PabloBotas/Phen2Gene

Phenotype driven gene prioritization for HPO

Phen2Gene

Phen2Gene is a phenotype driven gene prioritization tool, that takes HPO(Human Phenotype Ontology) ID(s) as inputs, searches and prioritize suspected genes.

Prerequisite

Python 3.7
Numpy

Installation

Python 3.7

Here shows installing Python 3.7 by Anaconda (Anaconda installation instruction: https://docs.anaconda.com/anaconda/install/). Usually Python 3.7 is installed at the same time Anaconda is installed. If you want to run Python 3 under different environment, you may create a new environment for Python 3 in commandline by conda create -n <environment name> python=3.7, then conda activate <environment name> (on Linux/Mac).

To exit the environment, source deactivate.

Numpy

Here shows installing in commandline by Anaconda: conda install numpy.

Phen2Gene

git clone https://github.com/WGLab/Phen2Gene.git

Install Time

It may take a few minutes to install Phen2Gene.

After Installation

cd YOUR/PATH/TO/PHEN2GENE

Usage

usage: phen2gene.py [-h] [-f [FILE.NAME [FILE.NAME ...]]]
                    [-m [HPID [HPID ...]]] [-w w|s] [-v] [-out OUTPUT]

optional arguments:
  -h, --help            show this help message and exit
  -f, --file [FILE.NAME [FILE.NAME ...]]
                        Input HPO as file.
  -m, --manual [HPID [HPID ...]]
                        Input HPO ID(s) one by one, with an empty space as seperation.
  -w, --method w|s  Methods to merge gene scores. 
                        'w' ( Default ) Weighted Score Merge 
                        's' Simple Score Merge
  -v, --verbosity       Display Phen2Gene workflow verbosely.
  -out, --output OUTPUT/PATH
                        Specify the path to store output files. 
                        Default directory path: ./out/

Input files

Input files to Phen2Gene should contains only HPO ID(s), seperated by new line character(\n).

Example

1. Input HPO ID(s) manually

python phen2gene.py -m HP:0000001 HP:0000021 HP:0000027 HP:0030905 HP:0030910 HP:0010628 -out out/out

2. Input HPO ID(s) by files

python phen2gene.py -f sample.txt -out out/out

3. Use Weighted Score Merge

python phen2gene.py -f sample.txt -w w -out out/out

4. Run Phen2gene verbosely

python phen2gene.py -f sample.txt -v -out out/out

Getting Help

Please use the GitHub's Issues page if you have questions.

Phenotype driven gene prioritization tool.

Phen2Gene reads HPO terms, and output a prioritized candidate gene list.

Env Requirments

1. Python3 and numpy

2. Linux environments recommended

Test

Input by file

python phen2gene.py -f sample.txt -v

Input by HPO terms

python phen2gene.py -m HP:0002779 HP:0001631 HP:0030718 HP:0005117 HP:0001156 HP:0000426 HP:0000316 -v

Use weighted human phenotype terms for scoring

python phen2gene.py -f sample.txt -w w -v

Use unweighted human phenotype terms for scoring

python phen2gene.py -f sample.txt -w u -v

Usage

python phen2gene.py [-h] [-f [FILE.NAME [FILE.NAME ...]]]

             [-m [HPID [HPID ...]]] [-w w|u] [-v] [-out OUTPUT]
             
optional arguments:

  -h, --help            show this help message and exit
  
  -f [FILE.NAME [FILE.NAME ...]], --file [FILE.NAME [FILE.NAME ...]]

                        Input HPO as file.
  -m [HPID [HPID ...]], --manual [HPID [HPID ...]]
                        Input HPO ID(s) one by one, seperated by an empty
                        space.
  -w w|u, --method w|u  Methods to merge gene scores. 
                        'w' ( Default ) Scoring by weighted Human-Phenotype terms.
                        'u' Scoring by Unweighted Human-Phenotype terms.
  -v, --verbosity       Display Phen2Gene workflow verbosely.
  -out OUTPUT, --output OUTPUT
                        Specify the path to store output files. Default
                        directory path: ./out/