faidx1

Fetch sequences from fasta

Usage

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 ...]]

Overview

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

Releases

Unchanged in 5 releases since Debian 9 (Stretch).

9–13