Add CASP-CAPRI parallel processing scripts

Author: amorehead

project/datasets/builder/compile_casp_capri_dataset_on_andes.sh

@@ -0,0 +1,33 @@
+#!/bin/bash
+
+####################### Batch Headers #########################
+#SBATCH -A BIF135
+#SBATCH -p batch
+#SBATCH -J make_casp_capri_dataset
+#SBATCH -t 0-24:00
+#SBATCH --mem 224G
+#SBATCH --nodes 4
+#SBATCH --ntasks-per-node 1
+###############################################################
+
+# Remote paths #
+export PROJDIR=/gpfs/alpine/scratch/"$USER"/bif135/Repositories/Lab_Repositories/DIPS-Plus
+export PSAIADIR=/ccs/home/"$USER"/Programs/PSAIA_1.0_source/bin/linux/psa
+export OMP_NUM_THREADS=8
+
+# Remote Conda environment #
+source "$PROJDIR"/miniconda3/bin/activate
+conda activate DIPS-Plus
+
+# Load CUDA module for DGL
+module load cuda/10.2.89
+
+# Default to using the Big Fantastic Database (BFD) of protein sequences (approx. 270GB compressed)
+export HHSUITE_DB=/gpfs/alpine/scratch/$USER/bif132/Data/Databases/bfd_metaclust_clu_complete_id30_c90_final_seq
+
+# Run dataset compilation scripts
+cd "$PROJDIR"/project || exit
+
+srun python3 "$PROJDIR"/project/datasets/builder/generate_hhsuite_features.py "$PROJDIR"/project/datasets/CASP-CAPRI/interim/parsed "$PROJDIR"/project/datasets/CASP-CAPRI/interim/parsed "$HHSUITE_DB" "$PROJDIR"/project/datasets/CASP-CAPRI/interim/external_feats --rank "$1" --size "$2" --num_cpu_jobs 4 --num_cpus_per_job 8 --num_iter 2 --source_type casp_capri --write_file
+
+#srun python3 "$PROJDIR"/project/datasets/builder/postprocess_pruned_pairs.py "$PROJDIR"/project/datasets/CASP-CAPRI/raw "$PROJDIR"/project/datasets/CASP-CAPRI/interim/pairs "$PROJDIR"/project/datasets/CASP-CAPRI/interim/external_feats "$PROJDIR"/project/datasets/CASP-CAPRI/final/raw --num_cpus 32 --rank "$1" --size "$2" --source_type CASP-CAPRI

project/datasets/builder/compile_evcoupling_dataset_on_andes.sh

@@ -31,11 +31,3 @@ cd "$PROJDIR"/project || exit
 srun python3 "$PROJDIR"/project/datasets/builder/generate_hhsuite_features.py "$PROJDIR"/project/datasets/EVCoupling/interim/parsed "$PROJDIR"/project/datasets/EVCoupling/interim/parsed "$HHSUITE_DB" "$PROJDIR"/project/datasets/EVCoupling/interim/external_feats --rank "$1" --size "$2" --num_cpu_jobs 4 --num_cpus_per_job 8 --num_iter 2 --source_type evcoupling --read_file
 
 #srun python3 "$PROJDIR"/project/datasets/builder/postprocess_pruned_pairs.py "$PROJDIR"/project/datasets/EVCoupling/raw "$PROJDIR"/project/datasets/EVCoupling/interim/pairs "$PROJDIR"/project/datasets/EVCoupling/interim/external_feats "$PROJDIR"/project/datasets/EVCoupling/final/raw --num_cpus 32 --rank "$1" --size "$2" --source_type EVCoupling
-
-#python3 "$PROJDIR"/project/datasets/builder/partition_dataset_filenames.py "$PROJDIR"/project/datasets/EVCoupling/final/raw --source_type EVCoupling --rank "$1" --size "$2"
-#python3 "$PROJDIR"/project/datasets/builder/collect_dataset_statistics.py "$PROJDIR"/project/datasets/EVCoupling/final/raw --rank "$1" --size "$2"
-#python3 "$PROJDIR"/project/datasets/builder/log_dataset_statistics.py "$PROJDIR"/project/datasets/EVCoupling/final/raw --rank "$1" --size "$2"
-#python3 "$PROJDIR"/project/datasets/builder/impute_missing_feature_values.py "$PROJDIR"/project/datasets/EVCoupling/final/raw --impute_atom_features False --num_cpus 32 --rank "$1" --size "$2"
-
-# Optionally convert each postprocessed (final 'raw') complex into a pair of DGL graphs (final 'processed') with labels
-#python3 "$PROJDIR"/project/datasets/builder/convert_complexes_to_graphs.py "$PROJDIR"/project/datasets/EVCoupling/final/raw "$PROJDIR"/project/datasets/EVCoupling/final/processed --num_cpus 32 --edge_dist_cutoff 15.0 --edge_limit 5000 --self_loops True --rank "$1" --size "$2"