my %patterns = 
(
  comment => qr/#.*/,
  leadingSpaces => qr{$^\s+},
  trailingSpaces => qr{\s+$},
  leadingComma => qr/^,/
);

while(my $line = <FILE1>)
{
  $line =~ s/$_// for %patterns{qw/comment trailingSpaces/};
}