FA_TOOL

Command line tool in python. It operates on fa/fasta etc. files. version: 0.0.1

fatool.py [-h] -f FAFILE {cut,extractNames,extractContigs,remContigs}

optional arguments: -h, --help show this help message and exit -f FAFILE, --fafile FAFILE file to be cut usualy *.fa

fatool commands: {cut,extractNames,extractContigs,remContigs} each has own params, for more details use: command -h

cut:

usage: fatool.py cut [-h] -r RANGE [-o OUTPUT] [-s STEP] [--log LOG]

optional arguments: -h, --help show this help message and exit -r RANGE, --range RANGE cutted sequence length -o OUTPUT, --output OUTPUT output file default: output.fa -s STEP, --step STEP step length default: 1 --log LOG log file if not supplied stdout

extractContigs:

usage: fatool.py extractContigs [-h] --list LIST -o OUTPUT [--log LOG] [--multifile]

optional arguments: -h, --help show this help message and exit --list LIST file containing list of contigs one contig per line -o OUTPUT, --output output file; if --multifile is set output directory --log LOG log file if not supplied stdout --multifile if this flag is set each contig will be saved inseparate file

extractNames:

usage: fatool.py extractNames [-h] [-o OUTPUT] [--log LOG]

optional arguments: -h, --help show this help message and exit -o OUTPUT, --output output file if not supplied stdout --log LOG log file if not supplied stdout

remContigs:

usage: fatool.py remContigs [-h] --list LIST -o OUTPUT [--log LOG]

optional arguments: -h, --help show this help message and exit --list LIST file containing list of contigs one contig per line -o OUTPUT, --output output file if not supplied stdout --log LOG log file if not supplied stdout