changeset 53:7b57a93ac594 draft

Uploaded

--- a/Marea/marea.py	Fri Mar 13 14:26:31 2020 -0400
+++ b/Marea/marea.py	Sun Mar 15 11:19:36 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 #############################################
 
@@ -812,9 +782,6 @@
 
     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 = {}