NAME

fatool

DESCRIPTION

Tool for analyze and manipulate fasta files

VERSION

0.2.1

LICENSE

APACHE 2.0 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: cmdfatool.py [-h] [-v] {cut,extractNames,extractContigs,remContigs,join,split,reverse,validate,stats}

optional arguments: -h, --help show this help message and exit -v, --version display version number and exit

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

cut                 split supplied sequence into smaller parts, according to given params
extractNames        extracting contigs names only
extractContigs      extracting contigs specified in file (output in new file)
remContigs          removing contigs specified in file (output in new file)
join                joining two or more files, yet not verifing duplicates
split               each cotig saved into separate file
reverse             reverse all sequences in file
validate            validates fa file
stats               show statistics of fa file


cut:

usage: cmdfatool.py cut [-h] -f FAFILE -r RANGE [-o OUTPUT] [-s STEP] [--log LOG] [--operator OPERATOR]

optional arguments: -h, --help show this help message and exit -f FAFILE, --fafile FAFILE file to be cut usualy *.fa -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 --operator OPERATOR user who have fired script it will be noted in log

extractNames:

usage: cmdfatool.py extractNames [-h] -f FAFILE [-o OUTPUT] [--log LOG] [--operator OPERATOR]

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

extractContigs:

usage: cmdfatool.py extractContigs [-h] -f FAFILE --list LIST -o OUTPUT [--log LOG] [--operator OPERATOR] [--multifile]

optional arguments: -h, --help show this help message and exit -f FAFILE, --fafile FAFILE file to be cut usualy *.fa --list LIST file containing list of contigs one contig per line -o OUTPUT, --output OUTPUT output file; if --multifile is set output directory --log LOG log file if not supplied stdout --operator OPERATOR user who have fired script it will be noted in log --multifile if this flag is set each contig will be saved in separate file

remContigs

usage: cmdfatool.py remContigs [-h] -f FAFILE --list LIST -o OUTPUT [--log LOG] [--operator OPERATOR]

optional arguments: -h, --help show this help message and exit -f FAFILE, --fafile FAFILE file to be cut usualy *.fa --list LIST file containing list of contigs one contig per line -o OUTPUT, --output OUTPUT output file if not supplied stdout --log LOG log file if not supplied stdout --operator OPERATOR user who have fired script it will be noted in log

join

usage: cmdfatool.py join [-h] -f FAFILE -o OUTPUT [--files [FILES [FILES ...]]] [--overwrite] [--log LOG] [--operator OPERATOR]

optional arguments: -h, --help show this help message and exit -f FAFILE, --fafile FAFILE file to be cut usualy *.fa -o OUTPUT, --output OUTPUT output file if not supplied stdout --files [FILES [FILES ...]] files to be joined --overwrite if set owerwrites contigs with same name --log LOG log file if not supplied stdout --operator OPERATOR user who have fired script it will be noted in log

split

usage: cmdfatool.py split [-h] -f FAFILE -d OUTPUTDIR [--log LOG] [--operator OPERATOR]

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

reverse

usage: cmdfatool.py reverse [-h] -f FAFILE -o OUTPUT [--log LOG] [--operator OPERATOR]

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

validate

usage: cmdfatool.py validate [-h] -f FAFILE -t TYPE [--details]

optional arguments: -h, --help show this help message and exit -f FAFILE, --fafile FAFILE file to be cut usualy *.fa -t TYPE, --type TYPE type of sequence 0 - general, 1 DNA, 2 - amino --details set if you want to see detaild validation info

stats

usage: cmdfatool.py stats [-h] -f FAFILE [--log LOG] [--operator [OPERATOR [OPERATOR ...]]]

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