Bioinformatics in Python: Retrieve GO annotations

Abstract: retrieve GO annotations with a given specie from ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/

We will  store the relationships between genes(DB_id) and GO terms(GO_id) into a dictionary.
Here is the introductions of the goa files:
Column No.    Contents
1.        DB
2.        DB_Object_ID
3.        DB_Object_Symbol
4.         Qualifier
5.        GO_ID
6.        DB:Reference
7.        Evidence Code
8.        With (or) From
9.        Aspect
10.        DB_Object_Name
11.        DB_Object_Synonym
12.        DB_Object_Type
13.        Taxon and Interacting taxon
14.        Date
15.        Assigned_By
16.        Annotation_Extension
17.        Gene_Product_Form_ID

The result:
Number of genes with GO annotations: 47355
ok
The script:
# -*- coding: utf-8 -*-
"""
Created on Thu Aug 13 16:28:44 2015

@author: yuan
"""

# -*- coding: utf-8 -*-
"""
Created on Thu Aug 13 14:52:00 2015

@author: yuan
"""
import re
import os.path
import urllib
import gzip

class GO:
    def __init__(self, specie, out_dir):
        file_name='gene_association.goa_'+specie.lower()+'.gz'
        self.file=out_dir+file_name
        if not os.path.isfile(self.file):
            linkage='ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/'+specie+'/'+file_name
            print 'Web linkage:', linkage
            #download file
            urllib.urlretrieve(linkage, self.file)
            print 'Download GO terms into', self.file
           
    def GO_annotation(self):
        if self.file.rfind('.gz')>0:
            in_obj=gzip.open(self.file, 'r')
        else:
            in_obj=open(self.file, 'r')
        #
        n=0
        GOannot={}
        for line in in_obj:
            line=line.rstrip("\n")
            if not line.find("!")==0:
                items=line.split("\t")
                DB_id=items[1]
                GO_id=items[4]
                if GOannot.has_key(DB_id):
                    GOannot[DB_id] += ','+GO_id
                else:
                    GOannot[DB_id]=GO_id
                    n+=1
        in_obj.close()
        print 'Number of genes with GO annotations:',n
        return GOannot
       
if __name__=="__main__":
    #other species: CHICHEN, COW, DICTY, DOG, FLY, MOUSE, PIG, RAT, YEAST, ZEBRAFISH
    specie='HUMAN'
    out_dir='/home/yuan/mysql_pre/cookbooks/'
    g=GO(specie, out_dir)
    GOannot=g.GO_annotation()
   
    print 'ok'