Hi, I want to compare two files on the basis of two different Ids, and want to print something, if the Ids matched.

I opened the two files and used while loop (i.e. while within while). The if condition of this prog. is working good, but else condition will give lots of lines, because of while within while.. "last;" is also not working here..

Please help me to solve this

file 1 

 
chr17    69112551
chr7    151046672
chr7    151047369

[download]
file 2 
chr1    66953622    66953654
chr1    67200451    67200472
chr1    67200475    67200478
chr1    67058869    67058880
chr1    67058881    67058885
chr1    67058887    67058895

[download]

Perl prog. 

#!/usr/bin/perl -w

$pwd = `pwd`;
chomp($pwd);

$file=$ARGV[0];
$file1=$ARGV[1];

open(IN,$file);
while ($line=<IN>){
chomp($line);

@ary = split(/\t/,$line);
chomp($ary[0]);chomp($ary[1]);

open(SK,$file1);
while($line1=<SK>)
{
    @any = split(/\t/,$line1);
    chomp($any[0]); chomp($any[0]);chomp($any[1]);chomp($any[2]);
if ($ary[0] eq $any[0] and $ary[1] == $any[1]) or ($ary[0] eq $any[0] 
+and $ary[1] == $any[2]) 
{
    print "$line\tE\n";
    
}
else
{ print "$line\tM\n";
}

}
}

[download]

In reply to compare two files on the basis of Two IDs by genome

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