Metadata-Version: 2.1
Name: mitos
Version: 1.0.3
Summary: MITOS
Home-page: http://mitos.bioinf.uni-leipzig.de
Author: Matthias Bernt
Author-email: bernt@informatik.uni-leipzig.de
License: UNKNOWN
Download-URL: https://gitlab.com/Bernt/MITOS
Description: Thes are 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 three 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: `conda install mitos -c bioconda -m -n mitos`
        2. via pip: `pip install mitos`
        3. manual: pip -r requirements.txt
        
        For the non-python requirements see README.MITOS.
        
        MITOS
        =====
        
        * runmitos.py: standalone CLI MITOS
        
        From runmitos.py help:
        
        ```
        mandatory options:
          -c CODE, --code CODE  the genetic code
          -o OUTDIR, --outdir OUTDIR
                                the directory where the output is written
          --linear              treat sequence as linear
          -r REFDIR, --refdir REFDIR
                                the directory where the reference data is found
        
        ```
        
        Please note that the reference data for the `-r` flag needs to be downloaded from Zenodo ([MITOS](https://zenodo.org/record/2683856), [MITOS2](https://zenodo.org/record/2672835)).
        
        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
        
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
Description-Content-Type: text/markdown
