---
name: "faidx"
section: "1"
platform: "linux"
package: "python3-pyfaidx"
version: "0.8.1.3-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/faidx"
---

# faidx(1)

Fetch sequences from FASTA

## NAME

faidx - Fetch sequences 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

Fetch sequences from FASTA. If no regions are specified, all entries in the input file are returned. Input FASTA file must be consistently line-wrapped, and line wrapping of output is based on input line lengths.

## OPTIONS

### Positional arguments

- fasta

  FASTA file

- regions

  space separated regions of sequence to fetch e.g. chr1:1-1000

### Optional arguments

- **-h**, **--help**

  show this help message and exit

- **-b** BED, **--bed** BED

  bed file of regions

- **-o** OUT, **--out** OUT

  output file name (default: stdout)

- **-i** {bed,chromsizes,nucleotide,transposed}, **--transform** {bed,chromsizes,nucleotide,transposed}

  transform the requested regions into another format. default: None

- **-c**, **--complement**

  complement the sequence. default: False

- **-r**, **--reverse**

  reverse the sequence. default: False

- **-n**, **--no-names**

  omit sequence names from output. default: False

- **-f**, **--full-names**

  output full names including description. default: False

- **-x**, **--split-files**

  write each region to a separate file (names are derived from regions)

- **-l**, **--lazy**

  fill in **--default-seq** for missing ranges. default: False

- **-s** DEFAULT\_SEQ, **--default-seq** DEFAULT\_SEQ

  default base for missing positions and masking. default: N

- **-d** DELIMITER, **--delimiter** DELIMITER

  delimiter for splitting names to multiple values (duplicate names will be discarded). default: None

- **-g** REGEX, **--regex** REGEX

  regular expression for filtering non-matching sequence names. default: .\*

- **-m**, **--mask-with-default-seq**

  mask the FASTA file using **--default-seq** default: False

- **-M**, **--mask-by-case**

  mask the FASTA file by changing to lowercase. default: False

- **--version**

  print pyfaidx version number

## SEE ALSO

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