phenoapt's Introduction

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.