mtoolnote
Variant annotator for MToolBox.
Free software: MIT license
GitHub repo: https://github.com/mitoNGS/mtoolnote
Features
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
Usage
Once installed, mtoolnote offers a CLI command and a Python function to annotate both human and non-human VCF files.
Human mitochondrial variant annotation
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.
Non-human mitochondrial variant annotation
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.
Installation
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 .
Testing
After installation, run all tests with:
$ pytest
or the full suite (tests using python3.6, python3.7, flake8) with:
$ tox
Credits
This package was created with Cookiecutter and the cc-pypackage project template.
History
0.1.0 (2019-08-27)
First development release.
0.1.1 (2019-09-02)
Add option to create csv from annotated vcf file.
0.1.2 (2019-09-17)
Fix requirements;
Relocate local database for human annotation.
0.1.3 (2019-09-25)
Add multi-threading processing for non-human annotations (fix #1).
0.1.4 (2019-11-30)
Add haplogroup-specific allele frequencies to final annotations (fix #4);
Add external predictors to final annotations (fix #5).
0.1.5 (2020-02-09)
Add locus name to basic information even for non-annotated human variants (fix #14);
Update requirements (fix #17);
Restructure code.
0.1.6 (2020-03-04)
Use the Loci table to provide basic locus annotations (fix #22).
0.1.7 (2020-04-04)
Add functional locus annotations using the FuncLoci table (fix #24).
0.2.0 (2020-04-08)
Add options to choose specific annotations to include in human data (fix #28).
1 maintainer
Metadata
1 maintainer
Release files for mtoolnote 0.2.0
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