wang-q / faops

faops operates fasta files

faops operates fasta files

faops is a lightweight tool for operating sequences in the fasta format.

This tool can be regarded as a combination of faCount, faSize, faFrag, faRc, faSomeRecords, faFilter and faSplit from UCSC Jim Kent's utilities.

Comparing to Kent's fa* utilities, faops is:

• much smaller (kilo vs mega bytes)
• easy to compile (only one external dependency)
• well tested
• contains only one executable file
• can operate gzipped (bgzipped) files
• and can be run under all major OSes (including Windows).

faops is also inspired/influenced/stealing from seqtk and ufasta.

$ ./faops

Usage:     faops <command> [options] <arguments>
Version:   0.8.21

Commands:
    help           print this message
    count          count base statistics in FA file(s)
    size           count total bases in FA file(s)
    masked         masked (or gaps) regions in FA file(s)
    frag           extract sub-sequences from a FA file
    rc             reverse complement a FA file
    one            extract one fa record
    some           extract some fa records
    order          extract some fa records by the given order
    replace        replace headers from a FA file
    filter         filter fa records
    split-name     splitting by sequence names
    split-about    splitting to chunks about specified size
    n50            compute N50 and other statistics
    dazz           rename records for dazz_db
    interleave     interleave two PE files
    region         extract regions from a FA file

Options:
    There're no global options.
    Type "faops command-name" for detailed options of each command.
    Options *MUST* be placed just after command.

Examples

• Reverse complement

    faops rc test/ufasta.fa out.fa       # prepend RC_ to names
    faops rc -n test/ufasta.fa out.fa    # keep original names
  

• Extract sequences with names in list.file, one name per line

    faops some test/ufasta.fa list.file out.fa
  

• Same as above, but from stdin and to stdout

    cat test/ufasta.fa | faops some stdin list.file stdout
  

• Sort by header strings

    faops order test/ufasta.fa \
        <(cat test/ufasta.fa | grep '>' | sed 's/>//' | sort) \
        out.fa
  

• Sort by lengths

    faops order test/ufasta.fa \
        <(faops size test/ufasta.fa | sort -n -r -k2,2 | cut -f 1) \
        out2.fa
  

• Tidy fasta file to 80 characters of sequence per line

    faops filter -l 80 test/ufasta.fa out.fa
  

• All content written on one line

    faops filter -l 0 test/ufasta.fa out.fa
  

• Convert fastq to fasta

    faops filter -l 0 in.fq out.fa
  

• Compute N50, clean result

    faops n50 -H test/ufasta.fa
  

• Compute N75

    faops n50 -N 75 test/ufasta.fa
  

• Compute N90, sum and average of contigs with estimated genome size

    faops n50 -N 90 -S -A -g 10000 test/ufasta.fa
  

Compiling

faops can be compiled under Linux, macOS (gcc or clang) and Windows (MinGW).

git clone https://github.com/wang-q/faops
cd faops
make

Installing with Homebrew or Linuxbrew

brew install wang-q/tap/faops

Tests

Done with bats. Useful articles:

• https://blog.engineyard.com/2014/bats-test-command-line-tools
• http://blog.spike.cx/post/60548255435/testing-bash-scripts-with-bats

# brew install bats-core
make test

Dependency

• zlib
• kseq.h and khash.h from klib (bundled)

AUTHOR

Qiang Wang <[e-mail]>

COPYRIGHT AND LICENSE

This software is copyright (c) 2014 by Qiang Wang.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.