iPRESTO refactor

Made the iPRESTO repo more workable. Bump iPRESTO to v1.1.0

auxiliary_scripts/run_multiple_lda.py

-#!/usr/bin/env python3
-"""
-Author: Joris Louwen
-Script to run LDA multiple times to find good parameters for applying LDA
-to identify modules.
-"""
-
-import subprocess
-
-if __name__ == '__main__':
-    command = 'python3 ~/thesis/scripts-thesis/presto_top/presto_top.py -i ipresto_output_build_models_all_sponge_gbks_biosynt_15-1/all_sponge_gbks_clusterfile_filtered_clusterfile.csv -o ipresto_output_build_models_all_sponge_gbks_biosynt_15-1/ipresto_out_100t_1000chnk -t 100 -C 1000 -I 2000 -c 5 --classes ipresto_output_all_sponge_gbks_10-1/all_classes.txt --known_subclusters /mnt/scratch/louwe015/subcluster_data/subclusterblast_data/subclusters_subclusterblast_domains_synt_subset.txt | tee log_ipresto_output_build_models_all_sponge_gbks_biosynt_15-1_ipresto_out_100t_1000chnk.txt'
-    topic_range= [50,75,100,150,200]
-    for i in topic_range:
-        #without -a
-        command_without_a = command.format(i,'','6000',i,'')
-        print(command_without_a)
-        try:
-            subprocess.check_call(command_without_a, shell=True)
-        except subprocess.CalledProcessError:
-            print(command_without_a)
-            print('all empty topics?')
-        
-        command_with_a = command.format(i,'x10_','60000',i,'-a 10 ')
-        print(command_with_a)
-        try:
-            subprocess.check_call(command_with_a, shell=True)
-        except subprocess.CalledProcessError:
-            print(command_with_a)
-            print('all empty topics?')