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.
- via conda:
conda install mitos -c bioconda -m -n mitos - via pip:
pip install mitos - 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
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
