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Tool to query hpo database and some other sources

Project description

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# phizz #

Tool to query HPO and OMIM

## Installation ##

```pip install phizz```


$git clone
$cd phizz
$python install

## Usage ##

Using command line utility:

Usage: phizz query [OPTIONS]

Query the hpo database.

Print the result in csv format as default.

-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'])
[{'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'}]

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