NAME

fatool

VERSION

0.3.1

LICENSE

APACHE 2.0 Specified in LICENSE.md file

INTRODUCTION

Package and Command line tool in python 2.7. It operates on fa/fasta/etc. files. version: 0.2.1. To install package use setup.py install.

PREREQUISITES

PYTHON 2.7

USAGE

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] [--report REPORT] [--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 --report REPORT 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] [--report REPORT] [--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 --report REPORT 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 [--report REPORT] [--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 --report REPORT 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 [--report REPORT] [--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 --report REPORT 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] [--report REPORT] [--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 --report REPORT 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 [--report REPORT] [--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 --report REPORT 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 [--report REPORT] [--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 --report REPORT 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 [--report REPORT] [--operator [OPERATOR [OPERATOR ...]]]

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

findPrimer

usage: cmdfatool.py findPrimer [-h] -f FAFILE --start START --stop STOP --mode {FF,FR} [--minlen MINLEN] [--maxlen MAXLEN] [--mml MML] [--report REPORT] [--operator [OPERATOR [OPERATOR ...]]]

optional arguments: -h, --help show this help message and exit -f FAFILE, --fafile FAFILE
file to show statistics usualy *.fa --start START first sequence to be found --stop STOP last sequence to be found --mode {FF,FR} FF (start - forward orientated, stop - forward orientated) or FR (start - forward orientated, stop - reverse orientated) --minlen MINLEN minimum length (detfault 50bp) --maxlen MAXLEN max length (detfault 1000bp) --mml MML mismatch level number of allowed missmatches in primers (detfault 0) --report REPORT report results into file if not supplied stdout --operator [OPERATOR [OPERATOR ...]] user who have fired script it will be noted in report

cutNameMarker

usage: cmdfatool.py cutNameMarker [-h] -f FAFILE -m MARKER -l LENGTH --keepMarker KEEPMARKER [-o OUTPUT]

optional arguments: -h, --help show this help message and exit -f FAFILE, --fafile FAFILE file to show statistics usualy *.fa -m MARKER, --marker MARKER marker that indicates start of cut -l LENGTH, --length LENGTH length of cut --keepMarker KEEPMARKER weather to keep marker or not default 1 (Yes) -o OUTPUT, --output OUTPUT output file default: output.fa

translateDNA2Proteins

usage: cmdfatool.py translateDNA2Proteins [-h] -f FAFILE [-o OUTPUT] [--startCodons [STARTCODONS [STARTCODONS ...]]] [--stopCodons [STOPCODONS [STOPCODONS ...]]] [--tdict {STD,VMTO,YMTO,BAPP}] [--nss] [--report REPORT] [--operator [OPERATOR [OPERATOR ...]]]

optional arguments: -h, --help show this help message and exit -f FAFILE, --fafile FAFILE file to show statistics usualy *.fa -o OUTPUT, --output OUTPUT output file default: output.fa --startCodons [STARTCODONS [STARTCODONS ...]] list of start codons separated by space bar --stopCodons [STOPCODONS [STOPCODONS ...]] list of stop codons separated by space bar --tdict {STD,VMTO,YMTO,BAPP} Which dictionary use for translation: STD - standard, VMTO - Vertebrate Mitochondrial, YMTO - Yeast Mitochondrial, BAPP - Bacterial Archaeal Plant and Plastid --nss No Start Stop --report REPORT report results into file if not supplied stdout --operator [OPERATOR [OPERATOR ...]] user who have fired script it will be noted in report