hmtnote 0.7.2
Human mitochondrial variants annotation using HmtVar.
License: MIT license
Keywords: hmtnote

=======
HmtNote
=======


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Human mitochondrial variants annotation using HmtVar.


* Free software: MIT license
* Documentation: https://hmtnote.readthedocs.io
* GitHub repo: https://github.com/robertopreste/HmtNote
* Publication: https://doi.org/10.1101/600619


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 >= 3.6!**

The preferred installation method for HmtNote is using ``pip``:

.. code-block:: console

    $ 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

It is also possible to convert the resulting annotated VCF file to CSV format, for a simpler visual inspection of the data, by simply specifying the ``--csv`` option **(please note that an output VCF file name must be provided)**::

    hmtnote annotate input.vcf annotated.vcf --csv

An additional ``annotated.csv`` file will be created in the same directory of ``annotated.vcf``.

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)

An additional annotated CSV can be produced from the output VCF using the ``csv=True`` argument::

    annotate("input.vcf", "annotated.vcf", csv=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.

.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`cc-pypackage`: https://github.com/robertopreste/cc-pypackage
.. _HmtVar: https://www.hmtvar.uniba.it
.. _Clinvar: https://www.ncbi.nlm.nih.gov/clinvar/
.. _OMIM: https://www.omim.org
.. _dbSNP: https://www.ncbi.nlm.nih.gov/snp
.. _`Mitomap Somatic Mutations`: https://www.mitomap.org/foswiki/bin/view/MITOMAP/MutationsSomatic
.. _Mitomap: https://www.mitomap.org/MITOMAP/MutationsCodingControl
.. _MutPred: http://mutpred.mutdb.org
.. _Panther: http://pantherdb.org
.. _`PhD SNP`: http://snps.biofold.org/phd-snp/phd-snp.html
.. _`SNPs & GO`: https://snps-and-go.biocomp.unibo.it/snps-and-go/
.. _Polyphen2: http://genetics.bwh.harvard.edu/pph2/
.. _Installation: https://hmtnote.readthedocs.io/en/latest/installation.html
.. _Usage: https://hmtnote.readthedocs.io/en/latest/usage.html


=======
History
=======

0.1.0 (2019-03-03)
==================

* First release on PyPI.


0.1.1 (2019-03-04)
------------------

* Clean installation requirements for conda;
* Update documentation.


0.1.2 (2019-03-15)
------------------

* Classes and methods are protected where needed;
* Code style is clean.


0.1.3 (2019-03-17)
------------------

* Fix issue with ``--predict`` annotation, which didn't retrieve the correct field from HmtVar.


0.1.4 (2019-03-19)
------------------

* Fix issue that prevented importing ``annotate_vcf()`` into Python scripts.


0.1.5 (2019-03-20)
------------------

* Add HmtVar ID of the variant in basic and full annotation;
* Change ``Disease Score`` annotation to ``DiseaseScore``.


0.2.0 (2019-03-25)
==================

* Add warnings to ``hmtnote`` command to be compliant with future versions;
* Check internet connection before trying to annotate variants.


0.3.0 (2019-03-27)
==================

* Add options to download the annotation database locally;
* Use local database to annotate variants (instead of calling HmtVar's API);
* Fallback to using local database when no internet connection is available;
* Check if local database actually exists before performing offline annotation;
* Databases are downloaded asynchronously.


0.3.1 (2019-03-29)
------------------

* Update installation requirements and documentation.


0.4.0 (2019-04-03)
==================

* Add support for insertion and deletion annotations;
* Add test suite and files for indels.


0.5.0 (2019-04-28)
==================

* Replace VCF parsing using VCFpy instead of cyvcf2;
* Rename ``hmtnote.annotate_vcf()`` to ``hmtnote.annotate()`` for compliance with CLI.


0.5.1 (2019-04-29)
------------------

* Fix issue with the new VCFpy implementation where new info where badly reported;
* Update test files restricting the number of entries to 80 for faster testing.

0.5.2 (2019-04-30)
------------------

* Fix requirements in setup.py file.

0.5.3 (2019-05-06)
------------------

* Update requirements in setup.py.

0.5.4 (2019-05-06)
------------------

* Fix installation issue.

0.5.5 (2019-05-06)
------------------

* Fix VCF record parsing issue.

0.6.0 (2019-06-25)
==================

* Use vcfpy2 for VCF files parsing;
* Dump annotation files directly from HmtVar instead of the original API call;
* Add annotation progress bar;
* Check internet connection using httpstat.us;
* Update tests and add more test cases;
* Update documentation with detailed API usage.

0.7.0 (2019-07-26)
==================

* Add ``--csv`` command line option to convert output to CSV format;
* Add homoplasmy annotations;
* Update all tests accordingly;
* Update documentation.

0.7.1 (2019-07-30)
------------------

* Fix issue with echoed string (#78);
* Fix issue with CSV format columns (#79);
* Update testfiles.

0.7.2 (2019-08-16)
------------------

* Remove pysam from requirements and fix dependencies;
* Change docstrings to Google style;
* Update documentation;
* Update testfiles.