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Script changed into python package, tests added. 

	modified:   README.md
	new file:   bin/cmdfatool.py
	new file:   build/lib/fatool/__init__.py
	new file:   build/lib/fatool/fa.py
	new file:   build/lib/fatool/fuzzy.py
	new file:   build/lib/fatool/sequence.py
	new file:   build/scripts-2.7/cmdfatool.py
	deleted:    fatool.py
	new file:   fatool/__init__.py
	new file:   fatool/fa.py
	new file:   fatool/fuzzy.py
	new file:   fatool/sequence.py
	new file:   fatool/tests/__init__.py
	new file:   fatool/tests/test_fa.py
	new file:   fatool/tests/test_sequence.py
	new file:   setup.py
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1 parent 5a1648e commit 6af1b970cdcae15a101c3ea0629806d083abf2d9 @blazejmarciniak blazejmarciniak committed Jun 12, 2016
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175 README.md
@@ -1,16 +1,20 @@
NAME
====
-FA_TOOL
+fatool
+
+DESCRIPTION
+===========
+
+Tool for analyze and manipulate fasta files
VERSION
=======
-0.1.0
+0.2.1
LICENSE
=======
-
-Specified in LICENSE.md file
+APACHE 2.0 Specified in LICENSE.md file
INTRODUCTION
============
@@ -25,80 +29,147 @@ PYTHON 2.7
COMMAND LINE
============
-usage: fatool.py [-h] -f FAFILE [--operator OPERATOR] [--log LOG]
- {cut,extractNames,extractContigs,remContigs,join,split} ...
+usage: cmdfatool.py [-h] [-v]
+ {cut,extractNames,extractContigs,remContigs,join,split,reverse,validate,stats}
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
+ -v, --version display version number and exit
-facutter commands:
- {cut,extractNames,extractContigs,remContigs,join,split} each has own params
+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 into list txt file
- extractContigs extracting contigs specified in file based on contigs names list (output in new file)
+ 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
- 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]
+ reverse reverse all sequences in file
+ validate validates fa file
+ stats show statistics of fa file
- 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
+
+ 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
+
-extractContigs:
+ extractNames:
- usage: fatool.py extractContigs [-h] --list LIST -o OUTPUT [--log LOG] [--multifile]
+usage: cmdfatool.py extractNames [-h] -f FAFILE [-o OUTPUT] [--log LOG]
+ [--operator OPERATOR]
- optional arguments:
+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 file; if --multifile is set output directory
+ -o OUTPUT, --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
+ --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
-extractNames:
- usage: fatool.py extractNames [-h] [-o OUTPUT] [--log LOG]
+ join
+
+usage: cmdfatool.py join [-h] -f FAFILE -o OUTPUT
+ [--files [FILES [FILES ...]]] [--overwrite]
+ [--log LOG] [--operator OPERATOR]
- optional arguments:
+optional arguments:
-h, --help show this help message and exit
- -o OUTPUT, --output output file if not supplied stdout
+ -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
-join:
-
- usage: fatool.py join [-h] -o OUTPUT [--files [FILES [FILES ...]]]
+usage: cmdfatool.py split [-h] -f FAFILE -d OUTPUTDIR [--log LOG]
+ [--operator OPERATOR]
- optional arguments:
- -h, --help show this help message and exit
- -o OUTPUT, --output OUTPUT output file
- --files [FILES [FILES ...]] files to be joined
-
-remContigs:
+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
+
- usage: fatool.py remContigs [-h] --list LIST -o OUTPUT [--log LOG]
+ reverse
+
+usage: cmdfatool.py reverse [-h] -f FAFILE -o OUTPUT [--log LOG]
+ [--operator OPERATOR]
- optional arguments:
+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
+ -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]
-split:
-
- usage: fatool.py split [-h] -d OUTPUTDIR
+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
- -d OUTPUTDIR, --outputDir output directory where splited contigs will be saved
+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
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