pwy nodes
A a b c d e f
B a b c

##</code><code>##

de A
ef A
ab B
ac B
bc B

##</code><code>##

my $in=$ARGV[0] || "pathways.col";
open (IN,$in) or die "cannot open $in\n";
my %HoCplx2ID; my %HoPwyPair;
while (my $lines=<IN>){
        next if ($lines =~/^#/);
        next if ($lines =~/^UNIQUE-ID/);
        chomp $lines;
        my @cols=split(/\t/,$lines);
        my $cmplxID=$cols[0];
        #print $cmplxID."\n";
        my $cmplxNm=$cols[1];
        my @restCols=@cols[2..$#cols];
        my @cycIDs=grep(/^GCXG-/, @restCols);
        @cycIDs=grep($_ ne '',@cycIDs);
        print "cycIDs array\n";
        print Dumper(@cycIDs);
        my $pwySize=scalar(@cycIDs);
        push (@{$HoCplx2ID{$cmplxID}},@cycIDs);
        for (my $i=0; $i < ($pwySize-1); $i++){
                my $pair =join("\t",$cycIDs[$i],$cycIDs[$i+1]);
                $HoPwyPair{$pair}{$cmplxID}=$pwySize;
        }

}
close(IN);
########## print out pairwise with PA01 locusIDs ######
my $org=$ARGV[1]|| "PA01";
my $outfile="$in.$org.pairwise.nxtNeighb.tab";
#open (OUT,">",$outfile);
### step 1 for each pair find smallest pathway
my %HoSmPwy;
foreach my $pair (keys %HoPwyPair){
        $HoSmPwy{$pair}=100;
        foreach my $pwy (keys %{$HoPwyPair{$pair}}){
                if ($HoPwyPair{$pair}{$pwy} < $HoSmPwy{$pair}) {
                        $HoSmPwy{$pair}=$HoPwyPair{$pair}{$pwy};
                }
        }
}
print "hash of smallest pathways\n";
#print Dumper(%HoSmPwy);
### step 2 for each pathway, look at each pair if that pwy size = smallest pathway , then print ##
print "output\n";
foreach my $pwy (keys(%HoCplx2ID)){
        my @units=@{$HoCplx2ID{$pwy}};
        my $pwySize=scalar(@units);
        for (my $i=0; $i < ($pwySize-1); $i++){
        my $pair =join("\t",$units[$i],$units[$i+1]);
                if ($pwySize = $HoSmPwy{$pair}) {
                #       print $pair."\n";
                }
        }
}

####