changeset 2:9bb153d42a1c draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sparql_uniprot.py	Mon May 02 16:50:00 2016 -0400
@@ -0,0 +1,230 @@
+from SPARQLWrapper import SPARQLWrapper, JSON
+import sys
+
+# Constante con los prefijos comunes a usar en queries
+COMMON_PREFIXES = """
+	PREFIX up:<http://purl.uniprot.org/core/>
+	PREFIX keywords:<http://purl.uniprot.org/keywords/>
+	PREFIX uniprotkb:<http://purl.uniprot.org/uniprot/>
+	PREFIX taxon:<http://purl.uniprot.org/taxonomy/>
+	PREFIX ec:<http://purl.uniprot.org/enzyme/>
+	PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+	PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
+	PREFIX skos:<http://www.w3.org/2004/02/skos/core#>
+	PREFIX owl:<http://www.w3.org/2002/07/owl#>
+	PREFIX bibo:<http://purl.org/ontology/bibo/>
+	PREFIX dc:<http://purl.org/dc/terms/>
+	PREFIX xsd:<http://www.w3.org/2001/XMLSchema#>
+	PREFIX faldo:<http://biohackathon.org/resource/faldo#>
+"""
+
+# Lista con los nombres de las variables que obtenemos de la base de datos.
+paramList = ['protein', 'proteinFullName', 'geneName', 'organismName', 'diseaseAnnotationText', 'domainFullName', 'similarityAnnotationText', 'locationAnnotationText', 'functionAnnotationText', 'pharmaceuticalAnnotationText'];
+
+def buildQuery(proteinId, proteinName, geneName, organismName, diseaseAnnotation, domainName, similarityAnnotation, locationAnnotation, functionAnnotation, pharmaceuticalAnnotation):
+	query = COMMON_PREFIXES
+	query += "select distinct \n"
+	query += "	?protein\n"
+	query += "	?proteinFullName\n"
+	query += "	?geneName\n"
+	query += "	?organismName\n"
+	query += "	?diseaseAnnotationText\n"
+	query += "	?domainFullName\n"
+	query += "	?similarityAnnotationText\n"
+	query += "	?locationAnnotationText\n"
+	query += "	?functionAnnotationText\n"
+	query += "	?pharmaceuticalAnnotationText\n"
+	query += "where{\n"
+
+	query += "	?protein a up:Protein .\n"
+
+	if (proteinId != ''):
+		query += "	VALUES ?protein {uniprotkb:"+ proteinId + "}\n"
+
+	query += "\n"
+
+	if (proteinName == ''):
+		query += "	OPTIONAL {\n"
+	query += "	?protein up:recommendedName ?proteinName .\n"
+	query += "	?proteinName up:fullName ?proteinFullName . \n"
+	if (proteinName !=''):
+		query += "	filter( regex(str(?proteinFullName), " + '"' + proteinName + '"' + ",\"i\" )) .\n"
+	if (proteinName == ''):
+		query += "	}\n"
+	query += "\n"
+
+	if (geneName == ''):
+		query += "	OPTIONAL {\n"
+	query += "	?protein up:encodedBy ?gene .\n"
+	query += "	?gene skos:prefLabel ?geneName .\n"
+	if (geneName != ''):
+		query += "	filter( regex(str(?geneName), " + '"' + geneName + '"' + ",\"i\" )) .\n"
+	if (geneName == ''):
+		query += "	}\n"
+
+	query += "\n"
+
+	if (organismName == ''):
+		query += "	OPTIONAL {\n"
+	query += "	?protein up:organism ?organism .\n"
+	query += "	?organism up:scientificName ?organismName .\n"
+	if (organismName != ''):
+		query += "	filter( regex(str(?organismName), " + '"' + organismName + '"' + ",\"i\" )) .\n"
+	if (organismName == ''):
+		query += "	}\n"
+
+	query += "\n"
+
+	if (diseaseAnnotation == ''):
+		query += "	OPTIONAL {\n"
+	query += "	?protein up:annotation ?diseaseAnnotation .\n"
+	query += "	?diseaseAnnotation a up:Disease_Annotation .\n"
+	query += "	?diseaseAnnotation up:disease ?disease .\n"
+	query += "	?disease rdfs:comment ?diseaseAnnotationText\n"
+	if (diseaseAnnotation != ''):
+		query += "	filter( regex(str(?diseaseAnnotationText), " + '"' + diseaseAnnotation + '"' + ",\"i\" )) .\n"
+	if (diseaseAnnotation == ''):
+		query += "	}\n"
+
+	query += "\n"
+
+	if (domainName == ''):
+		query += "	OPTIONAL {\n"
+	query += "	?protein up:domain ?domain .\n"
+	query += "	?domain up:recommendedName ?domainName .\n"
+	query += "	?domainName up:fullName ?domainFullName .\n"
+	if (domainName != ''):
+		query += "	filter( regex(str(?domainFullName), " + '"' + domainName + '"' + ",\"i\" )) .\n"
+	if (domainName == ''):
+		query += "	}\n"
+
+	query += "\n"
+
+	if (similarityAnnotation == ''):
+		query += "	OPTIONAL {\n"
+	query += "	?protein up:annotation ?similarityAnnotation .\n"
+	query += "	?similarityAnnotation a up:Similarity_Annotation .\n"
+	query += "	?similarityAnnotation rdfs:comment ?similarityAnnotationText .\n"
+	if (similarityAnnotation != ''):
+		query += "	filter( regex(str(?similarityAnotationText), " + '"' + similarityAnnotation + '"' + ",\"i\" )) .\n"
+	if (similarityAnnotation == ''):
+		query += "	}\n"
+
+	query += "\n"
+
+	if (locationAnnotation == ''):
+		query += "	OPTIONAL {\n"
+	query += "	?protein up:annotation ?locationAnnotation .\n"
+	query += "	?locationAnnotation a up:Subcellular_Location_Annotation .\n"
+	query += "	?locationAnnotation up:locatedIn ?location .\n"
+	query += "	?location up:cellularComponent ?cellComponent .\n"
+	query += "	?cellComponent rdfs:comment ?locationAnnotationText .\n"
+	if (locationAnnotation != ''):
+		query += "	filter( regex(str(?locationAnnotationText), " + '"' + locationAnnotation + '"' + ",\"i\" )) .\n"
+	if (locationAnnotation == ''):
+		query += "	}\n"
+
+	query += "\n"
+
+	if (functionAnnotation == ''):
+		query += "	OPTIONAL {\n"
+	query += "	?protein up:annotation ?functionAnnotation .\n"
+	query += "	?functionAnnotation a up:Function_Annotation .\n"
+	query += "	?functionAnnotation rdfs:comment ?functionAnnotationText .\n"
+	if (functionAnnotation != ''):
+		query += "	filter( regex(str(?functionAnnotationText), " + '"' + functionAnnotation + '"' + ",\"i\" )) .\n"
+	if(functionAnnotation == ''):
+		query += "	}\n"
+
+	query += "\n"
+
+	if (pharmaceuticalAnnotation == ''):
+		query += "	OPTIONAL {\n"
+	query += "	?protein up:annotation ?pharmaceuticalAnnotation .\n"
+	query += "	?pharmaceuticalAnnotation a up:Pharmaceutical_Annotation .\n"
+	query += "	?pharmaceuticalAnnotation rdfs:comment ?pharmaceuticalAnnotationText .\n"
+	if (pharmaceuticalAnnotation != ''):
+		query += "	filter( regex(str(?pharmaceuticalAnnotationText), " + '"' + pharmaceuticalAnnotation + '"' + ",\"i\" )) .\n"
+	if (pharmaceuticalAnnotation == ''):
+		query += "	}\n"
+	query += "}\n"
+	#query += "limit 30\n"
+
+	return query
+
+def printResults(json, output):
+	# Abrir fichero para escritura
+	fileRes = open(output, 'w')
+	# Imprimir cabecera
+	for param in paramList:
+		fileRes.write(param + "\t")
+	fileRes.write("\n")
+
+	# El formato json se puede recorrer de esta manera
+	# para ir obteniendo valores de la respuesta.
+	for entrada in json["results"]["bindings"]:
+		for param in paramList:
+			if (entrada.get(param)):
+				fileRes.write(entrada.get(param)["value"] + "\t")
+			else:
+				fileRes.write("\t")
+		fileRes.write("\n")
+	fileRes.close()
+
+def sparqlwrap(proteinId, proteinName, geneName, organismName, diseaseAnnotation, domainName, similarityAnnotation, locationAnnotation, functionAnnotation, pharmaceuticalAnnotation, output):
+	
+	query = buildQuery(proteinId, proteinName, geneName, organismName, diseaseAnnotation, domainName, similarityAnnotation, locationAnnotation, functionAnnotation, pharmaceuticalAnnotation)
+	print query
+
+	# Creamos un objeto del tipo SPARQLWrapper indicando en que
+	# direccion esta el servicio que recibe consultas en sparql
+	# y responde a estas.
+	sparql = SPARQLWrapper('http://sparql.uniprot.org/sparql')
+
+	# Especificamos la consulta que queremos hacer en sparql.
+	sparql.setQuery(query)
+
+	# Indicamos en que formato queremos que nos devuelva
+	# los resultados de la consulta. Puede ser json, xml,
+	# rfd, turtle... Simplemente son distintos formatos
+	# para representar los datos en ficheros de texto.
+	sparql.setReturnFormat(JSON)
+
+	# Esta es la instruccion que realiza la consulta a
+	# uniprot. Devuelve un objeto de python que hay que
+	# tratar.
+	print "Ejecutando query"
+	results = sparql.query()
+
+	# Con esto, convertimos el objeto devuelto por
+	# el servicio al formato que especificamos antes.
+	# En este caso, json.
+	print "Conviertiendo a json"
+	json = results.convert()
+	print "Fin conversion a json"
+
+	# Dentro de la variable results tenemos informacion
+	# (metadatos) de lo que ha devuelto el servidor de
+	# uniprot.
+	print results.info()
+
+	# Imprimir resultados
+	printResults(json, output)
+
+
+# Obtener parametros de la linea de comandos.
+proteinId = sys.argv[1]
+proteinName = sys.argv[2]
+geneName = sys.argv[3]
+organismName = sys.argv[4]
+diseaseAnnotation = sys.argv[5]
+domainName =sys.argv[6]
+similarityAnnotation = sys.argv[7]
+locationAnnotation = sys.argv[8]
+functionAnnotation = sys.argv[9]
+pharmaceuticalAnnotation = sys.argv[10]
+output = sys.argv[11]
+
+# Llamada a la funcion que realiza la consulta.
+sparqlwrap(proteinId, proteinName, geneName, organismName, diseaseAnnotation, domainName, similarityAnnotation, locationAnnotation, functionAnnotation, pharmaceuticalAnnotation, output)
+