--- a/Marea/marea.py	Mon Mar 16 07:47:12 2020 -0400
+++ b/Marea/marea.py	Mon Mar 16 08:21:29 2020 -0400
@@ -537,36 +537,6 @@
         warning('Warning: wrong format rule in ' + str(err_rules) + '\n')
     return (split_rules, list(set(tmp_gene_in_rule)))
 
-def make_recon(data):
-    try:
-        import cobra as cb
-        import warnings
-        with warnings.catch_warnings():
-            warnings.simplefilter('ignore')
-            recon = cb.io.read_sbml_model(data)
-        react = recon.reactions
-        rules = [react[i].gene_reaction_rule for i in range(len(react))]
-        ids = [react[i].id for i in range(len(react))]
-    except cb.io.sbml.CobraSBMLError:
-        try:
-            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')
-            if not len(data.columns) == 2:
-                warning('Warning: more than 2 columns in custom datarules.\n' +
-                        'Extra columns have been disregarded\n')
-            ids = list(data.iloc[:, 0])
-            rules = list(data.iloc[:, 1])
-        except pd.errors.EmptyDataError:
-            sys.exit('Execution aborted: wrong format of custom datarules\n')
-        except pd.errors.ParserError:
-            sys.exit('Execution aborted: wrong format of custom datarules\n')            
-    split_rules, tmp_genes = do_rules(rules)
-    gene_in_rule = {}
-    for i in tmp_genes:
-        gene_in_rule[i] = 'ok'
-    return (ids, split_rules, gene_in_rule)
 
 ############################ gene #############################################
 
@@ -666,7 +636,6 @@
 
     if comparison == "manyvsmany":
         for i, j in it.combinations(class_pat.keys(), 2):
-            
             tmp = {}
             count = 0
             max_F_C = 0
@@ -702,10 +671,6 @@
                         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')
     elif comparison == "onevsrest":
         for single_cluster in class_pat.keys():
@@ -739,8 +704,8 @@
             tmp_csv.to_csv(tab, sep = '\t', index = False, header = header)
             
             if create_svg or create_pdf:
-                if args.rules_selector == 'HMRcore' or (args.rules_selector == 'Custom'
-                                                        and args.yes_no == 'yes'):
+                if args.custom_rules == 'false' or (args.custom_rules == 'true'
+                                                        and args.custom_map != ''):
                     fix_map(tmp, core_map, threshold_P_V, threshold_F_C, max_F_C)
                     file_svg = 'result/' + single_cluster + '_vs_ rest (SVG Map).svg'
                     with open(file_svg, 'wb') as new_map:
@@ -756,6 +721,10 @@
                         
     elif comparison == "onevsmany":
         for i, j in it.combinations(class_pat.keys(), 2):
+            if i != control and j != control:
+                continue
+            if i == control and j == control:
+                continue
             tmp = {}
             count = 0
             max_F_C = 0
@@ -778,8 +747,8 @@
             tmp_csv.to_csv(tab, sep = '\t', index = False, header = header)
             
             if create_svg or create_pdf:
-                if args.rules_selector == 'HMRcore' or (args.rules_selector == 'Custom'
-                                                        and args.yes_no == 'yes'):
+                if args.custom_rules == 'false' or (args.custom_rules == 'true'
+                                                        and args.custom_map != ''):
                     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:
@@ -791,10 +760,6 @@
                         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')
         
         
@@ -812,9 +777,6 @@
 
     if os.path.isdir('result') == False:
         os.makedirs('result')
-        
-    if args.custom_rules == 'true':
-        ids, rules, gene_in_rule = make_recon(args.custom_rule)
 
     class_pat = {}
     
@@ -879,7 +841,13 @@
     else:
         core_map = ET.parse(args.tool_dir+'/local/HMRcoreMap.svg')
         
-    maps(core_map, class_pat, ids, args.pValue, args.fChange, create_svg, create_pdf, args.comparison, args.control)
+    class_pat_trim = {}
+    
+    for key in class_pat.keys():
+    	class_pat_trim[key.strip()] = class_pat[key]
+ 
+        
+    maps(core_map, class_pat_trim, ids, args.pValue, args.fChange, create_svg, create_pdf, args.comparison, args.control)
         
     print('Execution succeded')