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

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# Generate Statistics on Deactivated Genes when
# comparing to the IMS database.

import Config
import sys, string
import MySQLdb
import Database

from classes import Quick, Test

with Database.db as cursor :

	quick = Quick.Quick( Database.db, cursor )
	test = Test.Test( Database.db, cursor )

	geneHash = quick.fetchValidGeneIDHash( )

	cursor.execute( "SELECT complex_id, complex_participants FROM " + Config.DB_IMS + ".complex_matrix WHERE modification_type='ACTIVATED'" )

	deactivatedComplexes = set( )
	deactivatedGenes = set( )

	for (complexID, participants) in cursor.fetchall( ) :

		splitParticipants = participants.split( "|" )

		for participant in splitParticipants :

			if str(participant) not in geneHash :
				deactivatedGenes.add(participant)
				deactivatedComplexes.add(complexID)

	print "Number of Deactivated Complexes: " + str( len(deactivatedComplexes) )
	print "Number of Deactivated Genes: " + str( len(deactivatedGenes) )

	if len(deactivatedGenes) > 0 :
		sqlFormat = ",".join( ['%s'] * len(deactivatedGenes) )
		cursor.execute( "SELECT gene_id, organism_id, organism_common_name FROM " + Config.DB_OLDQUICK + ".quick_annotation WHERE gene_id IN (%s)" % sqlFormat, tuple(deactivatedGenes) )

	# organisms = { }
	# for (geneID, organismID, organismCommonName) in cursor.fetchall( ) :
		# if organismCommonName not in organisms :
			# organisms[organismCommonName] = set( )
		# organisms[organismCommonName].add(geneID)

	organisms = { }
	organismHash = { }
	for (geneID, organismID, organismCommonName) in cursor.fetchall( ) :
		if str(organismID) not in organisms :
			organisms[str(organismID)] = set( )
			organismHash[str(organismID)] = organismCommonName
		organisms[str(organismID)].add(geneID)

	# print "----------------------------------"
	# print deactivatedInteractions

	# print "----------------------------------"
	# print deactivatedGenes

	# print "----------------------------------"
	# for (organismName, geneSet) in organisms.items( ) :
		# print organismName + " => " + str(len(geneSet))
		# print geneSet

	for (organismID, geneSet) in organisms.items( ) :
		for gene in geneSet :
			replacementCandidates = test.findReplacementCandidateGenes( gene, organismID )

			replacementSet = "-"
			if len(replacementCandidates) > 0 :
				replacementSet = "|".join(replacementCandidates)

			print str(gene) + "\t" + replacementSet + "\t" + str(len(replacementCandidates)) + "\t" + str(organismID) + "\t" + organismHash[str(organismID)] + "\t" + str(test.fetchInteractionCount( gene )) + "\t" + str(test.fetchEntrezGeneID( gene))

sys.exit( )