Source Code for Module biana.BianaParser.MyDataParser

 1  from bianaParser import * 
 2                       
 3 -class MyDataParser(BianaParser):                                                         
 4      """              
 5      MyData Parser Class  
 6   
 7      Parses data in the following format (meaining Uniprot_id1 interacts with Uniprot_id2 and some scores are associated with both the participants and the interaction): 
 8   
 9              Uniprot_id1 Description1 Participant_score1 Uniprot_id2 Description2 Participant_score2 Interaction_Affinity_score 
10      """                  
11                                                                                            
12      name = "mydata" 
13      description = "This file implements a program that fills up tables in BIANA database from data in MyData format" 
14      external_entity_definition = "An external entity represents a protein" 
15      external_entity_relations = "An external relation represents an interaction with given affinity" 
16               
17 -    def __init__(self): 
18          """ 
19          Start with the default values 
20          """ 
21          BianaParser.__init__(self, default_db_description = "MyData parser",   
22                               default_script_name = "MyDataParser.py", 
23                               default_script_description = MyDataParser.description,      
24                               additional_compulsory_arguments = []) 
25                       
26 -    def parse_database(self): 
27          """                                                                               
28          Method that implements the specific operations of a MyData formatted file 
29          """ 
30          # Add affinity score as a valid external entity relation since it is not recognized by BIANA 
31          self.biana_access.add_valid_external_entity_attribute_type( name = "AffinityScore", 
32                                                                      data_type = "double", 
33                                                                      category = "eE numeric attribute") 
34   
35          # Add score as a valid external entity relation participant attribute since it is not recognized by BIANA  
36          # (Do not confuse with external entity/relation score attribute, participants can have their attributes as well) 
37          self.biana_access.add_valid_external_entity_relation_participant_attribute_type( name = "Score", data_type = "float unsigned" ) 
38   
39          # Since we have added new attributes that are not in the default BIANA distribution, we execute the following command 
40          self.biana_access.refresh_database_information() 
41   
42          self.input_file_fd = open(self.input_file, 'r') 
43          self.external_entity_ids_dict = {} 
44   
45          for line in self.input_file_fd: 
46                  (id1, desc1, score1, id2, desc2, score2, score_int) = line.strip().split() 
47                  # Create an external entity corresponding to Uniprot_id1 in database (if it is not already created) 
48                  if not self.external_entity_ids_dict.has_key(id1): 
49                          new_external_entity = ExternalEntity( source_database = self.database, type = "protein" ) 
50                          # Annotate it as Uniprot_id1 
51                          new_external_entity.add_attribute( ExternalEntityAttribute( attribute_identifier= "Uniprot", value=id1, type="cross-reference") ) 
52                          # Associate its description 
53                          new_external_entity.add_attribute( ExternalEntityAttribute( attribute_identifier= "Description", value=desc1) ) 
54                          # Insert this external entity into database 
55                          self.external_entity_ids_dict[id1] = self.biana_access.insert_new_external_entity( externalEntity = new_external_entity ) 
56                  # Create an external entity corresponding to Uniprot_id2 in database (if it is not already created) 
57                  if not self.external_entity_ids_dict.has_key(id2): 
58                          new_external_entity = ExternalEntity( source_database = self.database, type = "protein" ) 
59                          # Annotate it as Uniprot_id2 
60                          new_external_entity.add_attribute( ExternalEntityAttribute( attribute_identifier= "Uniprot", value=id2, type="cross-reference") ) 
61                          # Associate its description 
62                          new_external_entity.add_attribute( ExternalEntityAttribute( attribute_identifier= "Description", value=desc2) ) 
63                          # Insert this external entity into database 
64                          self.external_entity_ids_dict[id2] = self.biana_access.insert_new_external_entity( externalEntity = new_external_entity ) 
65   
66                  # Create an external entity relation corresponding to interaction between Uniprot_id1 and Uniprot_id2 in database 
67                  new_external_entity_relation = ExternalEntityRelation( source_database = self.database, relation_type = "interaction" ) 
68                  # Associate Uniprot_id1 as the first participant in this interaction 
69                  new_external_entity_relation.add_participant( externalEntityID =  self.external_entity_ids_dict[id1] ) 
70                  # Associate Uniprot_id2 as the second participant in this interaction 
71                  new_external_entity_relation.add_participant( externalEntityID =  self.external_entity_ids_dict[values[1]] ) 
72                  # Associate score of first participant Uniprot_id1 with this interaction 
73                  new_external_entity_relation.add_participant_attributes( externalEntityID = self.external_entity_ids_dict[id1], participantAttribute = ExternalEntityRelationParticipantAttribute( attribute_identifier = "Score", value = score1 ) ) 
74                  # Associate score of second participant Uniprot_id2 with this interaction 
75                  new_external_entity_relation.add_participant_attributes( externalEntityID = self.external_entity_ids_dict[id2], participantAttribute = ExternalEntityRelationParticipantAttribute( attribute_identifier = "Score", value = score2 ) ) 
76                  # Associate the score of the interaction with this interaction 
77                  new_external_entity_relation.add_attribute( ExternalEntityRelationAttribute( attribute_identifier = "AffinityScore", 
78                                                                                                               value = score_int ) ) 
79                  # Insert this external entity realtion into database 
80                  self.biana_access.insert_new_external_entity( externalEntity = new_external_entity_relation ) 
81   
82          input_file_fd.close() 
83