--- name: "leaff" section: "1" platform: "linux" package: "leaff" version: "0~20150903+r2013-9+b1" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/leaff" --- # leaff(1) sequence library utilities and applications ## 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