ptt.txt 
Location Strand Length PID Gene Synonym Code COG + Product 1..1524 + 507 15607143 dnaA Rv0001 - COG0 +593L chromosomal replication initiator protein DnaA 2052..3260 + 402 15607144 dnaN Rv0002 - COG0592L + DNA polymerase III subunit beta 3280..4437 + 385 15607145 recF Rv0003 - COG1195L + DNA replication/repair protein RecF

##</code><code>##

mapped.txt
gi|50953765|ref|NC_002755.2|-587160 83 gi|448814763|ref|NC_00096 +2.3| 1329307 

##</code><code>##


$file="mapped.txt";

open (FH1, "$file");
open (FA, ">>allassignment.txt");
while ($seq1=<FH1>)
{
@seq1=split (/\t/, $seq1);
$pos1=@seq1[3];



open (FH, "ptt.txt");
while ($seq=<FH>)
{
@seq=split (/\t/, $seq);
$pos=@seq[0];
$pos8=@seq[8];
chomp $pos8;
@pos=split(/\.\./, $pos);
$pos_start=@pos[0];
$pos_end=@pos[1];


for ($i=$pos_start, $i<=$pos_end, $i++)
{if ($i=~m/^$pos1$/)
{$position1=@seq1[0]; $position8=@seq1[8]; $position9=@seq1[9];

print FA $i."\t".$pos1."\t".$pos."\t".$pos8."\t".$pos1."\t".$position1."\t".$position8."\t".$position9."\n" ;
last;}
}


}}}