NORMALISEFASTA(1)

✨ normalisefasta ✨

okay bestie, gather round, because this little icon of a manual page is about to become your new fave 💖 it lives in the General Commands Manual section of your system (that's section 1, iykyk), and it's literally the glow-up artist for your FastA files 💅

🌸 NAME 🌸

normalisefasta — normalise line length in a FastA file 🎀

🦋 SYNOPSIS 🦋

normalisefasta [options]

💜 DESCRIPTION 💜

so here's the vibe: normalisefasta reads a FastA file from standard input and outputs a reformatted version of that file on standard output, where all the lines containing sequence information have a consistent length. it's giving "make my FASTA look put together" ✨

the program can either produce uncompressed output or BGZF compressed output. and here's the lil detail nobody expects: for uncompressed output, a FastA index (.fai) is produced on the standard error channel. yes bestie, stderr. that's not a typo, that's just how it is 🙈

the following key=value pairs can be given:

• cols=<[80]> — line width for the lines containing sequence information, measured in number of bases. heads up: this option is only considered for uncompressed output (i.e. bgzf=0) 👑
• bgzf=<0|1> — produce uncompressed (bgzf=0) or compressed (bgzf=1) output 🌈
• index=<> — if bgzf=1, this key can be used for giving the file name for the index file, allowing (pseudo) random access in the output file. if the key is not given when bgzf=1, then no index is written 🫶
• level=<-1|0|1|9|11> — set compression level of the output file if bgzf=1. valid values are:
  • -1: zlib/gzip default compression level
  • 0: uncompressed
  • 1: zlib/gzip level 1 (fast) compression
  • 9: zlib/gzip level 9 (best) compression

if libmaus has been compiled with support for igzip (see https://software.intel.com/en-us/articles/igzip-a-high-performance-deflate-compressor-with-optimizations-for-genomic-data) then an additional valid value is:

• 11: igzip compression

• minlength=<[0]> — Minimum length. Reads shorter than this will be discarded. By default all reads are kept. so if you want to yeet the lil short ones, this is your girl ✂️

👑 AUTHOR 👑

Written by German Tischler. 💫

😭 REPORTING BUGS 😭

Report bugs to <germant@miltenyibiotec.de>

🎀 COPYRIGHT 🎀

Copyright © 2009-2014 German Tischler, © 2011-2014 Genome Research Limited. License GPLv3+: GNU GPL version 3 <http://gnu.org/licenses/gpl.html>

This is free software: you are free to change and redistribute it.

There is NO WARRANTY, to the extent permitted by law.

bestie this is a legal moment, not a suggestion: no warranty, fr fr 💀

and that's the whole page, no cap 🧚 this beauty came to you courtesy of BIOBAMBAM, dated January 2014 — stay slay, stay normalised 💖🌸✨