Command Cheat Sheet

Command Cheat Sheet

Keep this page nearby once you know the basic workflow. It favors commands you can paste over explanations; each command page owns the details and edge cases.

General

z-fasta --help
z-fasta --version

Index

# Default .zfi index
z-fasta index genome.fa

# Samtools-compatible .fai for uniform FASTA
z-fasta index --emit-fai genome.fa > genome.fa.fai

Get

# Complete record
z-fasta get genome.fa chr1

# 1-based inclusive region
z-fasta get genome.fa chr1:1000-2000

# Open-ended region
z-fasta get genome.fa chr1:1000-

# Several regions in request order
z-fasta get genome.fa chr1:1-100 chr2:1-100

# Literal full-record names from a file or stdin
z-fasta get genome.fa --names ids.txt
printf 'chr1\nchr2\n' | z-fasta get genome.fa --names -

# BED from a file or stdin
z-fasta get genome.fa --bed regions.bed
awk '$5 >= 100' regions.bed | z-fasta get genome.fa --bed -

# BED strand
z-fasta get genome.fa --bed regions.bed --strand-aware

# Orientation
z-fasta get genome.fa chr1:1-100 --rc
z-fasta get genome.fa chr1:1-100 --reverse-only
z-fasta get genome.fa chr1:1-100 --complement-only
z-fasta get genome.fa chr1:1-100 --rc --annotate-rc

# Successful-run summary to stderr
z-fasta get genome.fa --bed regions.bed --summary > regions.fa

Validate

# Human report
z-fasta validate genome.fa

# Fail a warnings-only quality gate
z-fasta validate --strict genome.fa

# One JSON report
z-fasta validate --json genome.fa

# Header policies
z-fasta validate --schema refseq genome.fa
z-fasta validate --max-header-len 200 genome.fa
z-fasta validate --custom-alphabet ACGTN- aligned.fa

# Read standard input; bound the duplicate check's memory
zcat genome.fa.gz | z-fasta validate -
z-fasta validate --max-name-memory 268435456 proteins.fa

# Check that the index get loads still describes the FASTA
z-fasta validate --index genome.fa
z-fasta validate --index=genome.fa.fai genome.fa

# Name the alphabet instead of sampling it
z-fasta validate --type dna genome.fa
z-fasta validate --type protein proteins.fa

# Write a repaired copy, wrapped at 60 or at a chosen width
z-fasta validate --fix -o genome.clean.fa genome.fa
z-fasta validate --fix --width 80 -o genome.clean.fa genome.fa

Stats

z-fasta stats genome.fa

Coordinate reminder

• Positional GET: 1-based inclusive.
• BED input: 0-based half-open.
• GET FASTA headers: 1-based inclusive.

Warning

A present .zfi is authoritative. If it is stale or corrupt, z-fasta fails instead of falling back to a valid .fai.