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'
SOURCE FILE EXAMINATION
-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
-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)