YeoLab / SONAR

A program to construct SVM model and get classification scores for predicting RNA-binding proteins with given PPI network and RBP annotation list

SONAR

SONAR is an algorithm to predict proteins' RNA-binding capability based on their protein-protein interaction neighborhood. This program will run SONAR with your PPI network edge list and RBP annotation list and give you a score table which contains the classification scores for all the proteins appearing in the PPI network. The immediate result (i.e. feature table involved in the classification) will also be presented. The program may run for several hours, please be patient.

Install

cd SONAR_directory

python setup.py install

Usage:

sonar -e Edge_list_File -r RBP_annotation_list [-p num_processes] [--outfile_feature_table feature_table_filename] [-o score_table_filename] [-R num_repeats]

By default, the output files will be put in the SONAR software folder. If you wanna make them in other folders, please specify the path of the folder in front of the filenames.

Example:

sonar -p 16 -r SONAR_directory/SONAR/Demo/RBP_merged_list.txt -e SONAR_directory/SONAR/Demo/BioPlex_interactionList_v4_edgelist.txt --outfile_feature_table=BioPlex_PPI_feature_table.xls -o SONAR_score_table_BioPlex_human.xls

Alternative way for run the program (i.e. directly run python scripts):

Prerequisite:

    python2.7/python3.7+
    python packages: pandas, networkx, numpy, multiprocessing, argparse, sklearn. 

Usage:

    1. Enter the SONAR software folder
    2. python SONAR_directory/SONAR/Demo/sonar.py -e Edge_list_File -r RBP_annotation_list [-p num_processes] [--outfile_feature_table filename] [-o outfile] [-R num_repeats]
    3. If the input files are not in the SONAR software folder, you have to specify the paths of these files in front of the filenames. By default, the output files will be put in the SONAR software folder. If you wanna make them in other folders, please specify the path of the folder in front of the filenames.

Reference:

Brannan KW, Jin W, Huelga SC, Banks CA, Gilmore JM, Florens L, Washburn MP, Van Nostrand EL, Pratt GA, Schwinn MK, Daniels DL, Yeo GW. SONAR Discovers RNA-Binding Proteins from Analysis of Large-Scale Protein-Protein Interactomes. Molecular Cell. 2016 Oct 20;64(2):282-93.

Please contact me if you have any problem running this program. Email address: [e-mail] (Wenhao Jin)

Wenhao Jin

6 Oct, 2016