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Tool to query hpo database and some other sources

Project 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'}]
```

Release History

This version
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0.2.3

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0.2.2

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0.2.1

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0.2

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0.1.2

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0.1.1

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0.1

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0.0.6

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0.0.4

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0.0.3

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0.0.2

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0.0.1

Download Files

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Filename, Size & Hash SHA256 Hash Help File Type Python Version Upload Date
phizz-0.2.3-py2.py3-none-any.whl
(14.9 MB) Copy SHA256 Hash SHA256
Wheel 2.7 Mar 2, 2016
phizz-0.2.3.tar.gz
(14.8 MB) Copy SHA256 Hash SHA256
Source None Mar 2, 2016

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