genome-classifier's Introduction
*----------------------------------------------------------------------- * README.txt * * Instructions for running the SGE parallel job and SVM classifier for * Zach Wallace. * * Class: BOT 599 * Term: Spring 2018 *----------------------------------------------------------------------- * * * OVERVIEW * * All shell scripts to run are contained in the 'run_job' directory. * When running these scripts, stay in the top-level 'Wallace_Project' * directory where this README is located. Thus, all shell scripts will * have a 'run_job/' prefix. * * Commands to enter are labeled below as numbered steps. Here I briefly * describe what each will do: * * - Steps 1-3 build the first feature set to feed into the SVM. * - Steps 4-6 build the second feature set to feed into the SVM. * - Step 7 runs the classifer. * * I had to include command line arguments for some of the scripts, since * the bash wrappers and the python functions were not playing well together. * If you simply copy and paste to your terminal and hit enter separately * for each step below (omitting the "Step X: " portions), all scripts * should run smoothly. I apologize for any inconvenience. * Step 1: python3 run_job/1_delete_old_files.py Step 2: ./run_job/2_pipeline.sh FASTA/exonseq_upstream100_MT.txt Step 3: ./run_job/3_merge_files.sh class1.txt Step 4: python3 run_job/1_delete_old_files.py Step 5: ./run_job/2_pipeline.sh FASTA/flank_upstream100_MT.txt Step 6: ./run_job/3_merge_files.sh class2.txt Step 7: ./run_job/4_call_quick_svm.sh
genome-classifier's People
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