/IMSP-Parser

Primary LanguageJava

IMSP's Data parser

Parse raw data from NCBI Blastp into pair-wise similarity matrices

Installation

  • Clone the repository
  • Make sure you have JDK 1.7 or above installed

Usage

  • Collect protein FASTA files as shown in file FASTA.txt
  • Obtain XXX-Alignment-hitTable.csvfrom either online BLASTp or Local Blast
  • Put XXX-Alignment-hitTable.csv in Parser/protein data/layer_name/protein_name/
  • Navigate to src/Parser/driver.java
  • Run the main method, the result will be in Parser/Result/layer_name/protein_name-group_name.csv