README.md

Welcome to this site for the One-Class Support Vector Machine (OCSVM)-Splicing tool. This site will serve as a source code repository for OCSVM-Splicing pipeline.

Prerequisites

This program requires the following modules.

1. Python (=> 2.7 ): https://www.python.org/
2. NumPy : http://www.numpy.org/
3. scikit-learn : http://scikit-learn.org/stable/index.html
4. computed splicing strength scores using MaxEntScan
   • 5' splice sites : http://genes.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq.html
   • 3' splice sites : http://genes.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq_acc.html

Options

1. -m INT : OCSVM-Splicing model number (1,2,or 3)

2. -i STR : Input file name

3. -o STR : Output file name

   example:  python one_calss_SVM.py -m 1 -i model_1_input_example.txt -o model_1_output.txt
   
   

OCSVM-Splicing models

• Model 1 : Intornic SNVs at 5' splice sites (within 4bp next to GT)

• Input : score of 5’splice_MUT – 5’splice_WT and 5’splice_MUT – 3’splice_WT
• example input (tab-delimited format; order of columns should not change)

• Model 2 : Intornic SNVs at 3' splice sites (within 1bp next to AG)

• Input : score of 3’splice_MUT – 3’splice_WT and 3’splice_MUT –5’splice_WT
• example input (tab-delimited format; order of columns should not change)

• Model 3 : Exonic SNVs at 5' splice sites (within 2bp next to GT)

• Input : score of 5’splice_MUT – 5’splice_WT and 5’splice_MUT – 3’splice_WT
• example input (tab-delimited format; order of columns should not change)

Output Results

Each model annotes SNVs as "benign" or "deleterious".

• example