Found it: ...

...
 my $columnID = $column[0];
 foreach ( my $columnID )
 {
  while ( $columnID =~ /(^FBgn\d+)/ )
  {
   my $ID = $1;
   print $ID, "\n";
  }
 }
...
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I'm not sure if you mean that you've found a solution or a problem (or perhaps it refers to some out-of-band discussion, e.g., the Chatterbox), but the quoted loop code is puzzling:

• my $columnID = $column[0]; defines and assigns a value to a lexical that is never accessed in the remainder of its scope;
• foreach ( my $columnID ) { ... } defines a masking lexical that is assigned no value and so is undefined by default;
• while ( $columnID =~ /(^FBgn\d+)/ ) { ... } matches the undefined masking lexical (odd that this produced no warning message... you do have warnings enabled, don't you?) against a pattern that cannot possibly match it (if there were a match, the loop would run forever).

c:\@Work\Perl\monks>perl -le
"use strict;
 use warnings;
 ;;
 my $columnID = 'XXX';
 foreach ( my $columnID )
 {
  while ( $columnID =~ /(^X)/ )
  {
   my $ID = $1;
   print qq{$ID \n};
  }
 }
"
Use of uninitialized value in pattern match (m//) at -e line 1.
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