Metadata-Version: 2.1
Name: hmtnote
Version: 0.1.5
Summary: Human mitochondrial variants annotation using HmtVar. 
Home-page: https://github.com/robertopreste/hmtnote
Author: Roberto Preste
Author-email: robertopreste@gmail.com
License: MIT license
Description: =======
        HmtNote
        =======
        
        
        .. image:: https://img.shields.io/pypi/v/hmtnote.svg
                :target: https://pypi.python.org/pypi/hmtnote
        
        .. image:: https://travis-ci.com/robertopreste/HmtNote.svg?token=zzk3yyGKDnWjk4pFXFuz&branch=master
            :target: https://travis-ci.com/robertopreste/HmtNote
        
        .. image:: https://circleci.com/gh/robertopreste/HmtNote.svg?style=svg&circle-token=b910c3491e8df21fee34293ace05a35a116759c7
            :target: https://circleci.com/gh/robertopreste/HmtNote
        
        .. image:: https://codecov.io/gh/robertopreste/HmtNote/branch/master/graph/badge.svg
          :target: https://codecov.io/gh/robertopreste/HmtNote
        
        .. image:: https://readthedocs.org/projects/hmtnote/badge/?version=latest
                :target: https://hmtnote.readthedocs.io/en/latest/?badge=latest
                :alt: Documentation Status
        
        .. image:: https://pyup.io/repos/github/robertopreste/HmtNote/shield.svg
             :target: https://pyup.io/repos/github/robertopreste/HmtNote/
             :alt: Updates
        
        
        Human mitochondrial variants annotation using HmtVar.
        
        
        * Free software: MIT license
        * Documentation: https://hmtnote.readthedocs.io.
        
        
        Features
        --------
        
        HmtNote is a bioinformatics tool that can be used to annotate human mitochondrial variants from a VCF, using data available on HmtVar_.
        
        Annotations are grouped into basic, cross-reference, variability and predictions, depending on the type of information they provide.
        
        Basic
        =====
        
        Basic information about the variant; they include:
        
        * Locus: Locus to which the variant belongs
        * AaChange: Aminoacidic change determined
        * Pathogenicity: Pathogenicity predicted by HmtVar
        * DiseaseScore: Disease score calculated by HmtVar
        * HmtVar: HmtVar_ ID of the variant (can be used to view the related VariantCard on `https://www.hmtvar.uniba.it/varCard/<HmtVarID>`)
        
        Cross-reference
        ===============
        
        Cross-reference information about the variant; they include:
        
        * Clinvar: Clinvar_ ID of the variant
        * dbSNP: dbSNP_ ID of the variant
        * OMIM: OMIM_ ID of the variant
        * MitomapAssociatedDiseases: Diseases associated to the variant according to Mitomap_
        * MitomapSomaticMutations: Diseases associated to the variant according to `Mitomap Somatic Mutations`_
        
        Variability
        ===========
        
        Variability and allele frequency data about the variant; they include:
        
        * NtVarH: Nucleotide variability of the position in healthy individuals
        * NtVarP: Nucleotide variability of the position in patient individuals
        * AaVarH: Aminoacid variability of the position in healthy individuals
        * AaVarP: Aminoacid variability of the position in patient individuals
        * AlleleFreqH: Allele frequency of the variant in healthy individuals overall
        * AlleleFreqP: Allele frequency of the variant in patient individuals overall
        * AlleleFreqH_AF: Allele frequency of the variant in healthy individuals from Africa
        * AlleleFreqP_AF: Allele frequency of the variant in patient individuals from Africa
        * AlleleFreqH_AM: Allele frequency of the variant in healthy individuals from America
        * AlleleFreqP_AM: Allele frequency of the variant in patient individuals from America
        * AlleleFreqH_AS: Allele frequency of the variant in healthy individuals from Asia
        * AlleleFreqP_AS: Allele frequency of the variant in patient individuals from Asia
        * AlleleFreqH_EU: Allele frequency of the variant in healthy individuals from Europe
        * AlleleFreqP_EU: Allele frequency of the variant in patient individuals from Europe
        * AlleleFreqH_OC: Allele frequency of the variant in healthy individuals from Oceania
        * AlleleFreqP_OC: Allele frequency of the variant in patient individuals from Oceania
        
        Predictions
        ===========
        
        Pathogenicity prediction information of the variant from external resources; they include:
        
        * MutPred_Prediction: Pathogenicity prediction offered by MutPred_
        * MutPred_Probability: Confidence of the pathogenicity prediction offered by MutPred_
        * Panther_Prediction: Pathogenicity prediction offered by Panther_
        * Panther_Probability: Confidence of the pathogenicity prediction offered by Panther_
        * PhDSNP_Prediction: Pathogenicity prediction offered by `PhD SNP`_
        * PhDSNP_Probability: Confidence of the pathogenicity prediction offered by `PhD SNP`_
        * SNPsGO_Prediction: Pathogenicity prediction offered by `SNPs & GO`_
        * SNPsGO_Probability: Confidence of the pathogenicity prediction offered by `SNPs & GO`_
        * Polyphen2HumDiv_Prediction: Pathogenicity prediction offered by Polyphen2_ HumDiv
        * Polyphen2HumDiv_Probability: Confidence of the pathogenicity prediction offered by Polyphen2_ HumDiv
        * Polyphen2HumVar_Prediction: Pathogenicity prediction offered by Polyphen2_ HumVar
        * Polyphen2HumVar_Probability: Confidence of the pathogenicity prediction offered by Polyphen2_ HumVar
        
        Usage
        -----
        
        Command Line Interface
        ======================
        
        HmtNote can be used as a command line tool, by simply providing the original VCF and the filename where the annotated VCF will be saved::
        
            hmtnote input_vcf.vcf annotated_vcf.vcf
        
        By default, HmtNote 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 ``--basic``, ``--crossref``, ``--variab`` and ``--predict`` (or ``-b``, ``-c``, ``-v``, ``-p``)::
        
            hmtnote input_vcf.vcf annotated_basic_vcf.vcf --basic
            hmtnote input_vcf.vcf annotated_crossreferences_vcf.vcf --crossref
            hmtnote input_vcf.vcf annotated_variability_vcf.vcf --variability
            hmtnote input_vcf.vcf annotated_predictions_vcf.vcf --predict
        
        Python Module
        =============
        
        HmtNote can also be imported in a Python script and its function ``annotate_vcf()`` can be used to annotated a given VCF::
        
            from hmtnote import annotate_vcf
            annotate_vcf("input_vcf.vcf", "annotated_vcf.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::
        
            annotate_vcf("input_vcf.vcf", "annotated_basic_vcf.vcf", basic=True)
            annotate_vcf("input_vcf.vcf", "annotated_crossreferences_vcf.vcf", crossref=True)
            annotate_vcf("input_vcf.vcf", "annotated_variability_vcf.vcf", variab=True)
            annotate_vcf("input_vcf.vcf", "annotated_predictions_vcf.vcf", predict=True)
        
        Installation
        ------------
        
        **PLEASE NOTE: HmtNote only supports Python 3!**
        
        The preferred installation method for HmtNote is using ``pip`` in a conda environment:
        
        .. code-block:: console
        
            $ conda install requests
            $ conda install -c bioconda cyvcf2
            $ pip install hmtnote
        
        If you have issues, please refer to the Installation_ section of the Documentation_.
        
        
        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/
        .. _Documentation: https://hmtnote.readthedocs.io
        .. _Installation: https://hmtnote.readthedocs.io/en/latest/installation.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`.
        
        
        X.X.X (WIP)
        ===========
        
        * Add options to download the required databases locally;
        * Use local databases to annotate variants (instead of calling HmtVar's API);
        * Fallback to using local databases when web connection is not available?
        
Keywords: hmtnote
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 :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Description-Content-Type: text/x-rst
