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faidx - Fetch sequences from FASTA

FAIDX(1) User Commands FAIDX(1)

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
October 2015 faidx 0.4.2