...
 while($line = <$IFH> ){
     chomp $line;
     if(not($line eq "")) { ##### why does $line equal "" ?
       my @tmp = split(//,$line);
...
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what does $line = ""; mean?

If the "#####" comment is anything to go by, then a test for "not empty line" is being done in "not( $line eq "" )".

In that case your question is actually different than the comment, where you assign an empty string to $line variable.