| Previous changeset 27:875035bbe366 (2015-02-25) Next changeset 29:dd59731d50b5 (2015-02-25) |
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Commit message:
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removed:
conversion/gbk2rdf/tool_dependencies.xml genetic_elements/aragorn/aragorn.py genetic_elements/aragorn/tool_dependencies.xml |
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| diff -r 875035bbe366 -r 3501912295fb conversion/gbk2rdf/tool_dependencies.xml --- a/conversion/gbk2rdf/tool_dependencies.xml Wed Feb 25 08:16:43 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="biopython" version="1.61"> - <repository changeset_revision="ae9dda584395" name="package_biopython_1_61" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |
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| diff -r 875035bbe366 -r 3501912295fb genetic_elements/aragorn/aragorn.py --- a/genetic_elements/aragorn/aragorn.py Wed Feb 25 08:16:43 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,126 +0,0 @@ - -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. This is not an elegant solution but it works for now. -delete_galaxy() - -from rdflib import Graph, URIRef, Literal,Namespace, XSD, BNode,RDF,RDFS,OWL, ConjunctiveGraph, plugin - -# Import RDFLib's default Graph implementation. -from rdflib.graph import Graph - -import sys, os - -import rdflib -import subprocess -import hashlib -global URI -global SubClassOfDict -SubClassOfDict = {} - -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)) - #genomeGraph.add((coreURI["Feature"],RDFS.subClassOf,OWL.Thing)) - #genomeGraph.add((coreURI["Rna"],RDFS.subClassOf,coreURI["Feature"])) - #genomeGraph.add((uri,RDFS.subClassOf,coreURI["Rna"])) - return uri - -def tmp(): - import time - global tmpFolder - tmpFolder = "/tmp/"+str(time.time())+"/" - os.mkdir(tmpFolder) - -def query(): - global genomeGraph - genomeGraph = Graph() - filename = sys.argv[1] - genomeGraph.parse(filename, format="turtle") - qres = genomeGraph.query('select ?class ?sequence where {?class a ssb:DnaObject . ?class ssb:sequence ?sequence .}') - sequences = [] - for row in qres: - print ("Header:",row[0]) - sequences += [[">"+str(row[0]),str(row[1].strip())]] #.replace("/","-").replace("","") - - return sequences - -def aragorn(sequences): - for sequence in sequences: - #Call aragorn for each contig, for ease of parsing - open(tmpFolder+"tmp.seq","w").write('\n'.join(sequence)) - folder = os.path.realpath(__file__).rsplit("/",2)[0]+"/" - cmd = folder+"/tools/aragorn1.2.36/aragorn -fasta "+tmpFolder+"tmp.seq "+' '.join(sys.argv[3:-2])+" > "+tmpFolder+"aragorn.output" - print (cmd) - os.system(cmd) - aragorn = open(tmpFolder+"aragorn.output").readlines() -# string = ''.join(aragorn) - - contig = sequence[0].strip(">").replace("http://csb.wur.nl/genome/","") - dnaobjectURI = coreURI[contig] - #print (contig) - for line in aragorn: - if ">" in line: - print (line.split()) - try: - trna, pos = line.split()[1:] - except: - try: - trna, pos = line.split() - except: - if "(Permuted)" in line: - trna, permute, pos = line.split()[1:] - - if "tRNA-" in line: - trna, codon = (trna.strip(">)").split("(",1)) - else: - trna = trna.strip(">").strip() #Actually a tmRNA... - codon = '' - trnaClass = createClass(coreURI[trna.split("-")[0].title()]) #trna or tmrna - SubClassOfDict[trna.split("-")[0].title()] = 1 - if "c" in pos[0]: #complementary - stop, start = pos.split("[")[1].split("]")[0].split(",") - else: - start, stop = pos.split("[")[1].split("]")[0].split(",") - trnaURI = coreURI[contig+"/trna-aragorn_1_2_36-"+trna.lower() +"/"+ start +"_"+ stop] - genomeGraph.add((dnaobjectURI, coreURI["feature"] , trnaURI)) - genomeGraph.add((trnaURI, RDF.type,trnaClass)) - genomeGraph.add((trnaURI, coreURI["begin"] , Literal(start,datatype=XSD.integer))) - genomeGraph.add((trnaURI, coreURI["end"] , Literal(stop,datatype=XSD.integer))) - genomeGraph.add((trnaURI, coreURI["trna_type"] , Literal(trna))) - genomeGraph.add((trnaURI, coreURI["trna_anti"] , Literal(codon))) - genomeGraph.add((trnaURI, coreURI["tool"] , Literal("aragorn"))) - genomeGraph.add((trnaURI, coreURI["version"] , Literal("1.2.36"))) - genomeGraph.add((trnaURI, coreURI["sourcedb"], Literal(sys.argv[sys.argv.index("-sourcedb")+1]))) - -def subClassOfBuilder(): - for subclass in SubClassOfDict: - genomeGraph.add((coreURI["Feature"],RDFS.subClassOf,OWL.Thing)) - genomeGraph.add((coreURI["Rna"],RDFS.subClassOf,coreURI["Feature"])) - genomeGraph.add((coreURI[subclass],RDFS.subClassOf,coreURI["Rna"])) - genomeGraph.add((coreURI["Rna"], RDF.type,OWL.Class)) - -def save(): - #Create the subclass off instances - #subClassOfBuilder() - ## Saves the file - data = genomeGraph.serialize(format='turtle') - open(sys.argv[2],"wb").write(data) - -def main(): - tmp() - sequences = query() - aragorn(sequences) - save() - -main() |
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| diff -r 875035bbe366 -r 3501912295fb genetic_elements/aragorn/tool_dependencies.xml --- a/genetic_elements/aragorn/tool_dependencies.xml Wed Feb 25 08:16:43 2015 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,9 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="aragorn" version="1.2.36"> - <repository changeset_revision="f09e2902e6ed" name="package_aragorn_1_2_36" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <set_environment version="1.0"> - <environment_variable action="set_to" name="TRNAPRED_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable> - </set_environment> -</tool_dependency> |