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Human mitochondrial variants annotation using HmtVar.
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README.rst

HmtNote

Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public. https://travis-ci.com/robertopreste/HmtNote.svg?token=zzk3yyGKDnWjk4pFXFuz&branch=master https://circleci.com/gh/robertopreste/HmtNote.svg?style=svg&circle-token=b910c3491e8df21fee34293ace05a35a116759c7 Documentation Status Updates Downloads

Human mitochondrial variants annotation using HmtVar.

Features

HmtNote is a bioinformatics Python module and command line interface that can be used to annotate human mitochondrial variants from a VCF file, using data available on HmtVar.

Annotations are grouped into basic, cross-reference, variability and predictions, depending on the type of information they provide. It is possible to either use all of them to fully annotate a VCF file, or choose specific annotations of interest.

HmtNote works by pulling the required data from HmtVar on the fly, but if you're planning to annotate VCF files offline, it is possible to download the annotation database so that HmtNote can use it when no internet connection is available.

For more information, please refer to the Usage section of the documentation.

Installation

PLEASE NOTE: HmtNote only supports Python 3!

The preferred installation method for HmtNote is using pip:

$ pip install hmtnote

For more information, please refer to the Installation section of the documentation.

Usage

Command Line Interface

HmtNote can be used as a command line tool, using the annotate command and providing the input VCF file name and the file name or path where the annotated VCF will be saved:

hmtnote annotate input.vcf annotated.vcf

By default, HmtNote will annotate the VCF file using all four groups of annotations (basic, cross-reference, variability and predictions). If desired, you can select which specific annotation you want, using respectively --basic, --crossref, --variab and --predict (or -b, -c, -v, -p), or any combination of these options:

hmtnote annotate input.vcf annotated_basic.vcf --basic
hmtnote annotate input.vcf annotated_crossreferences.vcf --crossref
hmtnote annotate input.vcf annotated_variability.vcf --variab
hmtnote annotate input.vcf annotated_predictions.vcf --predict
hmtnote annotate input.vcf annotate_basic_variability.vcf --basic --variab

By default, HmtNote works by pulling the required data from HmtVar on the fly, but if you're planning to annotate VCF files offline, first download the annotation database using the dump command:

hmtnote dump

After that, HmtNote is capable of working even when no internet connection is available; this can be achieved using the --offline option after the usual annotation command:

hmtnote annotate input.vcf annotated.vcf --offline
hmtnote annotate input.vcf annotated_variability.vcf --variab --offline

For more information, please refer to the Usage section of the documentation.

Python Module

HmtNote can also be imported in a Python script and its function annotate_vcf() can be used to annotate a given VCF:

from hmtnote import annotate
annotate("input.vcf", "annotated.vcf")

By default, annotate_vcf() will annotate the VCF using all four groups of annotations (basic, cross-reference, variability and predictions). If desired, you can specify which kind of annotation you want, using respectively the basic=True, crossref=True, variab=True, predict=True arguments, or any combination of them:

annotate("input.vcf", "annotated_basic.vcf", basic=True)
annotate("input.vcf", "annotated_crossreferences.vcf", crossref=True)
annotate("input.vcf", "annotated_variability.vcf", variab=True)
annotate("input.vcf", "annotated_predictions.vcf", predict=True)

It is also possible to download the annotation database using the dump() function, and perform offline annotation of VCF files by simply adding the offline=True argument to annotate_vcf():

from hmtnote import dump
dump()
annotate("input.vcf", "annotated.vcf", offline=True)

For more information, please refer to the Usage section of the documentation.

Citing HmtNote

If you find HmtNote useful for your research, please cite this work:

Preste R. et al - Human mitochondrial variant annotation with HmtNote (doi: https://doi.org/10.1101/600619)

Credits

This package was created with Cookiecutter and the cc-pypackage project template.

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