Metadata-Version: 2.0
Name: mitos
Version: 1.0
Summary: MITOS
Home-page: https://gitlab.com/Bernt/MITOS
Author: Matthias Bernt
Author-email: bernt@informatik.uni-leipzig.de
License: UNKNOWN
Platform: UNKNOWN
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Dist: biopython (==1.73)
Requires-Dist: ete2 (==2.3.10)

This is the README file for the mitogenome related sources including MITOS and 
other (more or less) helpful tools. Note that some of the tools are unfinished 
and not in a production state. 

Clearly this README is a stub. We are happy to extend the documentation 
on request. So just send a message if you need further information. 

Installation
============

There are several ways to install. Prefered is the installation via conda
since this also takes care of non-python requirements of the main mitos script.

1. via conda: `TODO`
2. via pip: `pip install mitos`
3. pip -r requirements.txt

For the non-python requirements see README.MITOS.

MITOS
=====

* mitos.py
	standalone version 

see also `mitos.py --help` README.MITOS 


genbank file handling
=====================

* refseqsplit:
    - splits a file consisting of concatenated gb files into single genbank files
    - its possible to apply filters (taxonomy, prefix) 


skewness related programs
=========================

* skew:
	compute skewness values for a gene of given genbank files
* skewcum:
	compute cumulative skewness for given genbank files
* skewsvm:
	do svm classification of skewness values .. and try to relate misclassifications to rearrangements

MISC
====

* gcpp
	- pretty print and compare genetic code

Database handling
=================

* db2bed:
	tool to write Features from the Db in a bed file

* dbgetacc:
	print all accesions that in the Db

* db2mitos:
	tool to merge Features from the Db like Mitos and write in a bed file

* db2fasta:
	tool to write fasta with subsequences of genom from features in db.



