LEAFF(1)

NAME
leaff - sequence library utilities and applications

SYNOPSIS
leaff [-f fasta-file] [options]

DESCRIPTION
LEAFF (Let's Extract Anything From Fasta) is a utility program for working with multi-fasta files. In addition to providing random access to the base level, it includes several analysis functions.

OPTIONS
SOURCE FILES
   -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' OUTPUT OPTIONS
   -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
                  overlap).
   -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 SEQUENCE SELECTION
   -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) LONGER HELP
   -help analysis
   -help examples ANALYSIS FUNCTIONS
   --findduplicates a.fasta
                Reports sequences that are present more than once. Output
                is a list of pairs of deflines, separated by a newline.
   --mapduplicates a.fasta b.fasta
                Builds a map of IIDs from a.fasta and b.fasta that have
                identical sequences. Format is "IIDa <-> IIDb"
   --md5 a.fasta:
                Don't print the sequence, but print the md5 checksum
                (of the entire sequence) followed by the entire defline.
   --partition prefix [ n[gmk]bp | n ] a.fasta
   --partitionmap [ n[gmk]bp | n ] a.fasta
                Partition the sequences into roughly equal size pieces of
                size nbp, nkbp, nmbp or ngbp; or into n roughly equal sized
                partitions. Sequences larger that the partition size are
                in a partition by themself. --partitionmap writes a
                description of the partition to stdout; --partiton creates
                a fasta file 'prefix-###.fasta' for each partition.
                Example: -F some.fasta --partition parts 130mbp
                        -F some.fasta --partition parts 16
   --segment prefix n a.fasta
                Splits the sequences into n files, prefix-###.fasta.
                Sequences are not reordered; the first n sequences are in
                the first file, the next n in the second file, etc.
   --gccontent a.fasta
                Reports the GC content over a sliding window of
                3, 5, 11, 51, 101, 201, 501, 1001, 2001 bp.
   --testindex a.fasta
                Test the index of 'file'. If index is up-to-date, leaff
                exits successfully, else, leaff exits with code 1. If an
                index file is supplied, that one is tested, otherwise, the
                default index file name is used.
   --dumpblocks a.fasta
                Generates a list of the blocks of N and non-N. Output
                format is 'base seq# beg end len'. 'N 84 483 485 2' means
                that a block of 2 N's starts at space-based position 483
                in sequence ordinal 84. A '.' is the end of sequence
                marker.
   --errors L N C P a.fasta
                For every sequence in the input file, generate new
                sequences including simulated sequencing errors.
                L -- length of the new sequence. If zero, the length
                     of the original sequence will be used.
                N -- number of subsequences to generate. If L=0, all
                     subsequences will be the same, and you should use
                     C instead.
                C -- number of copies to generate. Each of the N
                     subsequences will have C copies, each with different
                     errors.
                P -- probability of an error.
                HINT: to simulate ESTs from genes, use L=500, N=10, C=10
                        -- make C=10 sequencer runs of N=10 EST sequences
                        of length 500bp each.
                      to simulate mRNA from genes, use L=0, N=10, C=10
                      to simulate reads from genomes, use L=800, N=10, C=1
                        -- of course, N= should be increased to give the
                        appropriate depth of coverage
   --stats a.fasta
                Reports size statistics; number, N50, sum, largest.
   --seqstore out.seqStore
                Converts the input file (-f) to a seqStore file (for instance,
                for use with the Celera assembler or sim4db).

NOTES
Please note that options are ORDER DEPENDENT. Sequences are printed whenever a SEQUENCE SELECTION option occurs on the command line. OUTPUT OPTIONS are not reset when a sequence is printed.

SEQUENCES are numbered starting at ZERO, not one!

EXAMPLES
1. Print the first 10 bases of the fourth sequence in file 'genes':
    leaff -f genes -e 0 10 -s 3 2. Print the first 10 bases of the fourth and fifth sequences:
    leaff -f genes -e 0 10 -s 3 -s 4 3. Print the fourth and fifth sequences reverse complemented, and the sixth
    sequence forward. The second set of -R -C toggle off reverse-complement:
    leaff -f genes -R -C -s 3 -s 4 -R -C -s 5 4. Convert file 'genes' to a seqStore 'genes.seqStore'.
    leaff -f genes --seqstore genes.seqStore

SEE ALSO
README.leaff
http://kmer.sourceforge.net/wiki/index.php/LEAFF_User%27s_Guide
http://kmer.sourceforge.net/wiki/index.php/LEAFF_Programming_Example