Metadata-Version: 1.2
Name: phenoapt
Version: 0.1.4
Summary: PhenoApt python client API library
Home-page: https://github.com/phenoapt/phenoapt
Author: PhenoApt Team
Author-email: phenoapt@ekitech.cn
License: MIT license
Description: ========
        phenoapt
        ========
        
        
        .. image:: https://img.shields.io/pypi/v/phenoapt.svg
                :target: https://pypi.python.org/pypi/phenoapt
        
        .. image:: https://img.shields.io/travis/phenoapt/phenoapt.svg
                :target: https://travis-ci.com/phenoapt/phenoapt
        
        
        Phenotype-based Gene Prioritization, modelled using Graph Embedding techniques
        
        This project contains the python client API library.
        
        Installation
        ------------
        
        You install phenoapt with pip:
        
            pip install phenoapt
        
        Or, if you prefer, clone the git repo and install from source::
        
            git clone https://github.com/phenoapt/phenoapt.git
            cd phenoapt
            python setup.py install
        
        Features
        --------
        
        * Rank by genes or diseases
        * Optional phenotype weights can be supplied
        
        Command line usage
        ------------------
        
        An example of top 10 gene rankings given phenotypes and weights::
        
            $ phenoapt rank-gene -p 'HP:0001193,HP:0001231,HP:0002999,HP:0003621' -w '1,2,2,1' -n 10
              rank    score  entrez_id    gene_symbol
            ------  -------  -----------  -------------
                 1  72.5097  EZ:8200      GDF5
                 2  73.8103  EZ:2697      GJA1
                 3  79.5231  EZ:51360     MBTPS2
                 4  85.5202  EZ:2316      FLNA
                 5  86.5767  EZ:10682     EBP
                 6  86.7231  EZ:8481      OFD1
                 7  86.9275  EZ:4010      LMX1B
                 8  87.2089  EZ:3930      LBR
                 9  91.1848  EZ:4000      LMNA
                10  92.2059  EZ:2273      FHL1
        
        and similarly, disease rankings can be obtained like this::
        
            $ phenoapt rank-disease -p 'HP:0001193,HP:0001231,HP:0002999,HP:0003621' -w '1,2,2,1' -n 10
              rank    score  disease_id    disease_name
            ------  -------  ------------  -------------------------------------------------------------------------------
                 1  63.2341  OMD:228900    FIBULAR HYPOPLASIA AND COMPLEX BRACHYDACTYLY
                 2  66.2116  OMD:215140    GREENBERG DYSPLASIA; GRBGD
                 3  66.3988  OMD:161200    NAIL-PATELLA SYNDROME; NPS
                 4  71.6026  OMD:308205    IFAP SYNDROME WITH OR WITHOUT BRESHECK SYNDROME
                 5  73.3633  OMD:302960    CHONDRODYSPLASIA PUNCTATA 2, X-LINKED DOMINANT; CDPX2
                 6  73.3904  OMD:135900    COFFIN-SIRIS SYNDROME 1; CSS1
                 7  74.5251  OMD:228930    FIBULAR APLASIA OR HYPOPLASIA, FEMORAL BOWING AND POLY-, SYN-, AND OLIGODACTYLY
                 8  75.0786  OMD:611816    TEMPLE-BARAITSER SYNDROME; TMBTS
                 9  75.1829  OMD:228520    FIBROCHONDROGENESIS 1; FBCG1
                10  78.0241  OMD:609945    OMD:609945
        
        For more information about tool usage, run phenoapt with --help.
        
        Code usage
        ------------------
        
        See `jupyter notebook example <https://github.com/phenoapt/phenoapt/blob/master/notebooks/phenoapt-example.ipynb>`_
        
        
        =======
        History
        =======
        
        0.1.0 (2020-09-06)
        ------------------
        
        * First release on PyPI.
        
Keywords: phenoapt
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
Classifier: Programming Language :: Python :: 3.8
Requires-Python: >=3.5
