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

faidx 0.4.2                                       October 2015                                          FAIDX(1)