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1 #!/usr/bin/env python3.4
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2 # Author: Jasper Jan Koehorst
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3 # Date created: Jan 22 2015
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4 # Function: generation of a RDF file from a genome fasta file
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5
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6
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7 # from io import StringIO
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8 from rdflib import Graph, URIRef, Literal,Namespace, RDF,RDFS,OWL, plugin
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9 # import rdflib
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10 from rdflib.store import Store
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11 import sys
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12
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13 store = plugin.get('IOMemory', Store)()
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14
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15 global URI
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16 URI = "http://csb.wur.nl/genome/"
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17 global seeAlso
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18 seeAlso = "rdfs:seeAlso"
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19 global coreURI
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20 coreURI = Namespace(URI)
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21 global genomeGraph
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22 store = plugin.get('IOMemory', Store)()
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23 genomeGraph = Graph(store,URIRef(URI))
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24 genomeGraph.bind("ssb",coreURI)
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25
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26 def delete_galaxy():
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27 for index, path in enumerate(sys.path):
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28 if "galaxy-dist/" in path:
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29 sys.path[index] = ''
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30
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31 def createClass(uri):
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32 genomeGraph.add((uri,RDF.type,OWL.Class))
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33 genomeGraph.add((uri,RDFS.subClassOf,OWL.Thing))
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34 return uri
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35
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36 def fasta_parser(input_file):
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37 createClass(coreURI["Genome"]) #Genome class
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38 createClass(coreURI["Type"]) #Type class (Chr,Pls,Scaffold)
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39
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40 genomeDict = {}
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41
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42 sequence = ""
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43 genomeID = sys.argv[sys.argv.index('-idtag')+1].replace(" ","_")
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44 if genomeID == 'None':
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45 genomeID = sys.argv[sys.argv.index('-id_alternative')+1].replace(" ","_").replace(".","_")
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46
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47 genomeURI = coreURI[genomeID]
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48 for index, element in enumerate(sys.argv):
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49 if '-organism' == element:
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50 genomeGraph.add((genomeURI, coreURI["organism"] , Literal(sys.argv[index+1])))
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51 if '-ncbi_taxid' == element:
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52 genomeGraph.add((genomeURI, coreURI["taxonomy"] , Literal(sys.argv[index+1])))
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53 if '-idtag' == element:
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54 genomeGraph.add((genomeURI, coreURI["id_tag"] , Literal(sys.argv[index+1])))
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55 if '-ids' == element:
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56 genomeGraph.add((genomeURI, coreURI["id_tag"] , Literal(sys.argv[index+1])))
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57
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58 genomeDict[genomeID] = {}
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59
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60 #Generating genome dictionary
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61 data = open(input_file).readlines()
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62 fastadict = {}
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63 key = ""
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64 for index, line in enumerate(data):
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65 if ">" == line[0]:
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66 key = line.strip(">").strip()
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67 fastadict[key] = ""
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68 else:
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69 fastadict[key] += line.strip()
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70
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71 genomeClass = createClass(coreURI["Genome"])
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72 typeClass = createClass(coreURI["DnaObject"])
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73 for index, genome in enumerate(fastadict):
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74 typeURI = coreURI[genomeID + "/dnaobject_" + str(index)]
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75 sequence = fastadict[genome]
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76 genomeGraph.add((genomeURI, coreURI["dnaobject"] , typeURI))
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77 genomeGraph.add((genomeURI, coreURI["sourcedb"], Literal(sys.argv[sys.argv.index("-sourcedb")+1])))
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78 genomeGraph.add((typeURI, coreURI["sequence"] , Literal(sequence)))
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79 genomeGraph.add((typeURI, coreURI["header"], Literal(genome)))
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80 genomeGraph.add((typeURI, coreURI["sourcedb"], Literal(sys.argv[sys.argv.index("-sourcedb")+1])))
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81 genomeGraph.add((genomeURI, RDF.type,genomeClass))
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82 genomeGraph.add((typeURI, RDF.type,typeClass))
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83
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84 def save():
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85 data = genomeGraph.serialize(format='turtle')
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86 open(sys.argv[sys.argv.index("-output")+1],"wb").write(data)
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87
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88 def main():
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89 input_file = sys.argv[sys.argv.index("-input")+1]
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90 fasta_parser(input_file)
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91 save()
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92
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93 if __name__ == '__main__':
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94 #Some modules that are required by RDFLIB are also in galaxy, this messes up the RDF import function.
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95 delete_galaxy()
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96 main()
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97
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