I have two files ptt.txt and mapped.txt : 
ptt.txt 
Location Strand Length PID Gene Synonym Code COG + Product 1..1524 + 5
+07 15607143 dnaA Rv0001 - COG0 +593L chromosomal replication initiato
+r 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

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

[download]
my code is 

$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;}
}


}}}

[download]
I want to find out if the third column of mapped.txt lies within the range of first column of ptt.txt

In reply to compare third column of one file with the first column of another by Anonymous Monk

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