FAIDX(1)

✨ NAME ✨

Okay so this is the FAIDX(1) page, a User Command bestie 🎀. faidx is how you fetch sequences straight from FASTA 🧬💖

🦋 SYNOPSIS 🦋

faidx [-h] [-b BED] [-o OUT] [-i {bed,chromsizes,nucleotide,transposed}]
[-c] [-r] [-n | -f] [-x] [-l] [-s DEFAULT_SEQ] [-d DELIMITER] [-g REGEX]
[-m | -M] [--version] fasta [regions [regions ...]]

🌸 DESCRIPTION 🌸

Okay so faidx pulls sequences out of a FASTA file for you 🫶. If you don't give it any regions, you get every single entry in the input file, no cap ✨. Your input FASTA has to be consistently line-wrapped 🙈, and the output's line wrapping copies whatever the input line lengths were. Main character energy 👑.

💅 OPTIONS 💅

🍓 Positional arguments

• fasta — the FASTA file you want to read 📄
• regions — space separated regions of sequence to fetch, e.g. chr1:1-1000 🧚

🌈 Optional arguments

• -h, --help — shows the help message and exits 💜
• -b BED, --bed BED — a bed file of regions 🗺️
• -o OUT, --out OUT — the output file name. Default is stdout ✨
• -i {bed,chromsizes,nucleotide,transposed}, --transform {bed,chromsizes,nucleotide,transposed} — transforms the requested regions into another format. Default is None 🔥
• -c, --complement — complements the sequence. Default is False 🦋
• -r, --reverse — reverses the sequence. Default is False 🔁
• -n, --no-names — leaves sequence names out of the output. Default is False 🙈
• -f, --full-names — outputs full names, description included. Default is False 📝
• -x, --split-files — writes each region to its own separate file. The file names come from the regions 🗂️
• -l, --lazy — fills in --default-seq for missing ranges. Default is False 🫧
• -s DEFAULT_SEQ, --default-seq DEFAULT_SEQ — the default base for missing positions and for masking. Default is N 🍬
• -d DELIMITER, --delimiter DELIMITER — the delimiter for splitting names into multiple values. Heads up, duplicate names get discarded 🙅. Default is None
• -g REGEX, --regex REGEX — a regular expression for filtering out sequence names that don't match 🔍. Default is .*
• -m, --mask-with-default-seq — masks the FASTA file using --default-seq 🎭. Default is False
• -M, --mask-by-case — masks the FASTA file by switching to lowercase 🌙. Default is False
• --version — prints the pyfaidx version number 🏷️

🫶 SEE ALSO 🫶

Okay bestie, please cite 📚✨: Shirley MD, Ma Z, Pedersen BS, Wheelan SJ. (2015) Efficient "pythonic" access to FASTA files using pyfaidx. PeerJ PrePrints 3:e1196 https://dx.doi.org/10.7287/peerj.preprints.970v1

That's the whole tea 🍵💖 This was faidx 0.4.2, from October 2015, FAIDX(1) forever 💅🌈