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

Source file:	faidx.1.en.gz (from python3-pyfaidx 0.8.1.3-1)
Source last updated:	2024-10-16T18:37:25Z
Converted to HTML:	2024-11-14T03:17:04Z