PYFASTX

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:

-h, --help

show this help message and exit

-v, --version

show program’s version number and exit

Commands:

	index		build index for fasta/q file
	stat		show detailed statistics information of fasta/q file
	split		split fasta/q file into multiple files
	fq2fa		convert fastq file to fasta file

subseq

get subsequences from fasta file by region

sample

randomly sample sequences from fasta or fastq file

extract

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.