Merge branch 'master' into secreton-2

src/parser/parser.py

@@ -5,7 +5,7 @@ Created on 27 dec. 2011
 
 @author: Bertrand Néron
 """
-
+from __future__ import print_function
 from collections import namedtuple
 from couchdbkit.client import Server
 from couchdbkit.exceptions import ResourceNotFound
@@ -26,7 +26,7 @@ def replicon_parser(replicon_data):
     :rtype: dict
     """
     replicon_db = {}
-    Replicon_info = namedtuple('Replicon_info', 'name, ncbi_id, taxid, strain, taxonomy, type')
+    Replicon_info = namedtuple('Replicon_info', ('name', 'taxid', 'strain', 'taxonomy', 'type'))
     with open(replicon_data, 'r') as replicon_file:
         for line in replicon_file:
             if not line.startswith('#'):
@@ -51,7 +51,6 @@ def replicon_parser(replicon_data):
                         raise Exception("Error during parsing line : {0} : {1}".format(line, err))
     return replicon_db
 
-
 def system_parser(system_data):
     """
     :param system_data: the path of secretion system information file
@@ -63,7 +62,9 @@ def system_parser(system_data):
 
     System_info = namedtuple('System_info', 'code, predicted_system, system_status, replicon,  genes')
     Gene = namedtuple('Gene',
-                      'code, id, protein_length, strand, begin, end, match, score, i-evalue, coverage, match_begin, match_end, name, description')
+                      ('code', 'id', 'protein_length', 'strand', 'begin', 'end', 'match',
+                       'score', 'i_evalue', 'coverage', 'match_begin', 'match_end', 'name', 'description')
+                      )
   
     with open(system_data, 'r') as system_file :
         for line in system_file:
@@ -181,9 +182,9 @@ def fill_db(server_uri, db_name, user, passwd, replicon_db, system_db, force_upd
         secretion_system.genes = genes
         secreton_db.save_doc(secretion_system, force_update=force_update)
 
-
+          
 if __name__ == '__main__':
-    from optparse import OptionParser, OptionGroup
+    import argparse
     import sys
     import getpass
    
@@ -197,60 +198,56 @@ if __name__ == '__main__':
        parse a file containing replicon informations and a file containing system informations
        and fill a couchDB data base with these informations 
 """
-    parser = OptionParser(usage=usage)
-    server_opt = OptionGroup(parser, "Server Options")
-    server_opt.add_option("-S", "--server",
-                          action="store",
-                          type="string",
-                          dest="server_url",
-                          help="the url of the couchDB server (with the port)")
-    server_opt.add_option("-d", "--database",
-                          action="store",
-                          type="string",
-                          dest="db_name",
-                          help="the name of the data base")
-    parser.add_option_group(server_opt)
-    
-    parsing_opt = OptionGroup(parser, "Parsing Options")
-    parsing_opt.add_option("-r", "--replicon",
-                           action="store",
-                           type="string",
-                           dest="replicon_path",
-                           help="the path to the replicon file to parse")
-    parsing_opt.add_option("-s", "--system",
-                           action="store",
-                           type="string",
-                           dest="system_path",
-                           help="the path to the system secretion file to parse")
-    parsing_opt.add_option("-f", "--force_update",
-                           action="store_true",
-                           dest="force_update",
-                           default=False,
-                           help="")
-    parser.add_option_group(parsing_opt)
-    
+    parser = argparse.ArgumentParser(usage=usage)
+    server_opt = parser.add_argument_group(title="Server Options")
+    server_opt.add_argument("-S", "--server",
+                            action="store",
+                            type="string",
+                            dest="server_url",
+                            help="the url of the couchDB server (with the port)")
+    server_opt.add_argument("-d", "--database",
+                            action="store",
+                            type="string",
+                            dest="db_name",
+                            help="the name of the data base")
+    parsing_opt = parser.add_argument_group(title="Parsing Options")
+    parsing_opt.add_argument("-r", "--replicon",
+                             action="store",
+                             type="string",
+                             dest="replicon_path",
+                             help="the path to the replicon file to parse")
+    parsing_opt.add_argument("-s", "--system",
+                             action="store",
+                             type="string",
+                             dest="system_path",
+                             help="the path to the system secretion file to parse")
+    parsing_opt.add_argument("-f", "--force_update",
+                             action="store_true",
+                             dest="force_update",
+                             default=False,
+                             help="insert document even if there is already a document with the same id (replace it)")
     options, args = parser.parse_args()
     
     if not options.server_url:
-        print >> sys.stderr, "You must specify a server url"
+        print("You must specify a server url", file=sys.stderr)
         parser.print_help(sys.stderr)
         sys.exit(1)
         
     if not options.db_name:
-        print >> sys.stderr, "You must specify a data base name"
+        print("You must specify a data base name", file=sys.stderr)
         parser.print_help(sys.stderr)
         sys.exit(1)
         
     if not options.replicon_path:
-        print >> sys.stderr, "You must specify the path to the replicon information file"
+        print("You must specify the path to the replicon information file", file=sys.stderr)
         parser.print_help(sys.stderr)
         sys.exit(1)
         
     if not options.system_path:
-        print >> sys.stderr, "You must specify the path to the secretion system information file"
+        print("You must specify the path to the secretion system information file", file=sys.stderr)
         parser.print_help(sys.stderr)
         sys.exit(1)
-
+    
     replicon_db = replicon_parser(options.replicon_path)
     system_db = system_parser(options.system_path)
    
@@ -261,11 +258,11 @@ if __name__ == '__main__':
             fill_db(options.server_url, options.db_name, user, password,
                     replicon_db, system_db, force_update=options.force_update)
             break
-        except restkit.errors.Unauthorized, err:
-            print >> sys.stderr, "Bad authentication, try again"
+        except restkit.errors.Unauthorized as err:
+            print("Bad authentication, try again", file=sys.stderr)
             try_again += 1
             if try_again > 2:
                 sys.exit("Authentication failure")
         except Exception, err:
-            print >> sys.stderr, err
+            print(err, file=sys.stderr)
             sys.exit(2)