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1
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17
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2 def delete_galaxy():
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3 import sys
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4 for index, path in enumerate(sys.path):
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5 if "galaxy-dist/" in path:
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6 sys.path[index] = ''
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7
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8 #Some modules that are required by RDFLIB are also in galaxy, this messes up the RDF import function. This is not an elegant solution but it works for now.
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9 delete_galaxy()
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10
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11 from rdflib import Graph, URIRef, Literal,Namespace, XSD, BNode,RDF,RDFS,OWL, ConjunctiveGraph, plugin
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12
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13 # Import RDFLib's default Graph implementation.
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14 from rdflib.graph import Graph
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15
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16 import sys, os
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17
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18 import rdflib
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19 import subprocess
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20 import hashlib
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21 global URI
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22 global SubClassOfDict
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23 SubClassOfDict = {}
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24
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25 URI = "http://csb.wur.nl/genome/"
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26 global seeAlso
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27 seeAlso = "rdfs:seeAlso"
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28 global coreURI
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29 coreURI = Namespace(URI)
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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 #genomeGraph.add((coreURI["Feature"],RDFS.subClassOf,OWL.Thing))
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35 #genomeGraph.add((coreURI["Rna"],RDFS.subClassOf,coreURI["Feature"]))
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36 #genomeGraph.add((uri,RDFS.subClassOf,coreURI["Rna"]))
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37 return uri
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38
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39 def tmp():
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40 import time
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41 global tmpFolder
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42 tmpFolder = "/tmp/"+str(time.time())+"/"
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43 os.mkdir(tmpFolder)
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44
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45 def query():
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46 global genomeGraph
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47 genomeGraph = Graph()
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48 filename = sys.argv[1]
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49 genomeGraph.parse(filename, format="turtle")
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50 qres = genomeGraph.query('select ?class ?sequence where {?class a ssb:DnaObject . ?class ssb:sequence ?sequence .}')
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51 sequences = []
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52 for row in qres:
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53 print ("Header:",row[0])
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54 sequences += [[">"+str(row[0]),str(row[1].strip())]] #.replace("/","-").replace("","")
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55
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56 return sequences
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57
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58 def aragorn(sequences):
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59 for sequence in sequences:
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60 #Call aragorn for each contig, for ease of parsing
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61 open(tmpFolder+"tmp.seq","w").write('\n'.join(sequence))
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62 folder = os.path.realpath(__file__).rsplit("/",2)[0]+"/"
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63 cmd = folder+"/tools/aragorn1.2.36/aragorn -fasta "+tmpFolder+"tmp.seq "+' '.join(sys.argv[3:-2])+" > "+tmpFolder+"aragorn.output"
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64 print (cmd)
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65 os.system(cmd)
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66 aragorn = open(tmpFolder+"aragorn.output").readlines()
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67 # string = ''.join(aragorn)
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68
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69 contig = sequence[0].strip(">").replace("http://csb.wur.nl/genome/","")
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70 dnaobjectURI = coreURI[contig]
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71 #print (contig)
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72 for line in aragorn:
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73 if ">" in line:
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74 print (line.split())
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75 try:
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76 trna, pos = line.split()[1:]
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77 except:
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78 try:
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79 trna, pos = line.split()
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80 except:
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81 if "(Permuted)" in line:
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82 trna, permute, pos = line.split()[1:]
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83
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84 if "tRNA-" in line:
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85 trna, codon = (trna.strip(">)").split("(",1))
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86 else:
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87 trna = trna.strip(">").strip() #Actually a tmRNA...
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88 codon = ''
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89 trnaClass = createClass(coreURI[trna.split("-")[0].title()]) #trna or tmrna
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90 SubClassOfDict[trna.split("-")[0].title()] = 1
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91 if "c" in pos[0]: #complementary
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92 stop, start = pos.split("[")[1].split("]")[0].split(",")
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93 else:
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94 start, stop = pos.split("[")[1].split("]")[0].split(",")
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95 trnaURI = coreURI[contig+"/trna-aragorn_1_2_36-"+trna.lower() +"/"+ start +"_"+ stop]
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96 genomeGraph.add((dnaobjectURI, coreURI["feature"] , trnaURI))
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97 genomeGraph.add((trnaURI, RDF.type,trnaClass))
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98 genomeGraph.add((trnaURI, coreURI["begin"] , Literal(start,datatype=XSD.integer)))
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99 genomeGraph.add((trnaURI, coreURI["end"] , Literal(stop,datatype=XSD.integer)))
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100 genomeGraph.add((trnaURI, coreURI["trna_type"] , Literal(trna)))
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101 genomeGraph.add((trnaURI, coreURI["trna_anti"] , Literal(codon)))
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102 genomeGraph.add((trnaURI, coreURI["tool"] , Literal("aragorn")))
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103 genomeGraph.add((trnaURI, coreURI["version"] , Literal("1.2.36")))
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104 genomeGraph.add((trnaURI, coreURI["sourcedb"], Literal(sys.argv[sys.argv.index("-sourcedb")+1])))
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105
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106 def subClassOfBuilder():
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107 for subclass in SubClassOfDict:
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108 genomeGraph.add((coreURI["Feature"],RDFS.subClassOf,OWL.Thing))
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109 genomeGraph.add((coreURI["Rna"],RDFS.subClassOf,coreURI["Feature"]))
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110 genomeGraph.add((coreURI[subclass],RDFS.subClassOf,coreURI["Rna"]))
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111 genomeGraph.add((coreURI["Rna"], RDF.type,OWL.Class))
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112
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113 def save():
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114 #Create the subclass off instances
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115 #subClassOfBuilder()
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116 ## Saves the file
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117 data = genomeGraph.serialize(format='turtle')
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118 open(sys.argv[2],"wb").write(data)
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119
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120 def main():
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121 tmp()
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122 sequences = query()
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123 aragorn(sequences)
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124 save()
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125
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126 main()
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