Scroll to navigation

PYFASTX(1) User Commands PYFASTX(1)

NAME

pyfastx - fast random access to sequences from FASTA/Q file

DESCRIPTION

usage: pyfastx COMMAND [OPTIONS]

A command line tool for FASTA/Q file manipulation

options:

show this help message and exit
show program's version number and exit

Commands:

build index for fasta/q file
show detailed statistics information of fasta/q file
split fasta/q file into multiple files
convert fastq file to fasta file
get subsequences from fasta file by region
randomly sample sequences from fasta or fastq file
extract full sequences or reads from fasta/q file

SEE ALSO

Each subcommand has its own on line help, which can be queried for instance with:


$ pyfastx index --help
usage: pyfastx index [-h] [-f] fastx [fastx ...]
positional arguments:


  fastx       fasta or fastq file, gzip support
options:


  -h, --help  show this help message and exit


  -f, --full  build full index, base composition will be calculated

Look up /usr/share/doc/pyfast/README.rst for more complete documentation.

November 2022 pyfastx version 0.8.4