Metadata-Version: 2.1
Name: mtoolnote
Version: 0.1.5
Summary: Variant annotator for MToolBox.
Home-page: https://github.com/mitoNGS/mtoolnote
Author: Roberto Preste
Author-email: robertopreste@gmail.com
License: MIT license
Description: =========
        mtoolnote
        =========
        
        
        .. image:: https://www.repostatus.org/badges/latest/wip.svg
            :alt: Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.
            :target: https://www.repostatus.org/#wip
        
        
        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.
        
        .. _Cookiecutter: https://github.com/audreyr/cookiecutter
        .. _`cc-pypackage`: https://github.com/robertopreste/cc-pypackage
        .. _Usage: https://mtoolnote.readthedocs.io/en/latest/usage.html
        .. _Installation: https://mtoolnote.readthedocs.io/en/latest/installation.html
        .. _HmtVar: https://www.hmtvar.uniba.it
        .. _BioMart: https://www.ensembl.org/biomart/martview
        
        
        =======
        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;
        * Update requirements;
        * Restructure code.
        
Keywords: mtoolnote
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Description-Content-Type: text/x-rst
