my $count = 0;
 44     my $priorScaffold;
 45     my $priorChr;
 46     my @finalArray;
 47     open (IN, '<', $fileName) or die "Cannot open $fileName\n";
 48     LINE: while (my $line = <IN>){
 49         chomp $line;
 50         if ($line =~ m/^>\w+/){
 51             next LINE;
 52         }
 53         my @dataLine = split /\t/, $line;
 54         my $chr = $dataLine[5];
 55         next LINE if ($chr !~ /^\d{1,2}?$/);
 56         my $scaffold = $dataLine[0];
 57         if ($count != 0){
 58             if ($scaffold ne $priorScaffold){                                       #If we found a new scaffoldd
 59                 push @{$global{$priorChr}{$priorScaffold}}, @finalArray;            #write to hash @finalArray using prior accumulated data for last scaffold    
 60                 $count = 0 ;
 61                 $allScaffolds{$priorScaffold}=0;                                    #Save priorScaffold in allScaffolds Hash for list use later- value is meaningless
 62                 @finalArray = ();
 63             }
 64             elsif ($chr != $priorChr){                                                 #If we just switched Chromosomes but are still on the same scaffold
 65                 push @{$global{$priorChr}{$priorScaffold}}, @finalArray;            #write to global the @finalArray accumulated to the point it switches chromosomes    
 66                 $count = 0;
 67                 @finalArray = ();
 68             }
 69         }
 70         push @{$finalArray[$count]},  @dataLine;
 71         $priorScaffold = $scaffold;
 72         $priorChr = $chr;
 73         $count ++;
 74         print "$line\n";
 75         print join ("\t", @dataLine)."\n";
 76     }


##</code><code>##

 DB<1> b 54 $dataLine[2] = uninitialized                                                                                                                                       
  DB<2> c                                                                                                                                                                       
This program requires 4 command line arguments
Input File from as MizBee output from SyntenyFinder as first
Input File listing all scaffolds and total lengths from the query genome
Output FILE name to be used as basis for creation of MizBee input file and tmp file you can deleteA NUMERIC integer value specifying the cut off value for scaffold EXCLUSION from visualization
This value is used to eliminate scaffolds with less then VAL hits on any given chromosome
THIS ONLY ELIMINATES THE SCAFFOLD VISUALIZATION FOR THAT CHROMOSOME



main::syntenyLoad(MizBEE_parseOUT.pl:54):
54:	        my $chr = $dataLine[5];
  DB<2> x $line                                                                                                                                                                 
0  "GL429767\cI42604\cI226589\cI0\cI1\cI7\cI100487615\cI100493753\cI550\cI-1\cI0.8748\cIENSMLUG00000029214\cIENSG00000087085\cI"
  DB<3> x split /\t/, $line                                                                                                                                                     
0  'GL429767'
1  42604
2  226589
3  0
4  1
5  7
6  100487615
7  100493753
8  550
9  '-1'
10  0.8748
11  'ENSMLUG00000029214'
12  'ENSG00000087085'
  DB<4> x @dataLine                                                                                                                                                             
0  'GL429767'
1  42604
2  'uninitialized'
3  0
4  1
5  7
6  100487615
7  100493753
8  550
9  '-1'
10  0.8748
11  'ENSMLUG00000029214'
12  'ENSG00000087085'
  DB<5>