faidx - 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.
- fasta
- FASTA file
- regions
- space separated regions of sequence to fetch e.g. chr1:1-1000
- -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
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