#!/usr/bin/awk -f
# Extract the sequences in a fasta file.
# One entire sequence per line out.

/^>/ { # then we have a; definition line.
  # Print out the previous sequence if there was one.
  if ( seq )  {
    print seq;
    seq = ""; # and start anew.
  }
  next; # Ignore (strip) the definition line.
}

# Ignore (strip) comment lines.
/^ *;/ { next; }

# Collect sequence.
{ seq = seq $0; }

END { if ( seq ) print seq; }