diff fasta2rdf/fastatordf.py @ 6:ec73c34af97b

FASTA2RDF

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fasta2rdf/fastatordf.py	Sat Feb 21 15:19:42 2015 +0100
@@ -0,0 +1,145 @@
+#!/usr/bin/env python3.4
+# Author: Jasper Jan Koehorst
+# Date created: Jan 22 2015
+# Function: generation of a RDF file from a genome fasta file
+
+def delete_galaxy():
+	import sys
+	for index, path in enumerate(sys.path):
+		if "galaxy-dist/" in path:
+			sys.path[index] = ''
+
+#Some modules that are required by RDFLIB are also in galaxy, this messes up the RDF import function.
+delete_galaxy()
+
+# from io import StringIO
+from rdflib import Graph, URIRef, Literal,Namespace, RDF,RDFS,OWL, plugin
+# import rdflib
+from rdflib.store import Store
+import sys
+
+store = plugin.get('IOMemory', Store)()
+
+global URI
+URI = "http://csb.wur.nl/genome/"
+global seeAlso
+seeAlso = "rdfs:seeAlso"
+global coreURI
+coreURI = Namespace(URI)
+
+def createClass(uri):
+	genomeGraph.add((uri,RDF.type,OWL.Class))
+	genomeGraph.add((uri,RDFS.subClassOf,OWL.Thing))
+	return uri
+
+def fasta_parser(input_file):
+	createClass(coreURI["Genome"])            #Genome class
+	createClass(coreURI["Type"])                #Type class (Chr,Pls,Scaffold)
+
+	genomeDict = {}
+	
+	#requires chromosome_1, chromosome_2, chromosome_1... #For multiple scaffolds
+# 	regex = re.compile('\[type=(.*?)\]')
+	sequence = ""
+	genomeID = sys.argv[sys.argv.index('-idtag')+1].replace(" ","_")
+	if genomeID == 'None':
+		genomeID = sys.argv[sys.argv.index('-id_alternative')+1].replace(" ","_").replace(".","_")
+
+	genomeURI = coreURI[genomeID]
+	for index, element in enumerate(sys.argv):
+		if '-organism' == element:
+			genomeGraph.add((genomeURI, coreURI["organism"] , Literal(sys.argv[index+1])))
+		if '-ncbi_taxid' == element:
+			genomeGraph.add((genomeURI, coreURI["taxonomy"] , Literal(sys.argv[index+1])))
+		if '-idtag' == element:
+			genomeGraph.add((genomeURI, coreURI["id_tag"] , Literal(sys.argv[index+1])))
+		if '-ids' == element:
+			genomeGraph.add((genomeURI, coreURI["id_tag"] , Literal(sys.argv[index+1])))
+
+	genomeDict[genomeID] = {}
+	# typDict = {"plasmid":0,"scaffold":0,"chromosome":0}
+	
+	#Generating genome dictionary
+	data = open(input_file).readlines()
+	fastadict = {}
+	key = ""
+	for index, line in enumerate(data):
+		if ">" == line[0]:
+			key = line.strip(">").strip()
+			fastadict[key] = ""
+		else:
+			fastadict[key] += line.strip()
+
+	# for line in fastadict:
+		# typ = regex.findall(line)
+		# value = 0
+		#If something is found
+		# if len(typ) > 0:
+			# typ = typ[0]
+		#If something is not found
+		# elif typ == []:
+		# typ = "scaffold"
+		#If something is found but does not contain a value
+		# elif "_" in typ:
+			# value = typ.split("_")[-1]
+			# try:
+				# value = int(value)
+			# except:
+				# value = 1
+				#Not a integer
+		
+		#If a value is not given it is automatically assigned as the first one
+		#If a value is given...
+		# if value > -1:
+			#If a second scaffold of a chromosome_1 is found
+		# if typ in genomeDict[genome]:
+			#Retrieve how many					
+			# value = len(genomeDict[genome][typ]) + 1
+			# genomeDict[genome][typ]["scaffold_"+str(value)] = {"contig":fastadict[line]}
+		# else:
+			# genomeDict[genome][typ] = {}
+			# genomeDict[genome][typ]["scaffold_1"] = {"contig":fastadict[line]}
+
+	#Genome dictionary to TTL
+	genomeClass = createClass(coreURI["Genome"])
+	typeClass = createClass(coreURI["DnaObject"])
+	for index, genome in enumerate(fastadict):
+		# for typ in genomeDict[genome]:
+			# for scaf in genomeDict[genome][typ]:
+				# for con in genomeDict[genome][typ][scaf]:
+					#A note is required here...
+					#Due to RDF performances we are reducing the amount of triples needed from a genome to a contig.
+					#Previously it was
+					# Genome > Class > Scaffold > Contig
+					#Now it will be
+					# Genome > Class/Scaffold/Contig
+					#typeURI = coreURI[genome + "/" + typ]
+					#scaffoldURI = coreURI[genome + "/" + typ + "/" + scaf]
+					#Was contigURI
+					typeURI = coreURI[genomeID + "/dnaobject_" + str(index)] # + "/" + scaf + "/" + con]
+					# sequence = genomeDict[genome][typ][scaf][con]
+					sequence = fastadict[genome]
+					genomeGraph.add((genomeURI, coreURI["dnaobject"] , typeURI))
+					genomeGraph.add((genomeURI, coreURI["sourcedb"], Literal(sys.argv[sys.argv.index("-sourcedb")+1])))
+					genomeGraph.add((typeURI, coreURI["sequence"] ,  Literal(sequence)))
+					genomeGraph.add((typeURI, coreURI["header"], Literal(genome)))
+					genomeGraph.add((typeURI, coreURI["sourcedb"], Literal(sys.argv[sys.argv.index("-sourcedb")+1])))
+					genomeGraph.add((genomeURI, RDF.type,genomeClass))
+					genomeGraph.add((typeURI, RDF.type,typeClass))
+
+def save():
+	data = genomeGraph.serialize(format='turtle')
+	open(sys.argv[sys.argv.index("-output")+1],"wb").write(data)
+
+def main():
+	store = plugin.get('IOMemory', Store)()
+	global genomeGraph
+	genomeGraph = Graph(store,URIRef(URI))
+	genomeGraph.bind("ssb",coreURI)
+	input_file = sys.argv[sys.argv.index("-input")+1]
+	fasta_parser(input_file)
+	save()
+
+if __name__ == '__main__':
+	main()
+