--- a/Marea/marea.py	Tue Oct 01 06:03:12 2019 -0400
+++ b/Marea/marea.py	Tue Oct 01 06:05:13 2019 -0400
@@ -1,4 +1,3 @@
-
 from __future__ import division
 import sys
 import pandas as pd
@@ -6,6 +5,7 @@
 import scipy.stats as st
 import collections
 import lxml.etree as ET
+import shutil
 import pickle as pk
 import math
 import os
@@ -13,7 +13,7 @@
 from svglib.svglib import svg2rlg
 from reportlab.graphics import renderPDF
 
-########################## argparse ###########################################
+########################## argparse ##########################################
 
 def process_args(args):
     parser = argparse.ArgumentParser(usage = '%(prog)s [options]',
@@ -71,6 +71,21 @@
                         type = str,
                         choices = ['yes', 'no'],
                         help = 'if make or not custom map')
+    parser.add_argument('-gs', '--generate_svg',
+                        type = str,
+                        default = 'true',
+                        choices = ['true', 'false'], 
+                        help = 'generate svg map')
+    parser.add_argument('-gp', '--generate_pdf',
+                        type = str,
+                        default = 'true',
+                        choices = ['true', 'false'], 
+                        help = 'generate pdf map')
+    parser.add_argument('-gr', '--generate_ras',
+                        type = str,
+                        default = 'true',
+                        choices = ['true', 'false'],
+                        help = 'generate reaction activity score')
     args = parser.parse_args()
     return args
 
@@ -85,7 +100,7 @@
 
 def read_dataset(data, name):
     try:
-        dataset = pd.read_csv(data, sep = '\t', header = 0)
+        dataset = pd.read_csv(data, sep = '\t', header = 0, engine='python')
     except pd.errors.EmptyDataError:
         sys.exit('Execution aborted: wrong format of ' + name + '\n')
     if len(dataset.columns) < 2:
@@ -536,7 +551,7 @@
         ids = [react[i].id for i in range(len(react))]
     except cb.io.sbml3.CobraSBMLError:
         try:
-            data = (pd.read_csv(data, sep = '\t', dtype = str)).fillna('')
+            data = (pd.read_csv(data, sep = '\t', dtype = str, engine='python')).fillna('')
             if len(data.columns) < 2:
                 sys.exit('Execution aborted: wrong format of '+
                          'custom datarules\n')
@@ -641,9 +656,28 @@
                         ', the class has been disregarded\n')
     return class_pat
 
+############################ create_ras #######################################
+
+def create_ras (resolve_rules, dataset_name):
+
+    if resolve_rules == None:
+        warning("Couldn't generate RAS for current dataset: " + dataset_name)
+
+    for geni in resolve_rules.values():
+        for i, valori in enumerate(geni):
+            if valori == None:
+                geni[i] = 'None'
+                
+    output_ras = pd.DataFrame.from_dict(resolve_rules)
+    output_to_csv = pd.DataFrame.to_csv(output_ras, sep = '\t', index = False)
+                
+    text_file = open("ras/Reaction_Activity_Score_Of_" + dataset_name + ".tsv", "w")
+    text_file.write(output_to_csv)
+    text_file.close()
+
 ############################ map ##############################################
 
-def maps(core_map, class_pat, ids, threshold_P_V, threshold_F_C):
+def maps(core_map, class_pat, ids, threshold_P_V, threshold_F_C, create_svg, create_pdf):
     args = process_args(sys.argv)
     if (not class_pat) or (len(class_pat.keys()) < 2):
         sys.exit('Execution aborted: classes provided for comparisons are ' +
@@ -663,52 +697,81 @@
                count += 1
             except (TypeError, ZeroDivisionError):
                count += 1
-        tab = 'table_out/' + i + '_vs_' + j + '.tsv'
+        tab = 'result/' + i + '_vs_' + j + ' (Tabular Result).tsv'
         tmp_csv = pd.DataFrame.from_dict(tmp, orient = "index")
         tmp_csv = tmp_csv.reset_index()
         header = ['ids', 'P_Value', 'Average']
         tmp_csv.to_csv(tab, sep = '\t', index = False, header = header)
-        if args.rules_selector == 'HMRcore' or (args.rules_selector == 'Custom'
-                                                and args.yes_no == 'yes'):
-            fix_map(tmp, core_map, threshold_P_V, threshold_F_C, max_F_C)
-            file_svg = 'map_svg/' + i + '_vs_' + j + '.svg'
-            with open(file_svg, 'wb') as new_map:
-                new_map.write(ET.tostring(core_map, encoding='UTF-8',
-                                          method='xml'))
-            file_pdf = 'map_pdf/' + i + '_vs_' + j + '.pdf'
-            renderPDF.drawToFile(svg2rlg(file_svg), file_pdf)
+        
+        if create_svg or create_pdf:
+            if args.rules_selector == 'HMRcore' or (args.rules_selector == 'Custom'
+                                                    and args.yes_no == 'yes'):
+                fix_map(tmp, core_map, threshold_P_V, threshold_F_C, max_F_C)
+                file_svg = 'result/' + i + '_vs_' + j + ' (SVG Map).svg'
+                with open(file_svg, 'wb') as new_map:
+                    new_map.write(ET.tostring(core_map))
+                    
+                
+                if create_pdf:
+                    file_pdf = 'result/' + i + '_vs_' + j + ' (PDF Map).pdf'
+                    renderPDF.drawToFile(svg2rlg(file_svg), file_pdf)
+                
+                if not create_svg:
+                    #Ho utilizzato il file svg per generare il pdf, 
+                    #ma l'utente non ne ha richiesto il ritorno, quindi
+                    #lo elimino
+                    os.remove('result/' + i + '_vs_' + j + ' (SVG Map).svg')
+                    
     return None
 
 ############################ MAIN #############################################
 
 def main():
     args = process_args(sys.argv)
-    os.makedirs('table_out')
-    if args.rules_selector == 'HMRcore':
-        os.makedirs('map_svg')
-        os.makedirs('map_pdf')
+    
+    create_svg = check_bool(args.generate_svg)
+    create_pdf = check_bool(args.generate_pdf)
+    generate_ras = check_bool(args.generate_ras)
+    
+    os.makedirs('result')
+
+    if generate_ras:
+        os.makedirs('ras')
+    
+    if args.rules_selector == 'HMRcore':        
         recon = pk.load(open(args.tool_dir + '/local/HMRcore_rules.p', 'rb'))
     elif args.rules_selector == 'Recon':
         recon = pk.load(open(args.tool_dir + '/local/Recon_rules.p', 'rb'))
     elif args.rules_selector == 'Custom':
         ids, rules, gene_in_rule = make_recon(args.custom)
+        
     resolve_none = check_bool(args.none)
+    
     class_pat = {}
+    
     if args.option == 'datasets':
         num = 1
-        #if len(args.names) != len(set(args.names)):
-        #    sys.exit('Execution aborted: datasets name duplicated')
         for i, j in zip(args.input_datas, args.names):
+
             name = name_dataset(j, num)
             dataset = read_dataset(i, name)
+
             dataset.iloc[:, 0] = (dataset.iloc[:, 0]).astype(str)
-            type_gene = gene_type(dataset.iloc[0, 0], name)
+
+            type_gene = gene_type(dataset.iloc[0, 0], name) 
+            
             if args.rules_selector != 'Custom':
                 genes = data_gene(dataset, type_gene, name, None)
                 ids, rules = load_id_rules(recon.get(type_gene))
             elif args.rules_selector == 'Custom':
                 genes = data_gene(dataset, type_gene, name, gene_in_rule)
+                
             resolve_rules, err = resolve(genes, rules, ids, resolve_none, name)
+
+            if generate_ras:
+                create_ras(resolve_rules, name)
+                
+            
             if err != None and err:
                 warning('Warning: gene\n' + str(err) + '\nnot found in class '
                     + name + ', the expression level for this gene ' +
@@ -738,10 +801,9 @@
                     'will be considered NaN\n')
         if resolve_rules != None:
             class_pat = split_class(classes, resolve_rules)
+            
     if args.rules_selector == 'Custom':
         if args.yes_no == 'yes':
-            os.makedirs('map_svg')
-            os.makedirs('map_pdf')
             try:
                 core_map = ET.parse(args.custom_map)
             except (ET.XMLSyntaxError, ET.XMLSchemaParseError):
@@ -750,8 +812,11 @@
             core_map = ET.parse(args.tool_dir + '/local/HMRcoreMap.svg')
     else:       
         core_map = ET.parse(args.tool_dir+'/local/HMRcoreMap.svg')
-    maps(core_map, class_pat, ids, args.pValue, args.fChange)
-    warning('Execution succeeded')
+        
+    maps(core_map, class_pat, ids, args.pValue, args.fChange, create_svg, create_pdf)
+        
+    print('Execution succeded')
+
     return None
 
 ###############################################################################