faidx(1)
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