phenoapt 0.1.6

PhenoApt python client API library

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.

Code usage

See jupyter notebook example

History

0.1.0 (2020-09-06)

• First release on PyPI.