Metadata-Version: 1.1
Name: phizz
Version: 0.0.2
Summary: Tool to query hpo database and some other sources
Home-page: https://github.com/moonso/query_hpo
Author: Måns Magnusson
Author-email: mans.magnusson@scilifelab.com
License: MIT
Description: 
        [![Build Status](https://travis-ci.org/moonso/phizz.svg)](https://travis-ci.org/moonso/phizz)
        
        # phizz #
        
        Tool to query HPO and OMIM
        
        ## Installation ##
        
        ```pip install phizz```
        
        or 
        
        ```
        $git clone https://github.com/moonso/phizz.git
        $cd phizz
        $python setup.py install
        ```
        
        ## Usage ##
        
        Using command line utility:
        
        ```
        Usage: phizz query [OPTIONS]
        
          Query the hpo database.
        
          Print the result in csv format as default.
        
        Options:
          -c, --config PATH
          -h, --hpo_term TEXT     Specify a hpo term
          -m, --mim_term TEXT     Specify a omim id
          -o, --outfile FILENAME  Specify path to outfile
          -j, --to_json           If output should be in json format
          --help                  Show this message and exit.
        ```
        
        so trying:
        
        ```
        $ phizz query -m OMIM:615373
        #hpo_id	description
        HP:0011675	Arrhythmia
        HP:0001644	Dilated cardiomyopathy
        HP:0001653	Mitral regurgitation
        HP:0000006	Autosomal dominant inheritance
        HP:0001711	Abnormality of the left ventricle
        ```
        to json:
        
        ```
        $ phizz query --hpo_term HP:0000002 --to_json
        [{"hpo_term": "HP:0000002", "description": "Abnormality of body height"}]
        ```
        
        Importing in python:
        
        ```
        In [1]: import phizz
        
        In [2]: phizz.query_disease(['OMIM:615373'])
        Out[2]:
        [{'description': u'Arrhythmia', 'hpo_term': u'HP:0011675'},
         {'description': u'Dilated cardiomyopathy', 'hpo_term': u'HP:0001644'},
         {'description': u'Mitral regurgitation', 'hpo_term': u'HP:0001653'},
         {'description': u'Autosomal dominant inheritance', 'hpo_term': u'HP:0000006'},
         {'description': u'Abnormality of the left ventricle',
          'hpo_term': u'HP:0001711'}]
        ```
        
        
        
Keywords: hpo omim hgnc
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: Topic :: Software Development
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Environment :: Console
