faidx(1) Fetch sequences from FASTA


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 ...]]


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.


Positional arguments

FASTA file
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
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
print pyfaidx version number