MITOS

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Project links

Environment
- Console
Intended Audience
- Science/Research
License
- OSI Approved :: MIT License
Operating System
- OS Independent
Programming Language
- Python :: 3
Topic
- Scientific/Engineering :: Bio-Informatics

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).

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

Project details

These details have not been verified by PyPI

Project links

Environment
- Console
Intended Audience
- Science/Research
License
- OSI Approved :: MIT License
Operating System
- OS Independent
Programming Language
- Python :: 3
Topic
- Scientific/Engineering :: Bio-Informatics

Release history Release notifications | RSS feed

2.1.9

Apr 29, 2024

2.1.8

Mar 21, 2024

2.1.7

Jan 24, 2024

2.1.6

Jan 7, 2024

2.1.5

Dec 22, 2023

2.1.4

Dec 20, 2023

2.1.3

Feb 25, 2023

2.1.2

Feb 23, 2023

2.1.1

Feb 22, 2023

2.1.0

Sep 9, 2022

2.0.8

May 21, 2020

2.0.7

May 21, 2020

2.0.6

Mar 27, 2020

2.0.5

Mar 26, 2020

2.0.4

Feb 9, 2020

2.0.3

Jan 7, 2020

2.0.2

Oct 15, 2019

2.0.1

May 2, 2019

1.1.7

Apr 29, 2024

1.1.6

Mar 21, 2024

1.1.5

Jan 24, 2024

1.1.4

Jan 7, 2024

1.1.3

Dec 22, 2023

1.1.2

Dec 20, 2023

1.1.1

Feb 23, 2023

1.1.0

Sep 9, 2022

This version

1.0.5

Feb 16, 2020

1.0.4

Feb 9, 2020

1.0.3

Jan 7, 2020

1.0.2

Oct 15, 2019

1.0.1

Apr 9, 2019

1.0

Apr 7, 2019

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