fix pep8 and python2.7 syntax

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
@@ -23,7 +23,7 @@ def replicon_parser( replicon_data ):
     @rtype: dict
     """
     replicon_db = {}
-    Replicon_info = namedtuple('Replicon_info', 'name, 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 line[0] != '#':
@@ -33,16 +33,20 @@ def replicon_parser( replicon_data ):
                     raise KeyError("duplicate replicon:" + fields[0])
                 else:
                     try:
-                        replicon_db[ fields[0] ] = Replicon_info( fields[0] , int(fields[1]) , fields[2] , fields[3].split('; ') , fields[4])
-                    except Exception, err:
-                        raise Exception( "Error during parsing line :"+line )
-                    #remove ending dot or semi-colon from the last term of taxonnomy
-                    if( replicon_db[ fields[0] ].taxonomy[-1].endswith('.') or replicon_db[ fields[0] ].taxonomy[-1].endswith(';')):
+                        replicon_db[fields[0]] = Replicon_info(fields[0],
+                                                               int(fields[1]),
+                                                               fields[2],
+                                                               fields[3].split('; '),
+                                                               fields[4])
+                    except Exception as err:
+                        raise Exception("Error during parsing line: {0}\n{1}".format(line, err))
+                    # remove ending dot or semi-colon from the last term of taxonomy
+                    tax_last_char = replicon_db[fields[0]].taxonomy[-1]
+                    if tax_last_char.endswith('.') or tax_last_char.endswith(';'):
                         replicon_db[fields[0]].taxonomy[-1] = replicon_db[fields[0]].taxonomy[-1][:-1]
     return replicon_db
                 
 
-
 def system_parser(system_data):
     """
     @param system_data: the path of secretion system information file
@@ -52,7 +56,9 @@ def system_parser( system_data ):
     """
     system_db = {}
     System_info = namedtuple('System_info', 'code, T3SS_family, replicon,  genes')
-    Gene = namedtuple( 'Gene', 'code, id, protein_length, strand, begin, end, match, full_score, e_value, best_domain_score, best_domain_evalue, c_value, coverage_profile, match_begin, match_end, name, description')
+    Gene = namedtuple('Gene', ('code', 'id', 'protein_length', 'strand', 'begin', 'end', 'match', 'full_score',
+                               'e_value', 'best_domain_score', 'best_domain_evalue', 'c_value', 'coverage_profile',
+                               'match_begin', 'match_end', 'name', 'description'))
   
     with open(system_data, 'r') as system_file:
         for line in system_file:
@@ -87,7 +93,7 @@ def system_parser( system_data ):
                             # append this gene to System_info genes
                             system_db[fields[16]].genes[gene.code] = gene
                     else:
-                        #create a new Sysem_info entry
+                        # create a new System_info entry
                         system_db[fields[16]] = System_info(fields[16], fields[17], fields[15], genes={gene.code: gene})
     return system_db
 
@@ -153,7 +159,7 @@ def fill_db( server_uri, db_name, user, passwd, replicon_db , system_db , force_
         secreton_db.save_doc(secretion_system, force_update=force_update)
           
 if __name__ == '__main__':
-    from optparse import OptionParser , OptionGroup
+    import argparse
     import sys
     import getpass
    
@@ -167,61 +173,56 @@ 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" ,
+    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_option( "-d" , "--database" ,
+    server_opt.add_argument("-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" ,
+    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_option( "-s" , "--system" ,
+    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_option( "-f" , "--force_update" ,
+    parsing_opt.add_argument("-f", "--force_update",
                              action="store_true",
                              dest="force_update",
                              default=False,
                              help="")
-    parser.add_option_group( parsing_opt )
-    
     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)
    
@@ -229,14 +230,12 @@ if __name__ == '__main__':
     while True:
         user, password = get_credentials()
         try:
-            fill_db(options.server_url, options.db_name, user, password, replicon_db, system_db, force_update = options.force_update)
+            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
-            sys.exit(2)