moonso / phizz

Query hpo with phenotypes and OMIM terms

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'}]