LEAFF(1)

🦋 NAME 🦋

okay so, bestie, meet leaff — sequence library utilities and applications 💖. This is the LEAFF(1) page from the General Commands Manual, and we're gonna read it together like it's a group chat, no cap ✨.

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🌸 SYNOPSIS 🌸

leaff [-f fasta-file] [options]

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✨ DESCRIPTION ✨

LEAFF stands for Let's Extract Anything From Fasta (yes, the name is literally iconic 💅) and it's a utility program for working with multi-fasta files. Not only does it give you random access to the base level, it also comes with a whole little friend group of analysis functions 🫶. It's giving swiss army knife. It's giving main character energy 🔥.

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🎀 OPTIONS 🎀

💜 SOURCE FILES

• -f file — use the sequence in file. (-F is also allowed, for historical reasons, so if you see -F don't panic, it's the same vibe 💀)
• -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 at all, queen 😌
• -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 — so pls don't, it will simply not slay 🙈
• -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 the 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).

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😭 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.

And the one that gets everybody: SEQUENCES are numbered starting at ZERO, not one! fr fr, zero. not one. zero 🫠

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🌟 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

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💖 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

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and that's the whole page, bestie 🎀 this was the LEAFF(1) manual from January 2016 — go extract literally anything from fasta, you got this 💅✨