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MITOS

Project 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, MITOS2).

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

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