#!/usr/bin/perl -w

# perl /home/xiangyang/Chen_genome/perl_bin/ANI_bacth_patall.pl 15 > jspecies.conf

my $subfile_number=$ARGV[0];
my $count1=0;
my $count2=0;
my %hash;
my @array_1;
my @array_3;

my $tt=1;

open (LIST, "/home/xiangyang/Chen_genome/chen_List");

my @left=<LIST>;
my $genome_num=scalar @left;
my $sub_total_ani=$genome_num*($genome_num-1)/2/$subfile_number;
###################################################################################################################### 
 for (my $q=1; $q<$sub_total_ani+1;$q++){
     my @array_2;
     $hash{$q}=\@array_2;                                                #####ref
                                        }

for (my $i=0; $i<$genome_num; $i++){
          push (@array_1, "GENOME=$left[$i]");
                                    }

for (my $i=0; $i<scalar @left; $i++){
for(my $k=$i+1; $k<scalar @left; $k++){
        $count1++;
        $count2++;
        if ($count1>$sub_total_ani){
            $tt=int ($count2/$sub_total_ani)+1;
            $count1=$count2-$sub_total_ani*($tt-1); 
                                  }
            $left[$i]=~s/(\s)*//g;
            $left[$k]=~s/(\s)*//g;

            push ($hash{$tt}, "ANIm=$left[$i]_vs_$left[$k].delta\n");    #####ref
                                       }
                                    }
###################################################################################################################### 
push(@array_3, 
"ANImM=mum
ANImB=200
ANImC=65
ANImG=90
ANImO=true
ANImI=20");

my @array_13=(@array_1,@array_3);
for (my $kk=1; $kk<$subfile_number+1; $kk++){
      open $kk, ">file_$kk.jspecies.conf";
      my @array_ref=@{$hash{$kk}};                                       #####ref
      my @array_123=(@array_1,@array_ref,@array_3);
      print $kk @array_123;
                                        }


# system ('java -jar -Xms1024m -Xmx1024m /home/xiangyang/Desktop/ANI_tool/jspecies1.2.1.jar');