NAME

FA_TOOL

VERSION

0.1.0

LICENSE

Specified in LICENSE.md file

INTRODUCTION

Command line tool in python 2.7. It operates on fa/fasta/etc. files. version: 0.1.0

PREREQUISITES

PYTHON 2.7

COMMAND LINE

usage: fatool.py [-h] -f FAFILE [--operator OPERATOR] [--log LOG] {cut,extractNames,extractContigs,remContigs,join,split} ...

optional arguments: -h, --help show this help message and exit -f FAFILE, --fafile file to be cut usualy *.fa --operator OPERATOR user who have fired script it will be noted in log --log LOG log file if not supplied stdout

facutter commands: {cut,extractNames,extractContigs,remContigs,join,split} each has own params

cut                 split supplied sequence into smaller parts, according to given params
extractNames        extracting contigs names only into list txt file
extractContigs      extracting contigs specified in file based on contigs names list (output in new file)
join                joining two or more files, yet not verifing duplicates
remContigs          removing contigs specified in file based on contigs names list (output in new file)
split               each cotig saved into separate file

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

join:

usage: fatool.py join [-h] -o OUTPUT [--files [FILES [FILES ...]]]

optional arguments: -h, --help show this help message and exit -o OUTPUT, --output OUTPUT output file --files [FILES [FILES ...]] files to be joined

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

split:

usage: fatool.py split [-h] -d OUTPUTDIR

optional arguments: -h, --help show this help message and exit -d OUTPUTDIR, --outputDir output directory where splited contigs will be saved