GO_parseDefinitions.py

# Parse all definitions for go from GO XML

import Config
import sys, string
import MySQLdb
import Database
import gzip

from xml.etree import ElementTree

with Database.db as cursor :
	
	cursor.execute( "TRUNCATE TABLE " + Config.DB_NAME + ".go_definitions" )
	cursor.execute( "TRUNCATE TABLE " + Config.DB_NAME + ".go_subsets" )
	cursor.execute( "TRUNCATE TABLE " + Config.DB_NAME + ".go_subset_mappings" )
	Database.db.commit( )
	
	with gzip.open( Config.GO_DEFINITIONS, 'r' ) as file :

		ontology = ElementTree.parse( file ).getroot( )
		goSubsets = { }
		
		for element in ontology.findall( 'header/subsetdef' ) :
		
			subsetID = element.find( 'id' ).text.strip( )
			subsetDesc = element.find( 'name' ).text.strip( )
			
			cursor.execute( "INSERT INTO " + Config.DB_NAME + ".go_subsets VALUES( '0', %s, %s, NOW( ), 'active' )", [subsetID, subsetDesc] )
			goSubsets[subsetID.upper( )] = cursor.lastrowid
			
		Database.db.commit( )
		
		insertCount = 0
		for element in ontology.findall( 'term' ) :
		
			goFullID = element.find( 'id' ).text.strip( )
			goName = element.find( 'name' ).text.strip( )
			goNamespace = element.find( 'namespace' ).text.strip( )
			goDefinition = element.find( 'def/defstr' )
			
			if None != goDefinition :
				goDefinition = goDefinition.text.strip( )
			else :
				goDefinition = ""
				
			goShortID = goFullID[3:]
			
			cursor.execute( "INSERT INTO " + Config.DB_NAME + ".go_definitions VALUES( %s, %s, %s, %s, %s, NOW( ), 'active' )", [goShortID, goFullID, goName, goDefinition, goNamespace] )
			
			for subset in element.findall( 'subset' ) :
			
				subsetName = subset.text.strip( )
				subsetID = goSubsets[subsetName.strip( ).upper( )]
				
				cursor.execute( "INSERT INTO " + Config.DB_NAME + ".go_subset_mappings VALUES ( '0',%s, %s,'active' )", [goShortID,subsetID] )
			
			insertCount = insertCount + 1
			if 0 == (insertCount % Config.DB_COMMIT_COUNT ) :
				Database.db.commit( )
			
	cursor.execute( "INSERT INTO " + Config.DB_STATS + ".update_tracker VALUES ( '0', 'GO_parseDefinitions', NOW( ) )" )
	Database.db.commit( )
	
sys.exit( )