modify batch scripts to allow for separate output directories and to …

…specify number of top genes and corresponding directories for output

scripts/msbatch.sh

@@ -1,9 +1,10 @@
 #!/usr/bin/env bash
 
 DATA_DIR=data/TCGA_PanCancer_Atlas_2018 ##TODO: SPECIFY DIR W/ MAF FILES
+DOUT=output/TOP_10_Genes ##TODO: SPECIFY OUTPUT DIR
 MAF_FILES=(${DATA_DIR}/*.maf) ## Array of all MAF files in the directory
 SCRIPT_DIR=$(dirname "$0") ## Directory of the current script
-SLURM_DIR=output/slurm_logs
+SLURM_DIR=${DOUT}/slurm_logs
 
 mkdir -p ${SLURM_DIR}
 

scripts/ssbatch.sh

@@ -14,15 +14,16 @@ cd ${DISCOVER_DIR}
 python setup.py install --user  # Use --user to install DISCOVER in user space
 cd ${ORIGINAL_DIR}
 
-K=100 ##TODO SPECIFY NUMBER OF TOP GENES
+K=10 ##TODO SPECIFY NUMBER OF TOP GENES
+DOUT=output/TOP_10_Genes ##TODO: SPECIFY OUTPUT DIR
 MAF_FILE=${1}                ## MAF file path
 SUBTYPE_NAME=$(basename ${MAF_FILE} .maf) ## Extract subtype name from MAF file
-OUTPUT_DIR=output/${SUBTYPE_NAME} ## Set output directory
+OUTPUT_DIR=${DOUT}/${SUBTYPE_NAME} ## Set output directory
 
 mkdir -p ${OUTPUT_DIR}
 
 ## Commands to run
-dialect generate -m ${MAF_FILE} -o ${OUTPUT_DIR}
+# dialect generate -m ${MAF_FILE} -o ${OUTPUT_DIR} ##TODO: UNCOMMENT TO RUN END TO END
 dialect identify -c ${OUTPUT_DIR}/count_matrix.csv -b ${OUTPUT_DIR}/bmr_pmfs.csv -o ${OUTPUT_DIR} -k ${K} -cb ${OUTPUT_DIR}/CBaSE_output/q_values.txt
 dialect compare -c ${OUTPUT_DIR}/count_matrix.csv -b ${OUTPUT_DIR}/bmr_pmfs.csv -o ${OUTPUT_DIR} -k ${K}
 dialect merge -d ${OUTPUT_DIR}/pairwise_interaction_results.csv -a ${OUTPUT_DIR}/comparison_interaction_results.csv -o ${OUTPUT_DIR}