar(@cycIDs);
        push (@{$HoCplx2ID{$cmplxID}},@cycIDs);
}
close(IN);
###########
my %HoP;
foreach my $pwy (keys %HoCplx2ID){
        my @genes=@{$HoCplx2ID{$pwy}};
        my $numbGenes=scalar(@genes);
                for (my $i=0;$i<$numbGenes;$i++){
                for (my $j=1;$j<$numbGenes;$j++){
                                                         my $pair=join("-",$HoCycID2Loc{$genes[$i]},$HoCycID2Loc{$genes[$j]});
                        my $rev_pair=join("-",$HoCycID2Loc{$genes[$j]},$HoCycID2Loc{$genes[$i]});
                        if (($genes[$i] ne $genes[$j]) && (!exists($HoP{$rev_pair}))){
                                print OUT join("\t",$HoCycID2Loc{$genes[$i]},$HoCycID2Loc{$genes[$i+1]},$j)."\n";
                                $HoP{$pair}=1;
                }
        }
        }
        }