>SEQUENCE-ID-STRING commentary string
SEQUENCE_LETTERS_AT_MOST_80_PER_LINE...

##</code><code>##

# require that there be three file name args on the command line:
#  -- input file1
#  -- input file2
#  -- output file

# for each input file:
#   open it
#   read one line at a time
#     chomp the line to remove final line-feed
#     if line starts with ">", it's the start of a new sequence, so:
#        if there was a sequence before this one, save it in  %seq_hash
#        set current sequence to an empty string

#     otherwise, line starts with a letter, so:
#        append contents of line to current sequence

# After reaching the end of the second file, save current sequence in %seq_hash

# open the output file
# Loop over the keys of %seq_hash
#    write the ID-string to the output file
#    if necessary, add line-feeds into the sequence string at 80-char intervals 
#    write the sequence string to the output file