BioGRID-Annotation/EG_parseExternals.py at master · BioGRID/BioGRID-Annotation · GitHub

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# Parse all external database ids for genes from Entrez Gene that
# are relevant to the organisms we want loaded
# via the organisms table.

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

from classes import EntrezGene

with Database.db as cursor :

	entrezGene = EntrezGene.EntrezGene( Database.db, cursor )
	existingEntrezGeneIDs = entrezGene.fetchExistingEntrezGeneIDs( )

	cursor.execute( "DELETE FROM " + Config.DB_NAME + ".gene_externals WHERE gene_external_source != 'GRID LEGACY'" )
	Database.db.commit( )
	cursor.execute( "OPTIMIZE TABLE " + Config.DB_NAME + ".gene_externals" )
	Database.db.commit( )

	insertCount = 0
	with gzip.open( Config.EG_GENEINFO, 'r' ) as file :
		for line in file.readlines( ) :

			line = line.strip( )

			# Ignore Header Line
			if "#" == line[0] :
				continue

			splitLine = line.split( "\t" )
			sourceID = splitLine[1].strip( )
			dbxrefs = (splitLine[5].strip( )).split( "|" )

			if sourceID in existingEntrezGeneIDs :
				currentGeneID = existingEntrezGeneIDs[sourceID]

				if "-" != splitLine[5].strip( ) :
					insertCount = insertCount + 1
					for dbxref in dbxrefs :
						dbxrefInfo = dbxref.split( ":", 1 )
						dbxrefInfo[1] = str(dbxrefInfo[1]).upper( ).replace( "HGNC:", "" ).replace( "MGI:", "" ).replace( "RGD:", "" )
						cursor.execute( "INSERT INTO " + Config.DB_NAME + ".gene_externals VALUES ( '0', %s, %s, 'active', NOW( ), %s )", [dbxrefInfo[1].strip( ), dbxrefInfo[0].strip( ).upper( ), currentGeneID] )

				cursor.execute( "INSERT INTO " + Config.DB_NAME + ".gene_externals VALUES ( '0', %s, 'ENTREZ_GENE', 'active', NOW( ), %s )", [sourceID, currentGeneID] )
				cursor.execute( "INSERT INTO " + Config.DB_NAME + ".gene_externals VALUES ( '0', %s, 'ENTREZ_GENE_ETG', 'active', NOW( ), %s )", ['ETG' + str(sourceID), currentGeneID] )

			if 0 == (insertCount % Config.DB_COMMIT_COUNT ) :
				Database.db.commit( )

	cursor.execute( "INSERT INTO " + Config.DB_NAME + ".gene_externals SELECT '0', gene_source_id, 'SGD', 'active', NOW( ), gene_id FROM " + Config.DB_NAME + ".genes WHERE gene_source='SGD'" )
	Database.db.commit( )

	cursor.execute( "INSERT INTO " + Config.DB_STATS + ".update_tracker VALUES ( '0', 'EG_parseExternals', NOW( ) )" )
	Database.db.commit( )

sys.exit( )