Variant annotator for MToolBox.
- Free software: MIT license
- GitHub repo: https://github.com/mitoNGS/mtoolnote
mtoolnote can annotate mitochondrial variants from:
- human genomes, using data stored in a local database derived from HmtVar;
- non-human genomes, using data from BioMart.
- Currently, only the following species are supported: oaries, ptroglodytes, scerevisiae, ecaballus, fcatus, cfamiliaris, pabelii, ggallus, mmulatta, rnorvegicus, btaurus, oanatinus, sscrofa, nleucogenys, chircus, mmusculus, tguttata, tnigroviridis, mgallopavo, mdomestica, drerio
Once installed, mtoolnote offers a CLI command and a Python function to annotate both human and non-human VCF files.
Using the CLI:
$ mtoolnote INPUT_VCF OUTPUT_VCF
where INPUT_VCF
and OUTPUT_VCF
represent file paths. Use the --csv
flag option to create an annotated CSV file in addition to the VCF output.
Using the Python module:
import mtoolnote mtoolnote.annotate("input.vcf", "output.vcf")
Use the csv=True
option to create an annotated CSV file in addition to the VCF output.
Using the CLI:
$ mtoolnote INPUT_VCF OUTPUT_VCF SPECIES
where SPECIES indicates the sample species, one of oaries
, ptroglodytes
, scerevisiae
,
ecaballus
, fcatus
, cfamiliaris
, pabelii
, ggallus
, mmulatta
,
rnorvegicus
, btaurus
, oanatinus
, sscrofa
, nleucogenys
, chircus
,
mmusculus
, tguttata
, tnigroviridis
, mgallopavo
, mdomestica
, drerio
. Use the --csv
flag option to create an annotated CSV file in addition to the VCF output.
Using the Python module:
import mtoolnote mtoolnote.annotate("input.vcf", "output_vcf", "species")
Use the csv=True
option to create an annotated CSV file in addition to the VCF output.
After cloning this repo, cd
in it and install mtoolnote using:
$ python setup.py install # in case this does not work: $ pip install -r requirements.txt $ pip install .
or in development mode:
$ pip install -r requirements_dev.txt $ pip install -e .
After installation, run all tests with:
$ pytest
or the full suite (tests using python3.6, python3.7, flake8) with:
$ tox
This package was created with Cookiecutter and the cc-pypackage project template.