That's a different question...

...the while(substr($line2, 0 , 3) ne "---") loop will certainly stop when $line2 is dashed. However, you enter the loop with $line2 set to the "Gene:" line you just processed, and at the top of the loop you read the next line. So, a dashed line is processed in the loop, and then brings the loop to a halt.

The inner loop could be recast:

while ($line2=<geneREAD>) {
  chomp $line2 ;
  if (substr($line2, 0 , 3) eq "---") { break ; } ;

  ....
} ;
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...mind you, you might want to check that the "Gene:" line is followed by something ? But that is part of the general problem of verifying the input.