# Print open reading frames.
# /[A-Z]+\*/ does not require a start codon, but does require a stop.
# /M[A-Z]*\*/ requires both a start and stop codon.
# /(^|M)[A-Z?]*(\*|$)/ requires start or beginning of line and stop or end of line.
# Prints an empty line if there are no ORFs in the line in.
# BUG: prints an extra space at the end of each line that has an ORF.
while (<>) {
  while ( /(^|M)[A-Z?]*(\*|$)/go ) {
    print "$& ";
  }
  print "\n";

# Why doesn't the following work? The list includes the submatches in all parentheses.
# @orfs, /(^|M)[A-Z?]*(\*|$)/g;

# This works pretty well, except can't get beginning of line.
# @orfs = /M[A-Z?]*\*?/g;
# print "@orfs\n";

# This below is the same as above:
# print join( ' ', /M[A-Z?]*\*?/g ), "\n";

}