humap_steps.sh

#!/bin/bash

mtype=humap
input_file_name=input_$mtype.yaml
graph_file=hu.MAP_network/input_data/humap_network_weighted_edge_lists.txt
input_training_file=hu.MAP_network/intermediate_data/training_CORUM_complexes_node_lists.txt
input_testing_file=hu.MAP_network/intermediate_data/testing_CORUM_complexes_node_lists.txt
mkdir results_$mtype
out_dir_name=./results_$mtype
train_results=$out_dir_name/train_results
pred_results=$out_dir_name/pred_results
id_map_path=convert_ids/humap_gene_id_name_map.txt

echo Training Algorithm....
python3 main_training.py --input_training_file $input_training_file --graph_file $graph_file --train_results $train_results

echo Predicting new complexes from known communities...
python3 main_prediction.py --graph_file $graph_file --train_results $train_results --out_dir_name $out_dir_name --pred_results $pred_results

echo Merging similar communities...
python3 postprocessing.py --input_file_name $input_file_name --graph_file $graph_file --out_dir_name $out_dir_name --pred_results $pred_results --train_results $train_results --input_training_file $input_training_file --input_testing_file $input_testing_file --id_map_path $id_map_path

echo Comparing predicted and known communitites...
python3 eval_complex_RL.py --input_file_name $input_file_name  --input_training_file $input_training_file --input_testing_file $input_testing_file --out_dir_name $out_dir_name --id_name_path $id_map_path