mitos 1.0

MITOS

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.