usage: leaff [-f fasta-file] [options]

   -f file:     use sequence in 'file' (-F is also allowed for historical reasons)
   -A file:     read actions from 'file'

   -d:          print the number of sequences in the fasta
   -i name:     print an index, labelling the source 'name'

   -6 <#>:      insert a newline every 60 letters
                  (if the next arg is a number, newlines are inserted every
                  n letters, e.g., -6 80.  Disable line breaks with -6 0,
                  or just don't use -6!)
   -e beg end:  Print only the bases from position 'beg' to position 'end'
                  (space based, relative to the FORWARD sequence!)  If
                  beg == end, then the entire sequence is printed.  It is an
                  error to specify beg > end, or beg > len, or end > len.
   -ends n      Print n bases from each end of the sequence.  One input
                  sequence generates two output sequences, with '_5' or '_3'
                  appended to the ID.  If 2n >= length of the sequence, the
                  sequence itself is printed, no ends are extracted (they
   -C:          complement the sequences
   -H:          DON'T print the defline
   -h:          Use the next word as the defline ("-H -H" will reset to the
                  original defline
   -R:          reverse the sequences
   -u:          uppercase all bases

   -G n s l:    print n randomly generated sequences, 0 < s <= length <= l
   -L s l:      print all sequences such that s <= length < l
   -N l h:      print all sequences such that l <= % N composition < h
                  (NOTE 0.0 <= l < h < 100.0)
                  (NOTE that you cannot print sequences with 100% N
                   This is a useful bug).
   -q file:     print sequences from the seqid list in 'file'
   -r num:      print 'num' randomly picked sequences
   -s seqid:    print the single sequence 'seqid'
   -S f l:      print all the sequences from ID 'f' to 'l' (inclusive)
   -W:          print all sequences (do the whole file)

   -help analysis
   -help examples