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Variant annotator for MToolBox.

Project description

mtoolnote

Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.

Variant annotator for MToolBox.

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).

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