Galaxy |

Changeset 26:6a858e304888 (2015-02-25)

Previous changeset 25:f1255292e929 (2015-02-21) Next changeset 27:875035bbe366 (2015-02-25)

Commit message:
Merge

removed:
.DS_Store
conversion/fasta2rdf/fastatordf.py
conversion/fasta2rdf/fastatordf.xml
conversion/fasta2rdf/test-data/NC_017117.fna
conversion/gbk2rdf/gbktordf.py
conversion/gbk2rdf/gbktordf.xml
conversion/gbk2rdf/test-data/CP009049.embl
conversion/gbk2rdf/test-data/NC_010067.gbk
conversion/gbk2rdf/tool_dependencies.xml
conversion/protein2rdf/protein_to_ttl.py
conversion/protein2rdf/protein_to_ttl.xml
conversion/protein2rdf/test-data/NC_017117.faa
fasta2rdf/fastatordf.py
fasta2rdf/fastatordf.xml
fasta2rdf/test-data/NC_017117.fna
gbk2rdf/gbktordf.py
gbk2rdf/gbktordf.xml
gbk2rdf/test-data/CP009049.embl
gbk2rdf/test-data/NC_010067.gbk
genetic_elements/aragorn.py
genetic_elements/aragorn.xml
genetic_elements/aragorn/aragorn.py
genetic_elements/aragorn/aragorn.xml
genetic_elements/aragorn/test-data/NC_017117.rdf
genetic_elements/aragorn/tool_dependencies.xml
protein2rdf/protein_to_ttl.py
protein2rdf/protein_to_ttl.xml
protein2rdf/test-data/NC_017117.faa

diff -r f1255292e929 -r 6a858e304888 .DS_Store

Binary file .DS_Store has changed

diff -r f1255292e929 -r 6a858e304888 conversion/fasta2rdf/fastatordf.py
--- a/conversion/fasta2rdf/fastatordf.py Sat Feb 21 22:35:02 2015 +0100
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,97 +0,0 @@
-#!/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
-
-
-# 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)
-global genomeGraph
-store = plugin.get('IOMemory', Store)()
-genomeGraph = Graph(store,URIRef(URI))
-genomeGraph.bind("ssb",coreURI)
-
-def delete_galaxy():
- for index, path in enumerate(sys.path):
- if "galaxy-dist/" in path:
- sys.path[index] = ''
-
-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 = {}
-
- 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] = {}
-
- #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()
-
- genomeClass = createClass(coreURI["Genome"])
- typeClass = createClass(coreURI["DnaObject"])
- for index, genome in enumerate(fastadict):
- typeURI = coreURI[genomeID + "/dnaobject_" + str(index)]
- 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():
- input_file = sys.argv[sys.argv.index("-input")+1]
- fasta_parser(input_file)
- save()
-
-if __name__ == '__main__':
- #Some modules that are required by RDFLIB are also in galaxy, this messes up the RDF import function.
- delete_galaxy()
- main()
-

diff -r f1255292e929 -r 6a858e304888 conversion/fasta2rdf/fastatordf.xml
--- a/conversion/fasta2rdf/fastatordf.xml Sat Feb 21 22:35:02 2015 +0100
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,38 +0,0 @@
-<tool id="SAPP_genome_to_ttl" name="FASTA to RDF" version="0.1">
-    <requirements>
-        <requirement type='package' version="3.4">python</requirement>
-        <requirement type='package' version="1.0">rdflib</requirement>
-    </requirements>
- <description></description>
- <command interpreter="python3">fastatordf.py '-input' '$input' '-output' '$output' '-organism' '$organism' '-ncbi_taxid' '$ncbi_taxid' '-idtag' '$identification_tag' -sourcedb SAPP
- #for $index, $id in enumerate( $ids )
- '-ids' '$id.id_tag'
- #end for
- '-id_alternative' '$input.name'
- </command>
- <inputs>
- <param size="60" name="input" type="data" format="fasta,fa" label="File for annotation, file types used fasta,fa"/>
- <param size="60" name="organism" type="text" format="text" label="organism name" optional="false"/>
- <param size="60" name="ncbi_taxid" type="text" format="text" label="NCBI taxonomy ID"/>
- <param size="60" name="identification_tag" type="text" format="text" label="An identification tag used for RDF storage !Needs to be very unique!" optional="false"/>
- <repeat name="ids" title="Identification tags">
- <param size="60" name="id_tag" type="text" format="text" label="An identification tag used by other consortiums"/>
- </repeat>
- </inputs>
-
- <outputs>
- <data format="rdf" name="output" label="genomeTTL: ${input.name}" />
- </outputs>
-
-    <tests>
-        <test>
-            <param name="input" value="test-data/NC_017117.fna"/>
-            <output name="$output" file="NC_017117.rdf"/>
-            <output name="$ncbi_taxid" value="634455"/>
-            <output name="$idtag" value="Acetobacter pasteurianus IFO 3283-22"/>
-            <output name="$organism" value="Acetobacter pasteurianus IFO 3283-22"/>
-        </test>
-    </tests>
-
-<help> Genome FASTA file to RDF</help>
-</tool>

diff -r f1255292e929 -r 6a858e304888 conversion/fasta2rdf/test-data/NC_017117.fna
--- a/conversion/fasta2rdf/test-data/NC_017117.fna Sat Feb 21 22:35:02 2015 +0100
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,2736 +0,0 @@\n->gi|384055705|ref|NC_017117.1| Acetobacter pasteurianus IFO 3283-22 plasmid pAPA22-010, complete sequence\n-CGCAGGTTGAGTTCCTGTTCCCGATAGATCCGATAAACCCGCTTATGATTCCAGAGCTGTCCCTGCACAT\n-TGCGCAGATACAGGAAACACAGACCAAATCCCCATCTCCTGTGAGCCTGGGTCAGTCCCACCAGAAGAGC\n-GGCAATCCTGTCGTTCTCCGCTGCCAGTCGCGGACGATAGCGAAAGCAGGTCTCGGATATCCCAAAAATC\n-CGACAGGCCAGCGCAATGCTGACCCCATGATGCGCCACAGCTTGTGCGGCCAGTTCCCGGCGCTGGGCTG\n-GCCGCTTCATTTTTTTCCAAGGGCTTCCTTCAGGATATCCGTCTGCATGCTCAAATCCGCATACATGCGC\n-TTCAGCCGACGGTTCTCCTCTTCCAAAGCCTTCATCTGACTGATCATCGAAGCATCCATGCCGCCATATT\n-TCGCGCGCCACCGGTAAAACGTGGCGTTGCTGATCCCATGCTCCCGACACAGGTCAGGAACCGGGACACC\n-GCCCTCAGCCTGGCGGATCACACCCATGATCTGGGCGTCAGTAAAGCGATCACTCTTCATCAGAATCTCC\n-TCAATTCTTACGCTGAGAAAATTCTCATTCAAAAGTCACTCTTTTTATGGGGGGATTACCACTCTAAATC\n-AATGCATTCCAATTAACTTATAAAATGCTTTGAGAGTCATCACCTACAGCAAAGAACTCTGCTGACACCT\n-CTGAAATCATTTTGAGCCATAAAAACTGGGCTCGATTGACGTCCTGAAACTCATCAGCCATCACGGCTGT\n-GAAACGGCGTGACCAGCGGTAGCGATAGGCATCATTGTGCAGCATTGCCAATGTCGGCCACATCAACAGA\n-TCCCCAAAATCTGCAGCATTCTGTTCGCGCAGCAAACTCTGGTAACGACCATACAACTCAACCACATAGC\n-GCCAGCCCGCATCGTCCATAAAACGTTTCTGGGCATGTGCTCGCGCTATCATGGCTTCAACATGATGCCC\n-TGCCATCTCAGGCGTCACCAGATCTTCCTTCAAACGAGATGGGGTGGTTGCCGTCCTCCCCGCACGGCAT\n-CGCAATGTGCCAGAATGGTCGTTGGAAGAAACGACTGCGCGAAAGGACGGCAGATGAAGGATACAGTGAT\n-AGGCGTTGATCTGGCAAAGAACATTTTCCAGGTTCATGGAGCTTCGCGTGCGGGCGAGGTGATGTTTCGC\n-AAAAAGCTGCGTCGTCAGCAGTTTATGCAGTTCATGGCCACGCAGCCGCCTGCTCTGGTCGTTCTTGAAG\n-CGTGCGGGAGCGCGCATTACTGGGCTCGCGAACTGGCAGGAGCTGGTCACGAGGTCAGACTGATCGCTCC\n-GCAGTATGTGAAGCCTTTCGTGAAGCGCCAGAAGAACGATGCTGCTGATGCGGAAGCGATCGTCATTGCG\n-GCCCGTCAGCCGGAAATGCGCTTTGTCGAACCACGCACTGAAGCGCAGCAGGCGCGTGGCGTTCTTTTCC\n-GGGCCCGGCAGCGTCTGGTGCACCAGCGCACGGAACTGGTGAATGCCCTGCGTGCCGTTCTGTATGAATT\n-CGGTCTCGTCGTGCCACAGGGGATTGCGCATATCAGACACATTGAAGCCATGCTGGATGAGGCGGTTCTG\n-CCAGAGGCTGTGAAGCAGGAATGCCTTGATCTGCTGCGACAGATTTCGGAGCAGAGTGTGCGGATTGATG\n-TCAGAACAAAGAAGATCAGGATGCTTGCCCAGGAAAGTGAAAACACCTGCAGATTGCAGAGCATGCCTGG\n-AGTGGGTCCTCTGACCGCTCTTGCGATTGAAGCTTTTGCGCCTGACCTGCAGAGCTTCCGGCGCGGGCGC\n-GACTTTGCTGCGTGGCTGGGGCTGGTGCCCCGTCAGTTCTCATCTGGCGGAAAGGAAAGGCTGGGGAAGA\n-TATCAAAAGCCGGGCAGGCTGATATCCGCAGGCTTCTCATCATGGGCGCCATGACCCAGGTGAACTGGGC\n-CAGCCGTAAGGCCCCTGCACCGGGAAGCTGGCTGGCACGGATGCTGGCCCGCAAGCCCCGTATGCTGGTA\n-GCCATTGCGCTGGCCAACAGGATGGCACGAGCCATCTGGGCCATGGCAACAAAACAGGAGGATTATCGGG\n-ATCCGGCCCTGTCCGTGGCAGCCTGAGCGATGGCTCGGCTCCCGCGGATGGAACCGGTAGGGGTGTGAGA\n-GGGCGATGACCTGAATGGGCGCATGATCGTCTGATCCGGATCGGAAAAACCAGTGGATTTCTCTGTGCTT\n-TAAAGCACGCCTGTGAGATTTGGATCTGATCCGCTGATCACCATACTGGCCAGTGGCTTCTGAAAGGCCA\n-CATCAACAGGCCTTACAGAAGACCGCACACGATCACACGTCAATATGGGTCAGAAAACTCTTGCATAACG\n-GACGGCAACCATATGTGGACGGCTCCCCCTTGCAAGAGGCTAGGCAAGAAAATGATCGGATCTTTGCTTC\n-CATATGTCCGGCCTGTTGATGCGGCCATAGGGTCGCTGGCCAAGATGGCTTCCGCAGCGTGAGCCCCAAA\n-CACAGAAGCGGTCTTTGATGACCACTGGTTGCCACGGGTTTTCTCACGCCATGGATCGATCGATCACACC\n-ATCTGCTCTATTACTTGCAAGCCACGACCTCAGCTCGGCACGAGAGCGTCAAATGTCAGCGCATCGTGCC\n-AGGCTAAGCTCAAACAGCAGCTGCGCCGGGTTGCTGCAGAAGGCGCTTATAGTGTTCGCCGCTGACCATC\n-AGTTTCCAAGCAATCCGCGCAATCTTATTGGCAAGGGCCACCGCTGCGAGTTTCGGTTTTTTGCGCTCCA\n-GCAATTCACGTAACCAAGATGAGGCATTCTTCCCATTGGTCCGCCGGGCATGCGACACGACTGCGGTCGC\n-GCCAACCACCAGCGTGCTTCGCAAGACCTCATCGCCAGCGCGTGTGATTCTGCCAAGCCTTGTTTTTCCA\n-CCGGTTGAGTGATCCCTGGGCGTCAATCCGATCCAGGCCGCAAAGGCTCGACCCGATTTGAACAGATGCG\n-GATCAGGCGTTTTCATCATCAGCAGCGCTGCGCCGATCGGGCCAACGCCCGGAATTTTCGCAAGACGCTG\n-ACTGCATTCGTTGGCGCGGTGCCATGCCATCACCTTGCCCTCAAGCTGTTCGATTTCACCTTGCAATTCA\n-GCATATTCCTTTGCGTGAAGGGCAAACAACTCGCGCGTCAATGTGGGCAGGCTTTCGTCCGCAGCGATCC\n-GATCAAGGAGTGCCTCAATCCGGCACATGCCTTTGGGCGCCGTGATCCCAAACTCGGCAGCATATCCCCG\n-GATCGTATTGGCGAGCTGTGTGCGGTTCCGGATAAGTCGTGCCCGCATTCCAATCAGCATCAACGCTGCC\n-TGCTCTTCCTCGCTCTTGAGCGGGACGAACCGCATTGTAGGCCGACTCATCGCTTCACAGAGGGCTTCCG\n-CGTCGGCGGCATCGTTTTTCCCGCGCTTGACATAAGGCTTCACGAGCTGCGGCGCGATCAGCTTCACTGT\n-GTGTCCCAGACACGAGAGCACCCGCCCCCAGTAATGGGAGGCGCCACAGGCCTCAATCGCGATTTCAATC\n-GGGGGCAGTTTCTCAAAAAACTTTACCATCTCCCGGCGGGATAGCTTCCTGCGCAAAACAGGCTGCTCCT\n-TCGCGTTTACACCGTGCAATTGGAAAACACTTTTTGACGTGTCCATGCCAATACGGATAATTTGTTCCAT\n-GGGTGGCCTCCTCTGTGAGTTCTGCAACGACTTCACCTTGGCACATCGCGATGCCG'..b'TTGCTCCGAAGGCCTGCATGTGTCCACACCACGGCGATTGCCTGCAACAAGGCGAATGGAT\n-AGAAACAGTCAGGAGAAAGGTCGTCTGGTTCGATGTTGAGGCTGGCCCAGGTCAGTTTCAGCCAAGAAGC\n-ATCATCTATGGTCCTAGGATTTACGCCAAGATATTTCGCAATATTCTTCGGTGTCGAGAGATGATATCGC\n-GGATTACACCTGAGCCGCGCCCATTCCCAACTCTGAATATCAGATAAAAACCGGCGCATAACCTGATAAT\n-AAGCAACTTTCGTTGGAGCCTGCAGAGGCTGGCCAACTGTTGGGATCAGACGATAATCAAAGGTGGAACC\n-GCCCCAATCGCCAACACGTAACCTGTCGACGGCGGCGAGATAGTCGGCACATACCGATACCGTCCATTGC\n-TCTGGTCCAGTGACCTCAGGGTGCTCGCGACCCAACCAGATTCCGATACGGGTTAGAGTGTTGTAAACTG\n-CTCGCCTCGACCCTTCTCGCAACGTTGTTGTTTCCAACCAACGTCGGCACCATGTCATCCACTCAGGATT\n-GATATTATCAGTTTCAGTTCCGTGACGAGGTGGATATGCCCGAAAATGGATAACCTTTGATGTTAATCCC\n-ATTGCCGCCAAACCGTTTGACAATATTCCAATCCGCTTGGCGATATGATTTCCTGTGTAACACTCTCGTG\n-TATGTTCCAGTATCTTCCTATCAAAACTTTCAAGTTTTGGATTCTCGCCTTGTAATGCAACTGCAGCAAA\n-TACTGATGGTACGAGGGGCCGAACGGTCTGACAGACGAAGCCGACACGGGTTAGGGCCGAGAACAGACGC\n-TCACATTCTGTATCAACAATCTCCGCTCCAAAAACCAATCGGGCAACGACAGCCGTCGCCACATTGCGTT\n-GAATTTTGTACACGCTTCGAAAACCACACAGAAGATAAGCGACTGCAATCAACTGCGGTACCATTCCGGT\n-TTTTTTCAGAACAGGACTATTATTGATAATCTCAACCCACAGGTCTTCACTCCACCCCCAGTAGGGTTTT\n-TCCTGGTGTGCGACCGTCAGAAGCAAATACTTCAAAGCACGATGGCTGTTAGCGCGGTCGAGATTGCTGC\n-GATACAGGATGTCCGTCAGAGGCTTATGAAGACGCGGAGCCTGCCGTTTCGTAATAACAAGATTTTCTTC\n-TTTCCAACGTCTGACAACTTTTAATTCGTCTGCAGACAATGTCGCCCGTCTGTCGTATTCATCGAGATTA\n-ATGTGGAATTTGTATTCGGGCTGGATGTGAGAAACCTGAGATTCTACCACTTTTCTATCCTCCGAAGACC\n-CTGTGACCAAGCTTCATATCCATCTGTTCGACTGAGTTTGCGATCTTGCGAAGCAGATCTTCACCGGAAA\n-GATGGATATAGAGTGTCGTGCTTTGAACATTGCGATGCCCGGCATACGTCGCAATATCGTGTAGACGCCA\n-GCCAGCACGGGCCAGATGCGTCAATCTCAGGTGACGCAAAGTGTGCGTACTGAACAATGGCATATCAGCC\n-TGGAGAGCAAGACGTCTGACAGTTTTGCTCCATGACCACTTCGTAATAGGCTGCCGAAAGTTCCGATCTG\n-ACTCAGAGAGAAACAGGGCCGCTGAATGAGTCGCTGCGTTGCGCCTTTGATGCAGATATACCGCCAACAC\n-AGGACAGAGCGCCGCTGAATAACAAACCACACGAGGGCGAGCGCTTTTACTTGTTTCGGCCCGAATGGTG\n-AGCAAACGTCTCGCAGGGTCGATATCCGAGACGCGCAAATTTACTACGGCGTGTCGTCAGTTAAGCCCTG\n-AGAGTGGCACGTGAGGGTTGTACTTTGTGTCTGCGTGTGCTGACTGTTTTCCCATTTTTTGGGGAGACAG\n-ACAGATGCGGCGCTATAGTTTACGCGATGACCAGTGGGAGCGGATAAAGGATCTTCTTCCTGGTCGAGAA\n-GGCTATGTCGGCGGCACTGCGGTGAACAACCGTCTGTTCGTGGAGGCGGTGCTGTATCGCTATCGCGCGG\n-GTATTCCATGGCGCGACCTTCCTGCCCGTTTCGGTGACTGGAAAAACGTGCACCGGCGTCTGCGCCGCTG\n-GTGTGAAAGCGGCGTCATCGAACGGATATTTCGTTATCTGGCCGCTGATTACGACAACGAATACATGATG\n-ATCGACAGCACAATTGTCCGAGCGCATCAGCATAGTGCCGGAGCTCTCAAAAAAGGGGCACGGATCAGGC\n-CATCGGACGATCACGGGCGGGCTAACTACAAAGATCCATGCCATCTGCGACGCTCTGGGCAATCCAGTGG\n-AACTCGGCATCACACCGGGACAGGATGCCGATATCACCCAGGCAGAACCACTTCTGGAAAACATCGAACC\n-GGATGCTTTCCTTGCTGACAAGGCGTATGACGCGGACAGGTTGATCGATCGGCTGATACAGCGCGGGATT\n-ACCCCGGTCATCCCGCCAAAACGCAACAGAACGACACGACGGGTAATCCCCCCATAAAAAGAGTGACTTT\n-TGAATGAGAATTTTCTCAGCGTAAGAATTGAGGAGATTCTGATGAAGAGTGATCGCTTTAGTGACGCCCA\n-GATCATGGGTGTGATCCGCCAGGCTGAGGGCGGTGTCCCGGTTCCTGACCTGTGCCGGGAGCATGGGATC\n-AGCAACGCCACGTTTTACCGGTGGCGCGCGAAATATGGCGGCATGGATGCTTCGATGATCAGTCAGATGA\n-AGGCTTTGGAAGAGGAGAACCGTCGGCTGAAGCGCATGTATGCGGATTTGAGCATGCAGACGGATATCCT\n-GAAGGAAGCCCTTGGAAAAAAATGAAGCGGCCAGCCCAGCGCCGGGAACTGGCCGCACAGGCTGTGGCGC\n-ATCATGGGGTCAGCATTGCGCTGGCCTGTCGGATTTTTGGGATATCCGAGACCTGCTTTCGCTATCGTCC\n-GCGACTGGCAGCGGAGAATGACAGGATTGCCGCTCTTCTGGTGGGACTGACCCAGGCTCACAGGAGATGG\n-GGATTTGGTCTGTGTTTCCTGTATCTGCGCAATGTGCAGGGACAGCTCTGGAATCATAAGCGGGTTTATC\n-GGATCTATCGGGAACTGGAGTTCAACCTGCGGATTAAACCCCGCAGGCGTCTGGTTCGCGAAAAGCCTGA\n-AAAGCTGTCGGTTCCGGCCCTTCCCAACACGGTCTGGTCCATGGATTTCATGGCGGACAGGCTTTTGGAT\n-GGACGCGCTTTTCGGCTCCTGAACATCCTGGATGAGTTCAATCGTGAAGGACTGGCGATCGAGGTTGATT\n-TTTCCCTGCCGGCCTGTCGGGTTGTCCGCTGGTAATCCCCCCATTTTTAGTGGGGCATTGAATGAGAATT\n-CAGGCAGCTGTTTTTAGTTTCTGGGCGGGGGTTAGCCCGCTGTTCCCCATGTTGGGTCTGTCATTGTTAT\n-ATGTCCAGAGCCATTGTGTTGCGACCTCCTGTACGTCCTGAATGCTTTCAAACAAATACTGCTCTAGCCA\n-TTCCTGCCGGACAGTTCTGTTGTAGCGTTCAATATAGGCGTTCTGCTGCGGATTGCCCGGTTGTGTATAG\n-ATCAGGGTAATCCCCTGCTTTTCGGCCCATGAAACCAACGTATGACTGACATATTCAGGGCCATTGTCCA\n-TTCGGATAGCCTCTGGCCTGCCACGCCACTCCATAACCTGTTCCAGACAGCGAACAACCCGACAGGCTGG\n-CAGGGAAAAATCAACCTCAATCGCCAGTCCTTCACGATTGAAATCATCCAGAATGTTCAGGAGCCGAAAA\n-GCACGTCCATCCATCAGCCTGTCCGCCATAAAATCCATGGACCAGACCCTGTTGGGAAGGGCCGGAACCG\n-ACAGCTTTTCAGGCTTTTCGCGAACCAGACGCCTGCGGGGTTTAATC\n'

diff -r f1255292e929 -r 6a858e304888 conversion/gbk2rdf/gbktordf.py
--- a/conversion/gbk2rdf/gbktordf.py Sat Feb 21 22:35:02 2015 +0100
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,360 +0,0 @@\n-#!/usr/bin/env python3.4\n-# Author: Jasper Jan Koehorst\n-# Date created: Feb 21 2015\n-# Function: generation of a RDF file from Genbank/EMBL\n-\n-import warnings\n-warnings.filterwarnings("ignore")\n-\n-def delete_galaxy():\n-\timport sys\n-\tfor index, path in enumerate(sys.path):\n-\t\tif "galaxy-dist/" in path:\n-\t\t\tsys.path[index] = \'\'\n-\n-#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.\n-delete_galaxy()\n-\n-from Bio import SeqIO\n-# Import RDFLib\'s default Graph implementation.\n-import os, sys\n-from Bio.Seq import Seq\n-\n-from rdflib import Graph, URIRef, Literal,Namespace,RDF,RDFS,OWL, plugin\n-from rdflib.store import Store\n-import hashlib\n-store = plugin.get(\'IOMemory\', Store)()\n-\n-global URI\n-URI = "http://csb.wur.nl/genome/"\n-global seeAlso\n-seeAlso = "rdfs:seeAlso"\n-global coreURI\n-coreURI = Namespace(URI)\n-\n-global SubClassOfDict\n-SubClassOfDict = {}\n-global SubClassOfDictRna\n-SubClassOfDictRna = {}\n-\n-def createClass(uri, root=True):\n-\tgenomeGraph.add((uri,RDF.type,OWL.Class))\n-\tif root:\n-\t\tgenomeGraph.add((uri,RDFS.subClassOf,OWL.Thing))\n-\treturn uri\n-\n-def tmp():\n-\timport time\n-\tglobal tmpFolder\n-\ttmpFolder = "/tmp/"+str(time.time())+"/"\n-\tos.mkdir(tmpFolder)\n-\n-def cleantmp():\n-\tos.system("ls "+tmpFolder)\n-\tos.system("rm -rf "+tmpFolder)\n-\n-def crawler():\n-\t#From input folder it looks for GBK file (gz files are in progress)\n-\tinput_file = sys.argv[sys.argv.index("-input")+1]\n-\tgbk_parser(input_file)\n-\n-def gbk_parser():\n-\tprevObjStart = -1\n-\tprevObjStop = -1\t\n-\tstore = plugin.get(\'IOMemory\', Store)()\n-\tglobal genomeGraph\n-\tgenomeGraph = Graph(store,URIRef(URI))\n-\tgenomeGraph.bind("ssb",coreURI)\n-\tinput_file = sys.argv[sys.argv.index("-input")+1]\n-\n-\t#CLASS definitions\n-\tgenomeClass = createClass(coreURI["Genome"], root=True)\n-\ttypeClass = createClass(coreURI["DnaObject"], root=True)\n-\tcreateClass(coreURI["Protein"], root=True)\n-\tpubmedClass = createClass(coreURI["Pubmed"], root=True)\n-\tmiscClass = createClass(coreURI["MiscFeature"], root=False)\n-\tcreateClass(coreURI["Feature"], root=True)\n-\tSubClassOfDict["MiscFeature"] = 1\n-\tSubClassOfDictRna["Trna"] = 1\n-\tSubClassOfDictRna["Rrna"] = 1\n-\tSubClassOfDictRna["Tmrna"] = 1\n-\tSubClassOfDictRna["Ncrna"] = 1\n-\n-# \tcodon = "11" #Default initialization if no CDS are present\n-\t##################\n-\tweird_chars = list(\'\'\',./?<>:;"\'|\\}]{[+=_-)(*&^%$#@!\xc2\xb1\xc2\xa7~` \'\'\')\n-\tscaf_value = 0\n-\t#Which files are already done\n-\t########\n-\tformatGBK = sys.argv[sys.argv.index("-format")+1]\n-\tfor record in SeqIO.parse(input_file, formatGBK):\n-\t\t#Read first feature for genome name and information...\n-\t\t#Ignore the empty GBK file due to the lack of features?\n-\n-\t\tfor index, feature in enumerate(record.features):\n-\t\t\tif index == 0:\n-\t\t\t\tif "-identifier" in sys.argv:\n-\t\t\t\t\tgenome = sys.argv[sys.argv.index("-identifier")+1]\n-\t\t\t\telse:\n-\t\t\t\t\ttry:\n-\t\t\t\t\t\tgenome = feature.qualifiers["organism"][0].replace(" ","_")\n-\t\t\t\t\texcept:\n-\t\t\t\t\t\t#BUG: THIS IS A TEMP FIX, USE GALAXY -IDENTIFIER TO CAPTURE THIS\n-\t\t\t\t\t\tgenome = "XNoneX"\n-\t\t\t\tfor char in weird_chars:\n-\t\t\t\t\tgenome = genome.replace(char,"_")\n-\n-\t\t\t\ttry:\n-\t\t\t\t\tgi = record.annotations["gi"]\n-\t\t\t\t\ttyp = str(gi)\n-\t\t\t\texcept:\n-\t\t\t\t\ttry:\n-\t\t\t\t\t\tgi = record.annotations["accessions"][0]\n-\t\t\t\t\t\ttyp = str(gi)\n-\t\t\t\t\texcept:\n-\t\t\t\t\t\tscaf_value += 1\n-\t\t\t\t\t\ttyp = "scaffold_"+str(scaf_value)\n-\t\t\t\tgenomeURI = coreURI[genome]\n-\t\t\t\tgbkURI = coreURI[genome + "/" + typ]\n-\t\t\t\t#To contig connection to connect all data to it\n-\t\t\t\tgenomeGraph.add((genomeURI, coreURI["dnaobject"] , gbkURI))\n-\n-\t\t\t\t#General genome features also stored in the class...\n-\t\t\t\tif "genome" in feature.qualifiers:\n-\t\t\t\t\tgenomeGraph.add((genomeURI, coreURI["organism"],Literal(feature.qualifiers["organism"][0])))\n-\t\t\t\tif "strain" in feature.qualifiers:\n-\t\t\t\t\tgenomeGraph.add((genomeURI, coreURI["strain"],Literal(feature.qualifiers["strain"][0])))\n-\t\t\t\tif "taxonomy" in record.annotations:\n-\t\t\t\t\tfo'..b'a" and feature_type.lower() != "ncrna":\n-\t\t\tSubClassOfDict[feature_type.lower().title()] = 1\n-\tfor key in feature.qualifiers:\n-\t\tvalues = feature.qualifiers[key]\n-\t\tif key == "translation":\n-\t\t\tpass\n-\t\telif type(values) == list:\n-\t\t\tfor v in values:\n-\t\t\t\tint_add(generalURI,coreURI[key.lower()],v)\n-\t\telse:\n-\t\t\tint_add(generalURI,coreURI[key.lower()],values)\n-\tif feature.type == "CDS":\n-\t\ttry:\n-\t\t\t#Feature is normally submitted to this function\n-\t\t\t#IF a subfeature is submitted it is submitted as a feature\n-\t\t\t#And subfeature variable will contain the superfeature\n-\t\t\tif superfeature:\n-\t\t\t\tcodon = superfeature.qualifiers["transl_table"][0]\n-\t\texcept:\n-\t\t\t#Default codon table 11\n-\t\t\tcodon = "11"\n-\t\t#Protein linkage\n-\t\ttranslation = ""\n-\t\ttry:\n-\t\t\ttranslation = feature.qualifiers["translation"][0].strip("*")\n-\t\texcept KeyError:\n-\t\t\t#When protein sequence is not given...\n-\t\t\tif len(feature.location.parts) > 1:\n-\t\t\t\t#Exon boundaries?\n-\t\t\t\tseq = \'\'\n-\t\t\t\tfor loc in feature.location:\n-\t\t\t\t\tseq += record.seq[loc]\n-\t\t\t\tif int(feature.location.strand) == -1:\n-\t\t\t\t\tseq = Seq(seq).complement()\n-\t\t\t\telse:\n-\t\t\t\t\tseq = Seq(seq)\n-\t\t\t\ttranslation = str(seq.translate(feature.qualifiers["transl_table"][0]))\n-\t\t\telif int(feature.location.strand) == -1:\n-\t\t\t\tif str(record.seq[feature.location.nofuzzy_start:feature.location.nofuzzy_end].reverse_complement().translate(codon)).strip("*") != translation:\n-\t\t\t\t\tif len(str(record.seq[feature.location.nofuzzy_start:feature.location.nofuzzy_end])) % 3 == 0:\n-\t\t\t\t\t\ttranslation = str(record.seq[feature.location.nofuzzy_start:feature.location.nofuzzy_end].reverse_complement().translate(codon))\n-\t\t\t\t\telse:\n-\t\t\t\t\t\ttranslation = \'\'\n-\t\t\telif int(feature.location.strand) == +1:\n-\t\t\t\t\tif len(str(record.seq[feature.location.nofuzzy_start:feature.location.nofuzzy_end])) % 3 == 0:\n-\t\t\t\t\t\ttranslation = str(record.seq[feature.location.nofuzzy_start:feature.location.nofuzzy_end].translate(codon))\n-\t\t\t\t\telse:\n-\t\t\t\t\t\ttranslation = \'\'\n-\t\t\t\n-\t\t\tif translation:\n-\t\t\t\ttranslation = list(translation)\n-\t\t\t\ttranslation[0] = "M"\n-\t\t\t\ttranslation = \'\'.join(translation).strip("*")\n-\t\t\t\tif "*" in translation:\n-\t\t\t\t\tpass\t\t\n-\n-\t\ttranslation = translation.encode(\'utf-8\')\n-\t\tmd5_protein = hashlib.md5(translation).hexdigest()\n-\t\tproteinURI = coreURI["protein/"+md5_protein]\n-\t\tgenomeGraph.add((generalURI,coreURI["protein"],proteinURI))\n-\t\tfor key in feature.qualifiers:\n-\t\t\tfor v in feature.qualifiers[key]:\n-\t\t\t\tif key == "translation":\n-\t\t\t\t\tgenomeGraph.add((proteinURI,coreURI["md5"],Literal(md5_protein)))\n-\t\t\t\t\tgenomeGraph.add((proteinURI,coreURI["sequence"],Literal(translation)))\n-\t\t\t\t\tgenomeGraph.add((proteinURI,RDF.type,proteinClass))\n-\t\t\t\telse:\n-\t\t\t\t\tfor v in feature.qualifiers[key]:\n-\t\t\t\t\t\tint_add(generalURI,coreURI[key.lower()],v)\n-\t\n-def int_add(subject, predicate, obj):\n-\ttry:\n-\t\tobject_float = float(obj.replace(\'"\',\'\'))\n-\t\tobject_int = int(obj.replace(\'"\',\'\'))\n-\t\tif object_int == object_float:\n-\t\t\tgenomeGraph.add((subject,predicate,Literal(object_int)))\n-\t\telse:\n-\t\t\tgenomeGraph.add((subject,predicate,Literal(object_float)))\n-\texcept:\n-\t\tgenomeGraph.add((subject,predicate,Literal(obj.replace(\'"\',\'\'))))\n-\t\t\t\t\n-def save():\n-\tdata = genomeGraph.serialize(format=\'turtle\')\n-\topen(sys.argv[sys.argv.index("-output")+1],"wb").write(data)\n-\n-def subClassOfBuilder():\n-\tfor subclass in SubClassOfDict:\n-\t\tgenomeGraph.add((coreURI["Feature"],RDFS.subClassOf,OWL.Thing))\n-\t\tgenomeGraph.add((coreURI[subclass],RDFS.subClassOf,coreURI["Feature"]))\n-\n-def subClassOfBuilderRna():\n-\tfor subclass in SubClassOfDictRna:\n-\t\tgenomeGraph.add((coreURI["Feature"],RDFS.subClassOf,OWL.Thing))\n-\t\tgenomeGraph.add((coreURI["Rna"],RDFS.subClassOf,coreURI["Feature"]))\n-\t\tgenomeGraph.add((coreURI[subclass],RDFS.subClassOf,coreURI["Rna"]))\n-\t\tgenomeGraph.add((coreURI[subclass],RDF.type,OWL.Class))\n-\n-def main():\n-\ttmp()\n-\tgbk_parser()\n-\tsubClassOfBuilder()\n-\tsubClassOfBuilderRna()\n-\tsave()\n-\tcleantmp()\n-\n-if __name__ == "__main__":\n-\tmain()\n\\ No newline at end of file\n'

diff -r f1255292e929 -r 6a858e304888 conversion/gbk2rdf/gbktordf.xml
--- a/conversion/gbk2rdf/gbktordf.xml Sat Feb 21 22:35:02 2015 +0100
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,38 +0,0 @@
-<tool id="SAPP_genbank_to_ttl" name="EMBL/GBK to RDF" version="0.1">
- <requirements>
-     <requirement type='package' version="3.4">python</requirement>
-     <requirement type='package' version="1.0">rdflib</requirement>
- </requirements>
- <description>Genbank to RDF conversion</description>
- <command interpreter="python3.4">gbktordf.py '-input' '$input' -output '$output' -sourcedb "$format" -format "$format"</command>
- <inputs>
- <param name="input" type="data" format="gbk,gb,genbank,embl" label="Genbank file"/>
- <param name="format" type="select" label="EMBL/GBK">
- <option value="genbank" selected="true"> Genbank</option>
- <option value="embl"> EMBL </option>
- </param>
- </inputs>
-
- <outputs>
- <data format="rdf" name="output" label="GBKttl: ${input.name}" />
- </outputs>
-
- <tests>
-     <test>
-       <param name="input" value="test-data/NC_010067.gbk"/>
-       <output name="$output" file="NC_010067.rdf"/>
-       <output name="$format" value="genbank"/>
-       <output name="$sourcedb" value="genbank"/>
-     </test>
-     <test>
-       <param name="input" value="test-data/CP009049.embl"/>
-       <output name="$output" file="CP009049.rdf"/>
-       <output name="$format" value="embl"/>
-       <output name="$sourcedb" value="embl"/>
-     </test>
-  </tests>
-
- <help>
- Genbank or EMBL to RDF conversion
- </help>
-</tool>

diff -r f1255292e929 -r 6a858e304888 conversion/gbk2rdf/test-data/CP009049.embl
--- a/conversion/gbk2rdf/test-data/CP009049.embl Sat Feb 21 22:35:02 2015 +0100
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,157312 +0,0 @@\n-ID CP009049; SV 1; circular; genomic DNA; STD; PRO; 4599018 BP.\n-XX\n-AC CP009049;\n-XX\n-PR Project:PRJNA255737;\n-XX\n-DT 13-FEB-2015 (Rel. 123, Created)\n-DT 13-FEB-2015 (Rel. 123, Last updated, Version 1)\n-XX\n-DE Salmonella enterica subsp. enterica serovar Paratyphi A strain CMCC 50973,\n-DE complete genome.\n-XX\n-KW .\n-XX\n-OS Salmonella enterica subsp. enterica serovar Paratyphi A\n-OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;\n-OC Enterobacteriaceae; Salmonella.\n-XX\n-RN [1]\n-RP 1-4599018\n-RA Wang B., Liang H., Liu X., Zhu L., Wang H., Zeng M.;\n-RT "Whole Genome Sequences of two Salmonella paratyphi A strains";\n-RL Unpublished.\n-XX\n-RN [2]\n-RP 1-4599018\n-RA Wang B., Liang H., Liu X., Zhu L., Wang H., Zeng M.;\n-RT ;\n-RL Submitted (24-JUL-2014) to the INSDC.\n-RL State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of\n-RL Biotechnology, 20 Dongdajie, Fengtai District, Beijing, Beijing 100071,\n-RL China\n-XX\n-DR MD5; e41a6215bf412b701febd8d4b182ec0c.\n-DR BioSample; SAMN02909989.\n-XX\n-CC Source DNA/bacteria are available from National Center for Medical\n-CC Culture Collection (CMCC) in China.\n-CC Annotation was added by the NCBI Prokaryotic Genome Annotation\n-CC Pipeline (released 2013). Information about the Pipeline can be\n-CC found here: http://www.ncbi.nlm.nih.gov/genome/annotation_prok/\n-CC ##Genome-Assembly-Data-START##\n-CC Assembly Method :: SOAPdenovo v. 2011.04\n-CC Assembly Name :: CMCC(B) 50973\n-CC Genome Coverage :: 133x\n-CC Sequencing Technology :: Illumina\n-CC ##Genome-Assembly-Data-END##\n-CC ##Genome-Annotation-Data-START##\n-CC Annotation Provider :: NCBI\n-CC Annotation Date :: 07/25/2014 13:43:31\n-CC Annotation Pipeline :: NCBI Prokaryotic Genome Annotation\n-CC Pipeline\n-CC Annotation Method :: Best-placed reference protein set;\n-CC GeneMarkS+\n-CC Annotation Software revision :: 2.6 (rev. 440435)\n-CC Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA;\n-CC repeat_region\n-CC Genes :: 4,309\n-CC CDS :: 4,016\n-CC Pseudo Genes :: 166\n-CC CRISPR Arrays :: 2\n-CC rRNAs :: 20 ( 5S, 16S, 23S )\n-CC tRNAs :: 100\n-CC ncRNA :: 7\n-CC Frameshifted Genes :: 106\n-CC ##Genome-Annotation-Data-END##\n-XX\n-FH Key Location/Qualifiers\n-FH\n-FT source 1..4599018\n-FT /organism="Salmonella enterica subsp. enterica serovar\n-FT Paratyphi A"\n-FT /host="Homo sapiens"\n-FT /sub_species="enterica"\n-FT /strain="CMCC 50973"\n-FT /mol_type="genomic DNA"\n-FT /country="China:Jiangsu"\n-FT /lat_lon="32.04 N 118.78 E"\n-FT /collection_date="2003-06-01"\n-FT /serovar="Paratyphi A"\n-FT /db_xref="taxon:54388"\n-FT /culture_collection="CMCC:50973"\n-FT gene complement(129..713)\n-FT /gene="mobA"\n-FT /locus_tag="IT63_00010"\n-FT CDS complement(129..713)\n-FT /codon_start=1\n-FT /transl_table=11\n-FT /gene="mobA"\n-FT /locus_tag="IT63_00010"\n-FT /product="molybdopterin-guanine dinucleotide biosynthesis\n-FT protein MobA"\n-FT /note="in Escherichia coli MobA links a guanosine\n-FT 5\'-phosphate to molydopterin to form molybdopterin guanine\n-FT dinucleotide during molybdenum cofactor biosynthesis;\n-FT Derived by automated c'..b'cgag cgaacgggga ggagcccaga gcctgaatca gcatgtgtgt 4596180\n- tagtggaagc gtctggaaag gcgcgcgata cagggtgaca gccccgtaca caaaagcgca 4596240\n- tgtgctgtga gctcgatgag tagggcggga cacgtggtat cctgtctgaa tatgggggga 4596300\n- ccatcctcca aggctaaata ctaattttgc tctttaaaaa tctggatcaa gctgaaaatt 4596360\n- gaaacacaga acaacgaaag ttgttcgtga gtctctcaaa ttttcgcaac acgatgatga 4596420\n- atcgtaagaa acatcttcgg gttgtgaggt taagcgacta agcgtacacg gtggatgccc 4596480\n- tggcagtcag aggcgatgaa ggacgtgcta atctgcgata agcgccggta aggtgatatg 4596540\n- aaccgttata accggcgatt tccgaatggg gaaacccagt gtgattcgtc acactatcat 4596600\n- taactgaatc cataggttaa tgaggcgaac cgggggaact gaaacatcta agtaccccga 4596660\n- ggaaaagaaa tcaaccgaga ttcccccagt agcggcgagc gaacggggag gagcccagag 4596720\n- cctgaatcag catgtgtgtt agtggaagcg tctggaaagg cgcgcgatac agggtgacag 4596780\n- ccccgtacac aaaagcgcat gtgctgtgag ctcgatgagt agggcgggac acgtggtatc 4596840\n- ctgtctgaat atggggggac catcctccaa ggctaaatac tcctgactga ccgatagtga 4596900\n- accagtaccg tgagggaaag gcgaaaagaa ccccggcgag gggagtgaaa aagaacctga 4596960\n- aaccgtgtac gtacaagcag tgggagcaca ggtttacctg tgtgactgcg taccttttgt 4597020\n- ataatgggtc agcgacttat attctgtagc aaggttaacc gtatagggga gccggaggga 4597080\n- aaccgagtct taaccgggcg ttaagttgca gggtatagac ccgaaacccg gtgatctagc 4597140\n- catgggcagg ttgaaggttg ggtaacacta actggaggac cgaaccgact aatgttgaaa 4597200\n- aattagcgga tgacctgtgg ctgggggtga aaggccaatc aaaccgggag atagctggtt 4597260\n- ctccccgaaa gctatttagg tagcgcctcg tgaattcatc tccgggggta gagcactgtt 4597320\n- tcggctaggg ggccatcccg gcttaccaac ccgatgcaaa ctgcgaatac cggagaatgt 4597380\n- tatcacggga gacacacggc gggtgctaac gtccgtcgtg aagagggaaa caacccagac 4597440\n- cgccagctaa ggtcccaaag tcatggttaa gtgggaaacg atgtgggaag gcccagacag 4597500\n- ccaggatgtt ggcttagaag cagccatcat ttaaagaaag cgtaatagct cactggtcga 4597560\n- gtcggcctgc gcggaagatg taacggggct aaaccatgca ccgaagctgc ggcagcgaca 4597620\n- ctcaggtgtt gttgggtagg ggagcgttct gtaagcctgt gaaggtggcc tgtgagggtt 4597680\n- gctggaggta tcagaagtgc gaatgctgac ataagtaacg ataaagcggg tgaaaagccc 4597740\n- gctcgccgga agaccaaggg ttcctgtcca acgttaatcg gggcagggtg agtcgacccc 4597800\n- taaggcgagg ccgaaaggcg tagtcgatgg gaaacgggtt aatattcccg tacttggtgt 4597860\n- tactgcgaag ggggggacgg agaaggctat gttggccggg cgacggttgt cccggtttaa 4597920\n- gcgtgtaggt gtgtgttcca ggtaaatccg gttcacttta acactgaggc gtgacgacga 4597980\n- ggcactacgg tgctgaagca acaaatgccc tgcttccagg aaaagcctct aagcatcagg 4598040\n- taacatcaaa tcgtacccca aaccgacaca ggtggtcagg tagagaatac caaggcgctt 4598100\n- gagagaactc gggtgaagga actaggcaaa atggtgccgt aacttcggga gaaggcacgc 4598160\n- tgacacgtag gtgaagtgat ttactcatgg agctgaagtc agtcgaagat accagctggc 4598220\n- tgcaactgtt tattaaaaac acagcactgt gcaaacacga aagtggacgt atacggtgtg 4598280\n- acgcctgccc ggtgccggaa ggttaattga tggggtcagc gcaagcgaag ctcctgatcg 4598340\n- aagccccggt aaacggcggc cgtaactata acggtcctaa ggtagcgaaa ttccttgtcg 4598400\n- ggtaagttcc gacctgcacg aatggcgtaa tgatggccag gctgtctcca cccgagactc 4598460\n- agtgaaattg aactcgctgt gaagatgcag tgtacccgcg gcaagacgga aagaccccgt 4598520\n- gaacctttac tatagcttga cactgaacat tgagccttga tgtgtaggat aggtgggagg 4598580\n- ctttgaagtg tggacgccag tctgcatgga gccgaccttg aaataccacc ctttaatgtt 4598640\n- tgatgttcta acgtggaccc gttacccggg ttgcggacag tgtctggtgg gtagtttgac 4598700\n- tggggcggtc tcctcctaaa gagtaacgga ggagcacgaa ggttggctaa tcctggtcgg 4598760\n- acatcaggag gttagtgcaa tggcataagc cagcttgact gcgagcgtga cggcgcgagc 4598820\n- aggtgcgaaa gcaggtcata gtgatccggt ggttctgaat ggaagggcca tcgctcaacg 4598880\n- gataaaaggt actccgggga taacaggctg ataccgccca agagttcata tcgacggcgg 4598940\n- tgtttggcac ctcgatgtcg gctcatccca tcccggggct gaagtaggtc ccaagggtat 4599000\n- ggctgttcgc catttaaa 4599018\n-//\n'

diff -r f1255292e929 -r 6a858e304888 conversion/gbk2rdf/test-data/NC_010067.gbk
--- a/conversion/gbk2rdf/test-data/NC_010067.gbk Sat Feb 21 22:35:02 2015 +0100
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b"@@ -1,259779 +0,0 @@\n-LOCUS NC_010067 4600800 bp DNA circular CON 20-AUG-2013\n-DEFINITION Salmonella enterica subsp. arizonae serovar 62:z4,z23:- str.\n- RSK2980 chromosome, complete genome.\n-ACCESSION NC_010067\n-VERSION NC_010067.1 GI:161501984\n-DBLINK Project: 58191\n- BioProject: PRJNA58191\n-KEYWORDS .\n-SOURCE Salmonella enterica subsp. arizonae serovar 62:z4,z23:- str.\n- RSK2980\n- ORGANISM Salmonella enterica subsp. arizonae serovar 62:z4,z23:- str.\n- RSK2980\n- Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;\n- Enterobacteriaceae; Salmonella.\n-REFERENCE 1 (bases 1 to 4600800)\n- CONSRTM NCBI Genome Project\n- TITLE Direct Submission\n- JOURNAL Submitted (03-DEC-2007) National Center for Biotechnology\n- Information, NIH, Bethesda, MD 20894, USA\n-REFERENCE 2 (bases 1 to 4600800)\n- AUTHORS McClelland,M., Sanderson,E.K., Porwollik,S., Spieth,J.,\n- Clifton,W.S., Fulton,R., Chunyan,W., Wollam,A., Shah,N., Pepin,K.,\n- Bhonagiri,V., Nash,W., Johnson,M., Thiruvilangam,P. and Wilson,R.\n- CONSRTM The Salmonella enterica serovar Arizonae Genome Sequencing Project\n- TITLE Direct Submission\n- JOURNAL Submitted (02-NOV-2007) Genetics, Genome Sequencing Center, 4444\n- Forest Park Parkway, St. Louis, MO 63108, USA\n-COMMENT PROVISIONAL REFSEQ: This record has not yet been subject to final\n- NCBI review. The reference sequence was derived from CP000880.\n- Salmonella enterica subspecies IIIa (Arizonae) serovar\n- 62:z4,z23:--Most bacteria in the species S. enterica belong to one\n- of seven subspecies; all but subspecies I normally grow only in\n- cold-blooded animals. Subspecies IIIa (S. Arizonae) is naturally\n- found in reptiles, but also causes outbreaks of salmonellosis in\n- turkeys and sheep and can occasionally produce both gastroenteritis\n- and serious disseminated disease in humans. Many human infections\n- can be traced to contact with reptiles or ingestion of various\n- reptile products, particularly from rattlesnakes. Fewer than ten\n- cases in humans are typically reported in the US each year.\n- \n- The strain of S. Arizonae (62:z4,z23:-) being sequenced is\n- CDC346-86; it was named RSK2980 by R.K. Selander and is strain\n- SARC5 of the Salmonella Reference C set. This serovar is of\n- interest because of its taxonomic position. It appears to be the\n- most divergent subspecies among the S. enterica. It can be obtained\n- from the American Type Culture Collection as ATCC BAA-731, or the\n- Salmonella Genetic Stock Centre as SGSC4693. The genome was\n- sequenced to 8X coverage, using plasmid and fosmid libraries and\n- was finished to an error rate of less than 1 per 10,000 bases.\n- Automated annotation was performed and manual annotation will\n- continue in the labs of Michael McClelland and Kenneth Sanderson.\n- The National Institute of Allergy and Infectious Diseases (NIAID),\n- National Institutes of Health (NIH) has funded this project.\n- \n- Coding sequences below are predicted using GeneMark v3.3 and\n- Glimmer2 v2.13.Intergenic regions not spanned by GeneMark and\n- Glimmer2 were blasted against NCBI's non-redundant (NR) database\n- and predictions generated based on protein alignments. RNA genes\n- were determined using tRNAscan-SE 1.23 or Rfam v8.0. This sequence\n- was finished as follows unless otherwise noted: all regions were\n- double stranded, sequenced with an alternate chemistries or covered\n- by high quality data(i.e., phred quality >=30);an attempt was made\n- "..b'1 acccgtcatc gtatcgtcct tgccgcaacg cttgcggaat ttcttacaca acttaatcct\n- 4597741 cttctgtaat cgtttgccct gacaggtgtg agagatctct tacaaggtct gtaggagatc\n- 4597801 gccaggatat cagagaatac ttagctacga ctttctcctg taaatatata taaatcaatc\n- 4597861 tattaaaata ttatttcgca ctttcatata caaatttact taaggtatcg tctgtaagcg\n- 4597921 tcttgtaaga caaggtgaaa caggcgattc tatattcatc gacagggagt cgtacaacga\n- 4597981 agcgaacgtc aggaagatgg cgcttctgca ggacacgcca ggagggcgtt acatggaaag\n- 4598041 gcttcaggat gaggcaaagt ggaaagcgca ggatgcgtta aaggacacct ccaggacgga\n- 4598101 gaacgagagc cgattaggat ggtcggcggg tctggatgac cagggacgct tcgggatgaa\n- 4598161 gctatcacat cggggcgatg tgcgcaggat gcaaacgttc aggatgagca ggccgcaggg\n- 4598221 tcacaggaaa agttgtcacg gatgagcagg gagcatgaaa agtagctgga atgctgcgaa\n- 4598281 acgaaccggg agcactgttt atacagtgct cccttttttt gttattcttc gcgccagatt\n- 4598341 tccattattg aggttcttaa catgacgact catgaccgtg tgcgtcagca gttacatgcg\n- 4598401 cttgaaacgc tgctgcgtga gcatcatcac tggcggctgg atgcgccgca ggcgcacctg\n- 4598461 tttaccagca cgcagccgtt ttgtatggat accatggaac cgctggaatg gctgcaatgg\n- 4598521 gtattgatcc cgcgtatgca taccctgctt gataatgcgc agccgttacc tgaggcgttt\n- 4598581 gccgtcgccc cttattatga aatggcgctg acggcggatt atccgcagcg ggaagcgatc\n- 4598641 ctgacggttt tgcaggatct ggatgcgcta tttacccgcg ataaatcctg atgctggaga\n- 4598701 tcctctatca ggacgcgtgg ctggttgccg ttaataaacc tgcaggctgg cttgttcacc\n- 4598761 ggagctggct ggatcgcgac gaaaaagttg tggtcatgca aacggtgcgc gaccaaatcg\n- 4598821 gccagcatgt ttttaccgcc caccgtctcg acagacccac atcgggcgta ctactgatgg\n- 4598881 ggctgtccag cgaagcggga cgccgcctgg cgcagcagtt cgagcagcac catatccgta\n- 4598941 aacgttacca tgccatagtg cgcggctggc tgatggatga tgcgctactg gattatcctc\n- 4599001 tgctggaaga gcgcgataaa attgccgata agttcgcgcg tgaggataaa gcgccccagc\n- 4599061 cagccgtaac gcagtatcgc gggctggcga cggtcgaaat ggcagtgccg accgggcgtt\n- 4599121 atcccactac gcgttatggc ctggttgagc tggaaccgaa aacggggcgc aaacaccagc\n- 4599181 tccgccgtca tctggcgcat ctacgccatc ctatcatcgg cgacagtaaa cacggtgatt\n- 4599241 tgcggcaaaa ccgtagcgcg gcggaacatt ttgcttgtcg tcgcctgatg cttcatgcca\n- 4599301 gtcggcttga actgacgcat cccttcaccg gacagccatt aattattcag gccggactgg\n- 4599361 atgaaacctg gatgcaggcg ctaacacagt ttggctggcg gggacttctc cctgataatg\n- 4599421 aaagggttga gtttacgacg gcgtcccggc aggatgagtc ttatcagaca taattcaggg\n- 4599481 agatacgcat aatggcggaa attggtattt ttgtcggtac gatgtatggc aactcactgt\n- 4599541 tggtggcgga ggaagcggaa gcgatcctgg ccagacaggg ccatagcgcg actgtgtttg\n- 4599601 aagatcctga actgtccgac tggcggcaat atcaggacaa ggtggcattg gttgtcacct\n- 4599661 caacgaccgg acagggcgat ctaccggata gtattgcgcc gctctttcac ggtattaaag\n- 4599721 atacgttagg ttttcaacca aacctgcgtt acggggtgat tgcgttaggt gatagcagct\n- 4599781 accccaattt ctgtaatggc ggcaagcagt ttgatgccct gttgcaggag caaagcgcgc\n- 4599841 aacgggtggg ggaaatgtta ctcattgacg ccagcgaaca tccggagccg gagagccaat\n- 4599901 ccaatccctg ggtagaaaac tggggaacct tactttcctg aggtaaatcc ctccccctac\n- 4599961 cgggagggta ccttttcgtt tgattgcatt gccagtaagc aaaataacga cctgtatgta\n- 4600021 gtttaaagaa actgaatcgt gttagctttg tgcatatgcc tgcaaaagca gcagtttttt\n- 4600081 acgggcgttt tcatgtaatc aagcgacctg tttcacattc ttctcttttt attcctcctg\n- 4600141 cgtcgacgcc tgacgccttc tgatttcatt tccgtgaagt ggcttccact gtcctgggct\n- 4600201 tttgccacaa acaggcgtaa ttcattgcca aaatactgtg ttgttgcacg gtgagtgtgc\n- 4600261 gtgacgcgct ttttatactt ctcctgccag tgaataaaag aatgcagcat gcaaagcaaa\n- 4600321 cgacctaata aaagctgcaa caaggaaacg ttatctctga ttccctaccg gttgtgcagt\n- 4600381 tcagagtgag cgtagctaac gcgaaatttc aggagtgcaa caatgagttc attaagtcac\n- 4600441 gcggcgagta gtgcggagaa tcgcacgaac gcccgctact ggatagtggt gatgctgttt\n- 4600501 atcgtcacat cctttaacta tggcgatcgc gccacattgt ccattgccgg ctcagaaatg\n- 4600561 gccaaagata ttggtcttga cccggtaggc atgggctacg ttttctctgc gttttcatgg\n- 4600621 gcctatgtta tcggacagat ccctggcggc tggctgctgg accgctttgg ttccaaacgc\n- 4600681 gtctatttct ggtctatttt catctggtcg gtcttcaccc tgttgcaggg ttttgtcgat\n- 4600741 atttttagcg gtttcggcat tgttgtcgcc ctctttacgc ttcgtttcct ggtcggtctg\n-//\n'

diff -r f1255292e929 -r 6a858e304888 conversion/gbk2rdf/tool_dependencies.xml
--- a/conversion/gbk2rdf/tool_dependencies.xml Sat Feb 21 22:35:02 2015 +0100
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -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>

diff -r f1255292e929 -r 6a858e304888 conversion/protein2rdf/protein_to_ttl.py
--- a/conversion/protein2rdf/protein_to_ttl.py Sat Feb 21 22:35:02 2015 +0100
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,130 +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.
-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
-import hashlib
-
-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["Protein"])
-
- genome = sys.argv[sys.argv.index('-idtag')+1].replace(" ","_")
- if genome == '':
- genome = sys.argv[sys.argv.index('-id_alternative')+1].replace(" ","_").replace(".","_")
-
- genomeURI = coreURI[genome]
- 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 '-diagnosis' == element:
- genomeGraph.add((genomeURI, coreURI["diagnosis"] , Literal(sys.argv[index+1])))
- if '-country' == element:
- genomeGraph.add((genomeURI, coreURI["country"] , Literal(sys.argv[index+1])))
- if '-location' == element:
- genomeGraph.add((genomeURI, coreURI["location"] , Literal(sys.argv[index+1])))
- if '-date' == element:
- genomeGraph.add((genomeURI, coreURI["date"] , Literal(sys.argv[index+1])))
- if '-ids' == element:
- genomeGraph.add((genomeURI, coreURI["id_tag"] , Literal(sys.argv[index+1])))
-
-
-
- data = (open(input_file).readlines())
- fastadict = {}
- sequence = ""
- key = ""
- for index, line in enumerate(data):
- if ">" == line[0]:
- if sequence:
- fastadict[key] = sequence
- key = line
- sequence = ""
- fastadict[key] = ""
- else:
- sequence += line.strip()
- fastadict[key] = sequence
-
- #Create a class, to be the same as all the other genome conversions...
- #TODO: Proteins are part of cds, cds are part of dnaobject
- #If CDS is not there... how then?
- classURI = coreURI[genome + "/" + "protein_fasta"]
- proteinClass = createClass(coreURI["Protein"])
- genomeClass = createClass(coreURI["Genome"])
- typeClass = createClass(coreURI["DnaObject"])
- cdsClass = createClass(coreURI["Cds"])
- #A theoretical begin, end is created to have a workable GBK generation
- begin = 0
- end = 0
- genomeGraph.add((genomeURI, RDF.type, genomeClass))
- genomeGraph.add((genomeURI, coreURI["sourcedb"], Literal(sys.argv[sys.argv.index("-sourcedb")+1])))
- genomeGraph.add((genomeURI, coreURI["dnaobject"] , classURI))
- genomeGraph.add((classURI, RDF.type, typeClass))
-
- for protein in fastadict:
- sequence = fastadict[protein]
- sequence = sequence.encode('utf-8')
- end = begin + len(sequence)
- md5_protein = hashlib.md5(sequence).hexdigest()
- proteinURI = coreURI["protein/"+md5_protein]
-
- cdsURI = coreURI[genome + "/protein_fasta/" + str(begin)+"_"+str(end)]
- genomeGraph.add((classURI, coreURI["feature"] , cdsURI))
- genomeGraph.add((cdsURI, coreURI["begin"] , Literal(begin)))
- genomeGraph.add((cdsURI, coreURI["end"] , Literal(end)))
- genomeGraph.add((cdsURI, coreURI["sourcedb"] , Literal(sys.argv[sys.argv.index("-sourcedb")+1])))
- genomeGraph.add((cdsURI, coreURI["protein"] , proteinURI))
- genomeGraph.add((cdsURI, RDF.type, cdsClass))
-
-
-
- genomeGraph.add((proteinURI,coreURI["md5"],Literal(md5_protein)))
- genomeGraph.add((proteinURI,coreURI["sequence"],Literal(sequence)))
- genomeGraph.add((proteinURI,RDF.type,proteinClass))
- genomeGraph.add((proteinURI, coreURI["sourcedb"], Literal(sys.argv[sys.argv.index("-sourcedb")+1])))
- genomeGraph.add((proteinURI, RDF.type, proteinClass))
- begin = end
-
-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()
-

diff -r f1255292e929 -r 6a858e304888 conversion/protein2rdf/protein_to_ttl.xml
--- a/conversion/protein2rdf/protein_to_ttl.xml Sat Feb 21 22:35:02 2015 +0100
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,42 +0,0 @@
-<tool id="SAPP_protein_rdf" name="Protein FASTA to RDF" version="0.1">
-    <requirements>
-        <requirement type='package' version="3.4">python</requirement>
-        <requirement type='package' version="1.0">rdflib</requirement>
-    </requirements>
- <description></description>
- <command interpreter="python3.4">protein_to_ttl.py '-input' '$input' '-output' '$output' '-organism' '$organism' '-ncbi_taxid' '$ncbi_taxid' '-idtag' '$identification_tag' '-diagnosis' '$diagnosis' '-country' '$country' '-location' '$location' '-date' '$date' -sourcedb SAPP
- #for $index, $id in enumerate( $ids )
- '-ids' '$id.id_tag'
- #end for
- '-id_alternative' '$input.name'
- </command>
- <inputs>
- <param size="60" name="input" type="data" format="fasta,fa" label="File for annotation, file types used fasta,fa"/>
- <param size="60" name="organism" type="text" format="text" label="organism name"/>
- <param size="60" name="diagnosis" type="text" format="text" label="Diagnosis of host if applicable"/>
- <param size="60" name="ncbi_taxid" type="text" format="text" label="NCBI taxonomy ID"/>
- <param size="60" name="country" type="text" format="text" label="Country of sample"/>
- <param size="60" name="location" type="text" format="text" label="Location of sample e.g., river, city, hospital"/>
- <param size="60" name="date" type="text" format="text" label="Sample date"/>
- <param size="60" name="identification_tag" type="text" format="text" label="An identification tag used for RDF storage !Needs to be very unique!"/>
- <repeat name="ids" title="Identification tags">
- <param size="60" name="id_tag" type="text" format="text" label="An identification tag used by other consortiums"/>
- </repeat>
- </inputs>
-
- <outputs>
- <data format="rdf" name="output" label="proteinTTL: ${input.name}" />
- </outputs>
-    <tests>
-        <test>
-            <param name="input" value="test-data/NC_017117.faa"/>
-            <output name="$output" file="NC_017117.rdf"/>
-            <output name="$ncbi_taxid" value="634455"/>
-            <output name="$idtag" value="Acetobacter pasteurianus IFO 3283-22"/>
-            <output name="$organism" value="Acetobacter pasteurianus IFO 3283-22"/>
-        </test>
-    </tests>
- <help>
- RDF creation from a multi protein fasta file
- </help>
-</tool>

diff -r f1255292e929 -r 6a858e304888 conversion/protein2rdf/test-data/NC_017117.faa
--- a/conversion/protein2rdf/test-data/NC_017117.faa Sat Feb 21 22:35:02 2015 +0100
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,993 +0,0 @@\n->gi|384055706|ref|YP_005485330.1| transposase [Acetobacter pasteurianus IFO 3283-22]\n-MKSDRFTDAQIMGVIRQAEGGVPVPDLCREHGISNATFYRWRAKYGGMDASMISQMKALEEENRRLKRMY\n-ADLSMQTDILKEALGKK\n->gi|384055707|ref|YP_005485331.1| DNA helicase II UvrD/Rep [Acetobacter pasteurianus IFO 3283-22]\n-MAGHHVEAMIARAHAQKRFMDDAGWRYVVELYGRYQSLLREQNAADFGDLLMWPTLAMLHNDAYRYRWSR\n-RFTAVMADEFQDVNRAQFLWLKMISEVSAEFFAVGDDSQSIL\n->gi|384055708|ref|YP_005485332.1| transposase [Acetobacter pasteurianus IFO 3283-22]\n-MVVGRNDCAKGRQMKDTVIGVDLAKNIFQVHGASRAGEVMFRKKLRRQQFMQFMATQPPALVVLEACGSA\n-HYWARELAGAGHEVRLIAPQYVKPFVKRQKNDAADAEAIVIAARQPEMRFVEPRTEAQQARGVLFRARQR\n-LVHQRTELVNALRAVLYEFGLVVPQGIAHIRHIEAMLDEAVLPEAVKQECLDLLRQISEQSVRIDVRTKK\n-IRMLAQESENTCRLQSMPGVGPLTALAIEAFAPDLQSFRRGRDFAAWLGLVPRQFSSGGKERLGKISKAG\n-QADIRRLLIMGAMTQVNWASRKAPAPGSWLARMLARKPRMLVAIALANRMARAIWAMATKQEDYRDPALS\n-VAA\n->gi|384055709|ref|YP_005485333.1| transposase [Acetobacter pasteurianus IFO 3283-22]\n-MEQIIRIGMDTSKSVFQLHGVNAKEQPVLRRKLSRREMVKFFEKLPPIEIAIEACGASHYWGRVLSCLGH\n-TVKLIAPQLVKPYVKRGKNDAADAEALCEAMSRPTMRFVPLKSEEEQAALMLIGMRARLIRNRTQLANTI\n-RGYAAEFGITAPKGMCRIEALLDRIAADESLPTLTRELFALHAKEYAELQGEIEQLEGKVMAWHRANECS\n-QRLAKIPGVGPIGAALLMMKTPDPHLFKSGRAFAAWIGLTPRDHSTGGKTRLGRITRAGDEVLRSTLVVG\n-ATAVVSHARRTNGKNASSWLRELLERKKPKLAAVALANKIARIAWKLMVSGEHYKRLLQQPGAAAV\n->gi|384055710|ref|YP_005485334.1| DNA resolvase [Acetobacter pasteurianus IFO 3283-22]\n-MVPPKPGKTPVGGRLIGYARVSTDDQGTDAQLNELRDAGCTMIFEKHASGADRNRPVLIRLLRDMNAGDT\n-LVVVRLDRLARSVSHLLAVIEQLDYAGAHFRSLDDPIDTTTPQGMFSLQVLGAVAQLDADFFCDGVDGSQ\n-RHRDVPR\n->gi|384055711|ref|YP_005485335.1| transposase [Acetobacter pasteurianus IFO 3283-22]\n-MLTSRIHRRKPMGKPMSKATARANAAKSSIRAHVEHVFAHQKNRFNLFIRTIGLARAEAKLTLCNLAYNF\n-NRLIFHERLETAG\n->gi|384055712|ref|YP_005485336.1| D-mannonate oxidoreductase [Acetobacter pasteurianus IFO 3283-22]\n-MNLNRNAISHVPDTVYTPRYDPALLRPGIVHLGCGNFHRGHQVVATQAAIDAEGRDGLRWGIVSATMRRP\n-DLATVLQSQDNLYTLLTREPANTVASVMAAITEAVYAGDDNANLAARIADPATAIVTLTVTASGYYLSAD\n-GRLDPTFEAIQADLTAITPRTAPGIIAAGLAQVRQRGGVPPVILCCDNVNSNGATLRQAVIDLAALKGDD\n-LLAAWIETNVQFPDTMVDRIVPTATPDDIADACRLLGGIEDRAPISAEPWFQWVIGEFDGPRPRWVAHPG\n-TKFVSDVGVFERAKLQMLNGTHMLLAYVGALANLNTVSEAASDDALGRIAARFMRNEQTADVSLDTDELD\n-RYTVDLMQRFRNPGIVHEVTRIGRNGSAKMASRIVQPMRSNIEAGRPVDGAVLLIASWIRWFALHEQDEF\n-DIALTDPRAETLRGLCADARDDHKAQAEAFLAMEEVFGAPLPDHGKQVEAIASMLRRLTEESVPELLRTI\n-AH\n->gi|384055713|ref|YP_005485337.1| phosphatase/phosphohexomutase [Acetobacter pasteurianus IFO 3283-22]\n-MTDTVFPAHLLKHKQEPVHGVVFDMDGLLLDSESLAMEALVFAARDLNYDIPMSFCRTMIGVPADGCRTM\n-VRKTYGQDFPLERFFELQEVHLRNFVDTGKLALKKGVLPLLDLLDTYKIPRAIATSSSRVRTDHHLKLVN\n-LFHRFNAIVTRDDVSKGKPDPEPYLTAAKKIGVNPAHALALEDSHSGARAAHAAGIRVIVVPDLLEATDE\n-IRGKALAIVQDLSIVEAYLKHAITGQA\n->gi|384055714|ref|YP_005485338.1| hypothetical protein APA22_40090 [Acetobacter pasteurianus IFO 3283-22]\n-MRRDMDLVRQLLLKLEGIEKGPHDVLLIGGNSEEVAVDGRTSDEIYFHLTKIEEAGFLERVGGGAMTAVT\n-FRALSWKGQEFLDTIRDDSIWKKTKEKAGSASFDILAAVAKAVIKDRIKSLTGLDIG\n->gi|384055715|ref|YP_005485339.1| hypothetical protein APA22_40100 [Acetobacter pasteurianus IFO 3283-22]\n-MRPLGSGLSVRTYGCSEADDQENDGWAKKDTGEIVALYEMSSPVMPSGLVSISRWKIKGCYPKSGLSRAM\n-LCPTKIPQSASNIALLIGSDWSFIEENVFCNHIEWQTCLPVFVMNLDHPA\n->gi|384055716|ref|YP_005485340.1| DNA helicase superfamily I [Acetobacter pasteurianus IFO 3283-22]\n-MSSKPSHHSVLSYWHSALLDDAQMKISFSRDNLVALDEEGFEKGKLPPDKTQALRKMHPASRDLAPDDSI\n-IAMAGIRILLGQVSHSTEHSKQPALFCMAMLVNVSPEGTIQPLKDAPPWINRELLEPSDGDVLIGDLATM\n-DTWLQLNPFEGGSLGKTLEWAEKLWNAVTGEDGLPDGYELWERVALQPAEASIGMIATLHQRRFYDTVLA\n-DTGLVTPLLARYIDGGPEPAVVDESQKWAAAGRARGTMTFAYGMSSSQSEAMTAFCSVKDGDILAVNGPP\n-GTGKTTLLQGIVATELVTRALEGGDPAVIVGTSTNNQAVTNIIDAMKKAMASKDSRPWARRWIEGADALG\n-LYFPSGEKEKEALKAGYLIASPGRGLGTMEWKGFPERERDTVDAWASRDAWINGYYGSFYPGVTPPLRKE\n-HLSGHGPQGARHDISLVEDGIAKIRARMKVLVETGRVCAGEARKLNQLYVASGYGTYPDITKAIAQREAL\n-LQERRPREDALKSDLKEKEAAAAVPRARINEENRKTRDLLKQRDDAVHAAGQKVEEVGAHAVALIAALPG\n-GGFFSNLMSGRNWANVERLVAEGRQGSFFRSLMQAQVKSKREWMDAINEMTASAERELATVRESREETRQ\n-ARDTLIQKLEREVAAADLVSKTARAEYDHYVGGSYVLAGRELEKLVTLKHQILQQLQDCCTAIETVLAPS\n-DWAAMFDMPEEKLPWRQSNWTGRLDVIEDFLDR'..b'DEVAPAV\n-RHLISQIQTTIA\n->gi|384055875|ref|YP_005485499.1| multidrug resistance transporter EmrB/QacA [Acetobacter pasteurianus IFO 3283-22]\n-MGTSMTSSRVTNPLFVLLAASTGCALTVLDTNVVAIILPTIAREFRASFADIEWVISTYVLCFASLLLPA\n-GAIADRYGRRRIYLIGITTFALTSLFCGAAPSATALYLARALQGVSAAFLLAPALAIIGHTFHNPDERNR\n-AWAIWGSIMGLTMVLAPIIGGIIAYALGWRWAFYINIPICVLLAGAVFILVKESRDTDARRLDPVGIIFF\n-AAFMFGLTWGMINGQASGWTSWNALNGFIGGSISLGIFIASERAQSRPMLDLGLFSNPRFLGAVWAMFAY\n-AASAQVMASMLPLFLQNGLGRSALQAGFAMLPFALAMLIFPHIGRLLERHISSSGILAGGLSCVAIGNGI\n-TAWGAYVGSWIIVMAGMVVIGSGGGLLNGETQKAIMSVVPKERSGMASGISTTSRFSGILLGFAMLSGIL\n-ATMVRKWVAAFGCGTGCHHPSDFADAIVAGDLPSAISGLEGSNQEIAIQHAHHAFSYGFAVALLVASIFA\n-LGSSITVFTLMQSKMKQNIT\n->gi|384055876|ref|YP_005485500.1| transposase, partial [Acetobacter pasteurianus IFO 3283-22]\n-MLAYAVMASVRYQANSLKPKKTQLRTRQSLSAGPFRRSGASS\n->gi|384055877|ref|YP_005485501.1| transposase [Acetobacter pasteurianus IFO 3283-22]\n-MQTECSAGAYEFPASCGRRVVARFDGGRMSSDGGVILVKQADDILGLSRRFAACFRDKRHPGFVEYRVED\n-LVRQRIMGLALGYEDLNDHDALRHDLIFGLASGRLSGGRANCAALAGKSTLNRLERSGQQADRYCRIIAD\n-HEALATLFVTLFLDQHEHAPARIVLDVDATDDRIHGHQEGRAFHGYYGHNCYLPLYVFCGDHLLSATLRT\n-ADRDPGKEALADIRRIVEQIRSRWPRVRILVRGDSGFARDSLMTWCEDNHVDFLFGLAGNTRLYDRIASL\n-SAEVRDEAATTGRAARGFASFDWITKDSWTRRRRVVAKAEWRHGNRYHRFIVTTLPQGMSDPRHLYEQIY\n-CARGDMENRIKECQMDLFSDRTSSHTIRANQLRLWFSAAAYVLLTALQRLALGQTSLETATCGTIRARLL\n-KIATRVTLSVRRIVLSMPDMFPCQHEFALAHARLRRLRQAI\n->gi|384055878|ref|YP_005485502.1| transposase [Acetobacter pasteurianus IFO 3283-22]\n-MQTECSAGAYEFPASCGRRVVARFDGGRMSSDGGVIVVKQADDILGLSRRFAACFRDKRHPGFVEYRVED\n-LVRQRIMGLALGYEDLNDHDALRHDLIFGLASGRLSGGRANCAALAGKSTLNRLERSGHKADRYCRIIAD\n-HEALATLFVTLFLDQHEHAPARIVLDVDATDDRIHGHQEGRAFHGYYGHNCYLPLYVFCGDHLLSATLRT\n-ADRDPGKEALADIRRIVEQIRSRWPRVRILVRGDSGFARDSLMTWCEDNHVDFLFGLAGNTRLYDRIASL\n-SAEVRDEAATTGRAARGFASFDWITKDSWTRRRRVVAKAEWRHGNRYHRFIVTTLPQGMSDPRHLYEQIY\n-CARGDMENRIKECQMDLFSDRTSSHTIRANQLRLWFSAAAYVLLTALQRLALGQTSLETATCGTIRARLL\n-KIATRVTLSVRRIVLSMPDMFPCQHEFALAHARLRRLRQAI\n->gi|384055879|ref|YP_005485503.1| DNA helicase II UvrD/Rep [Acetobacter pasteurianus IFO 3283-22]\n-MLQFSYMSEEADAIAAEIGRRAASGCAWHDIAVIYRQNRLSRAIEEALIQARVPYEIVGDVGFYQRVAVK\n-DALALLSLAARPDDRQSDEAFRADFSHLRQFRVIL\n->gi|384055880|ref|YP_005485504.1| DNA helicase RecD/TraA [Acetobacter pasteurianus IFO 3283-22]\n-MTSAVVGEQCQTEALAGLVERVTFHNAENGFCVLRVKVRGQRDLVTVVGHAAMISAGEFVQMSGRWFNDH\n-THGLQFKAEFLKASPPTTVEGIERYLGSGMIRGIGPVYAKKLVKAFGEAVFDLIEQEPHRLREVTGIGPK\n-RAERIVGGWADQKVIREIMLFLHSNGVGTSRAVRIFKTYGQDAVRLISENPYRLAKDIRGIGFKTADQIA\n-RKMGIAPDAMIRVRAGISYALGEAMDEGHCGLPVGELLTSTAELLEVAAPLIETALALELEAGDVVADSV\n-GETSCIFLAGLYRAEQSIAERLRACAVGRPPWPEIDAEKAMTWVEGKTGLAMAPSQQEAVRLALRSKVLV\n-ITGGPGVGKTTLVNAILKIVTAKGTDVQLCAPTGRAAKRLSESTGLEGKTIHRLLETDPGNGSFKRDDTN\n-PLTCDLLVVDEASMVDVLLMRSLLRALPDSASLLIVGDVDQLPSVGPGQVLADIIGSDAVPVVRLTEVFR\n-QAAQSRIITNAHRINEGKMPELSAEEGSDFYFVEAAEPEVGLRKLLAVVKDRIPARFGLDPVRDVQVLCP\n-MNRGGLGARSLNIELQQALNPAGDVKVERFGWTYGPGDKVMQIANDYDRDVFNGDLGVIDKIDVEEGELT\n-VLFDGREVVYGFGELDELVLAYATTIHKSQGSEYPVVVIPLVTQHYTMLARNLLYTGVTRGRKLVVLVGQ\n-KKALAIAVRNQGGRLRWSKLRDWLVGTSGTGHLSRLKKP\n->gi|384055881|ref|YP_005485505.1| phage integrase [Acetobacter pasteurianus IFO 3283-22]\n-MVESQVSHIQPEYKFHINLDEYDRRATLSADELKVVRRWKEENLVITKRQAPRLHKPLTDILYRSNLDRA\n-NSHRALKYLLLTVAHQEKPYWGWSEDLWVEIINNSPVLKKTGMVPQLIAVAYLLCGFRSVYKIQRNVATA\n-VVARLVFGAEIVDTECERLFSALTRVGFVCQTVRPLVPSVFAAVALQGENPKLESFDRKILEHTRECYTG\n-NHIAKRIGILSNGLAAMGLTSKVIHFRAYPPRHGTETDNINPEWMTWCRRWLETTTLREGSRRAVYNTLT\n-RIGIWLGREHPEVTGPEQWTVSVCADYLAAVDRLRVGDWGGSTFDYRLIPTVGQPLQAPTKVAYYQVMRR\n-FLSDIQSWEWARLRCNPRYHLSTPKNIAKYLGVNPRTIDDASWLKLTWASLNIEPDDLSPDCFYPFALLQ\n-AIAVVWTHAGLRSNEIARLRVGCTREQSEDVVDQSGNVVPAGQVCWLDVPEGKTSVAYTKPVGHAVHKYI\n-TAWMKKRASPRKHLDRRTGEHVHFLFQLRNRPIAKEVLNQTVIPLLCKKAGIPIEDSKGRITSHRGRASA\n-VSMLASVPQGMTIFDLAKWCGHTSVQSTMSYVRSKPTQLASAFAKADQAARMIEIVIDNEVIAAGATKDG\n-APWKYYDLGDSYCSNAFWSTCPHRMACARCYFNIPKPSAKGVVLAAQQAANRLLEEVWLSPEERDAVSGD\n-VEALEGMLNKLRDKPALDGRTPGEISATCGSQVSSPFTESE\n->gi|384055882|ref|YP_005485506.1| transposase [Acetobacter pasteurianus IFO 3283-22]\n-MELGITPGQDADITQAEPLLENIEPDAFLADKAYDADRLIDRLIQRGITPVIPPKRNRTTRRVIPP\n'

diff -r f1255292e929 -r 6a858e304888 fasta2rdf/fastatordf.py
--- a/fasta2rdf/fastatordf.py Sat Feb 21 22:35:02 2015 +0100
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

diff -r f1255292e929 -r 6a858e304888 fasta2rdf/fastatordf.xml
--- a/fasta2rdf/fastatordf.xml Sat Feb 21 22:35:02 2015 +0100
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

diff -r f1255292e929 -r 6a858e304888 fasta2rdf/test-data/NC_017117.fna
--- a/fasta2rdf/test-data/NC_017117.fna Sat Feb 21 22:35:02 2015 +0100
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

diff -r f1255292e929 -r 6a858e304888 gbk2rdf/gbktordf.py
--- a/gbk2rdf/gbktordf.py Sat Feb 21 22:35:02 2015 +0100
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

diff -r f1255292e929 -r 6a858e304888 gbk2rdf/gbktordf.xml
--- a/gbk2rdf/gbktordf.xml Sat Feb 21 22:35:02 2015 +0100
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

diff -r f1255292e929 -r 6a858e304888 gbk2rdf/test-data/CP009049.embl
--- a/gbk2rdf/test-data/CP009049.embl Sat Feb 21 22:35:02 2015 +0100
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

diff -r f1255292e929 -r 6a858e304888 gbk2rdf/test-data/NC_010067.gbk
--- a/gbk2rdf/test-data/NC_010067.gbk Sat Feb 21 22:35:02 2015 +0100
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

diff -r f1255292e929 -r 6a858e304888 genetic_elements/aragorn.py
--- a/genetic_elements/aragorn.py Sat Feb 21 22:35:02 2015 +0100
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,125 +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()

diff -r f1255292e929 -r 6a858e304888 genetic_elements/aragorn.xml
--- a/genetic_elements/aragorn.xml Sat Feb 21 22:35:02 2015 +0100
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,77 +0,0 @@
-<tool id="SAPP_aragorn_trna" name="tRNA and tmRNA" version="0.3">
-    <requirements>
-        <requirement type='package' version="3.4">python</requirement>
-        <requirement type='package' version="1.0">rdflib</requirement>
-        <requirement type="package" version="1.2.36">aragorn</requirement>
-    </requirements>
-    <description>Aragon</description>
-    <command interpreter="python3.4">aragorn.py '$input' '$output' '-gc$genbank_gencode' '$tmRNA' '$tRNA' '$topology' '-fon' '-sourcedb' 'SAPP'
-    </command>
-    <inputs>
-        <param name="input" type="data" format="rdf" label="RDF Genome"/>
-
-        <param name="genbank_gencode" type="select" label="Genetic code">
-            <option value="1" select="True">1. Standard</option>
-            <option value="2">2. Vertebrate Mitochondrial</option>
-            <option value="3">3. Yeast Mitochondrial</option>
-            <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
-            <option value="5">5. Invertebrate Mitochondrial</option>
-            <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
-            <option value="9">9. Echinoderm Mitochondrial</option>
-            <option value="10">10. Euplotid Nuclear</option>
-            <option value="11">11. Bacteria and Archaea</option>
-            <option value="12">12. Alternative Yeast Nuclear</option>
-            <option value="13">13. Ascidian Mitochondrial</option>
-            <option value="14">14. Flatworm Mitochondrial</option>
-            <option value="15">15. Blepharisma Macronuclear</option>
-            <option value="16">16. Chlorophycean Mitochondrial</option>
-            <option value="21">21. Trematode Mitochondrial</option>
-            <option value="22">22. Scenedesmus obliquus mitochondrial</option>
-            <option value="23">23. Thraustochytrium Mitochondrial</option>
-            <option value="24">24. Pterobranchia mitochondrial</option>
-        </param>
-        <param name="topology" type="select" label="Topology">
-            <option value="-c">Assume that each sequence has a circular topology</option>
-            <option value="-l">Assume that each sequence has a linear topology</option>
-        </param>
-        <param name='tmRNA' type='boolean' label='Search for tmRNA genes (-m)' truevalue='-m' falsevalue='' checked="true" help='' />
-        <param name='tRNA' type='boolean' label='Search for tRNA genes (-t)' truevalue='-t' falsevalue='' checked="true" help='' />
-    </inputs>
-    <outputs>
-        <data format="rdf" name="output" label="Aragorn: ${input.name}"></data>
-    </outputs>
-    <help>
-
-**What it does**
-
-Aragorn_ predicts tRNA (and tmRNA) in nucleotide sequences.
-
-.. _Aragorn: http://mbio-serv2.mbioekol.lu.se/ARAGORN/
-
------
-
-It requires an RDF genome file
-
-    </help>
-    <citations>
-        <citation type="bibtex">
-            @article{Laslett2004,
-abstract = {A computer program, ARAGORN, identifies tRNA and tmRNA genes. The program employs heuristic algorithms to predict tRNA secondary structure, based on homology with recognized tRNA consensus sequences and ability to form a base-paired cloverleaf. tmRNA genes are identified using a modified version of the BRUCE program. ARAGORN achieves a detection sensitivity of 99\% from a set of 1290 eubacterial, eukaryotic and archaeal tRNA genes and detects all complete tmRNA sequences in the tmRNA database, improving on the performance of the BRUCE program. Recently discovered tmRNA genes in the chloroplasts of two species from the 'green' algae lineage are detected. The output of the program reports the proposed tRNA secondary structure and, for tmRNA genes, the secondary structure of the tRNA domain, the tmRNA gene sequence, the tag peptide and a list of organisms with matching tmRNA peptide tags.},
-author = {Laslett, Dean and Canback, Bjorn},
-doi = {10.1093/nar/gkh152},
-file = {:Users/koeho006/Library/Application Support/Mendeley Desktop/Downloaded/Laslett, Canback - 2004 - ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences.pdf:pdf},
-isbn = {1362-4962 (Electronic)$\backslash$n1362-4962 (Linking)},
-issn = {03051048},
-journal = {Nucleic Acids Research},
-mendeley-groups = {VAPP Application note},
-pages = {11--16},
-pmid = {14704338},
-title = {{ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences}},
-volume = {32},
-year = {2004}
-}
-</citation>
-</citations>
-
-</tool>
-

diff -r f1255292e929 -r 6a858e304888 genetic_elements/aragorn/aragorn.py
--- a/genetic_elements/aragorn/aragorn.py Sat Feb 21 22:35:02 2015 +0100
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

diff -r f1255292e929 -r 6a858e304888 genetic_elements/aragorn/aragorn.xml
--- a/genetic_elements/aragorn/aragorn.xml Sat Feb 21 22:35:02 2015 +0100
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,88 +0,0 @@
-<tool id="SAPP_aragorn_trna" name="tRNA and tmRNA" version="0.3">
-    <requirements>
-        <requirement type='package' version="3.4">python</requirement>
-        <requirement type='package' version="1.0">rdflib</requirement>
-        <requirement type="package" version="1.2.36">aragorn</requirement>
-    </requirements>
-    <description>Aragon</description>
-    <command interpreter="python3.4">aragorn.py '$input' '$output' '-gc$genbank_gencode' '$tmRNA' '$tRNA' '$topology' '-fon' '-sourcedb' 'SAPP'
-    </command>
-    <inputs>
-        <param name="input" type="data" format="rdf" label="RDF Genome"/>
-
-        <param name="genbank_gencode" type="select" label="Genetic code">
-            <option value="1" select="True">1. Standard</option>
-            <option value="2">2. Vertebrate Mitochondrial</option>
-            <option value="3">3. Yeast Mitochondrial</option>
-            <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
-            <option value="5">5. Invertebrate Mitochondrial</option>
-            <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
-            <option value="9">9. Echinoderm Mitochondrial</option>
-            <option value="10">10. Euplotid Nuclear</option>
-            <option value="11">11. Bacteria and Archaea</option>
-            <option value="12">12. Alternative Yeast Nuclear</option>
-            <option value="13">13. Ascidian Mitochondrial</option>
-            <option value="14">14. Flatworm Mitochondrial</option>
-            <option value="15">15. Blepharisma Macronuclear</option>
-            <option value="16">16. Chlorophycean Mitochondrial</option>
-            <option value="21">21. Trematode Mitochondrial</option>
-            <option value="22">22. Scenedesmus obliquus mitochondrial</option>
-            <option value="23">23. Thraustochytrium Mitochondrial</option>
-            <option value="24">24. Pterobranchia mitochondrial</option>
-        </param>
-        <param name="topology" type="select" label="Topology">
-            <option value="-c">Assume that each sequence has a circular topology</option>
-            <option value="-l">Assume that each sequence has a linear topology</option>
-        </param>
-        <param name='tmRNA' type='boolean' label='Search for tmRNA genes (-m)' truevalue='-m' falsevalue='' checked="true" help='' />
-        <param name='tRNA' type='boolean' label='Search for tRNA genes (-t)' truevalue='-t' falsevalue='' checked="true" help='' />
-    </inputs>
-    <outputs>
-        <data format="rdf" name="output" label="Aragorn: ${input.name}"></data>
-    </outputs>
-    <tests>
-        <test>
-            <param name="input" value="test-data/NC_017117.fna"/>
-            <output name="$output" file="NC_017117.rdf"/>
-            <output name="$genbank_gencode" value="11"/>
-            <output name="$tmRNA" value="-m"/>
-            <output name="$tRNA" value="-t"/>
-            <output name="$topology" value="-c"/>
-        </test>
-    </tests>
-
-    <help>
-
-**What it does**
-
-Aragorn_ predicts tRNA (and tmRNA) in nucleotide sequences.
-
-.. _Aragorn: http://mbio-serv2.mbioekol.lu.se/ARAGORN/
-
------
-
-It requires an RDF genome file
-
-    </help>
-    <citations>
-        <citation type="bibtex">
-            @article{Laslett2004,
-abstract = {A computer program, ARAGORN, identifies tRNA and tmRNA genes. The program employs heuristic algorithms to predict tRNA secondary structure, based on homology with recognized tRNA consensus sequences and ability to form a base-paired cloverleaf. tmRNA genes are identified using a modified version of the BRUCE program. ARAGORN achieves a detection sensitivity of 99\% from a set of 1290 eubacterial, eukaryotic and archaeal tRNA genes and detects all complete tmRNA sequences in the tmRNA database, improving on the performance of the BRUCE program. Recently discovered tmRNA genes in the chloroplasts of two species from the 'green' algae lineage are detected. The output of the program reports the proposed tRNA secondary structure and, for tmRNA genes, the secondary structure of the tRNA domain, the tmRNA gene sequence, the tag peptide and a list of organisms with matching tmRNA peptide tags.},
-author = {Laslett, Dean and Canback, Bjorn},
-doi = {10.1093/nar/gkh152},
-file = {:Users/koeho006/Library/Application Support/Mendeley Desktop/Downloaded/Laslett, Canback - 2004 - ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences.pdf:pdf},
-isbn = {1362-4962 (Electronic)$\backslash$n1362-4962 (Linking)},
-issn = {03051048},
-journal = {Nucleic Acids Research},
-mendeley-groups = {VAPP Application note},
-pages = {11--16},
-pmid = {14704338},
-title = {{ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences}},
-volume = {32},
-year = {2004}
-}
-</citation>
-</citations>
-
-</tool>
-

diff -r f1255292e929 -r 6a858e304888 genetic_elements/aragorn/test-data/NC_017117.rdf
--- a/genetic_elements/aragorn/test-data/NC_017117.rdf Sat Feb 21 22:35:02 2015 +0100
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,25 +0,0 @@\n-@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .\n-@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .\n-@prefix ssb: <http://csb.wur.nl/genome/> .\n-@prefix xml: <http://www.w3.org/XML/1998/namespace> .\n-@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .\n-\n-ssb:NC_017117 a ssb:Genome ;\n- ssb:dnaobject <http://csb.wur.nl/genome/NC_017117/dnaobject_0> ;\n- ssb:id_tag "NC_017117" ;\n- ssb:sourcedb "SAPP" .\n-\n-ssb:Type a <http://www.w3.org/2002/07/owl#Class> ;\n- rdfs:subClassOf <http://www.w3.org/2002/07/owl#Thing> .\n-\n-ssb:DnaObject a <http://www.w3.org/2002/07/owl#Class> ;\n- rdfs:subClassOf <http://www.w3.org/2002/07/owl#Thing> .\n-\n-ssb:Genome a <http://www.w3.org/2002/07/owl#Class> ;\n- rdfs:subClassOf <http://www.w3.org/2002/07/owl#Thing> .\n-\n-<http://csb.wur.nl/genome/NC_017117/dnaobject_0> a ssb:DnaObject ;\n- ssb:header "gi|384055705|ref|NC_017117.1| Acetobacter pasteurianus IFO 3283-22 plasmid pAPA22-010, complete sequence" ;\n- ssb:sequence "CGCAGGTTGAGTTCCTGTTCCCGATAGATCCGATAAACCCGCTTATGATTCCAGAGCTGTCCCTGCACATTGCGCAGATACAGGAAACACAGACCAAATCCCCATCTCCTGTGAGCCTGGGTCAGTCCCACCAGAAGAGCGGCAATCCTGTCGTTCTCCGCTGCCAGTCGCGGACGATAGCGAAAGCAGGTCTCGGATATCCCAAAAATCCGACAGGCCAGCGCAATGCTGACCCCATGATGCGCCACAGCTTGTGCGGCCAGTTCCCGGCGCTGGGCTGGCCGCTTCATTTTTTTCCAAGGGCTTCCTTCAGGATATCCGTCTGCATGCTCAAATCCGCATACATGCGCTTCAGCCGACGGTTCTCCTCTTCCAAAGCCTTCATCTGACTGATCATCGAAGCATCCATGCCGCCATATTTCGCGCGCCACCGGTAAAACGTGGCGTTGCTGATCCCATGCTCCCGACACAGGTCAGGAACCGGGACACCGCCCTCAGCCTGGCGGATCACACCCATGATCTGGGCGTCAGTAAAGCGATCACTCTTCATCAGAATCTCCTCAATTCTTACGCTGAGAAAATTCTCATTCAAAAGTCACTCTTTTTATGGGGGGATTACCACTCTAAATCAATGCATTCCAATTAACTTATAAAATGCTTTGAGAGTCATCACCTACAGCAAAGAACTCTGCTGACACCTCTGAAATCATTTTGAGCCATAAAAACTGGGCTCGATTGACGTCCTGAAACTCATCAGCCATCACGGCTGTGAAACGGCGTGACCAGCGGTAGCGATAGGCATCATTGTGCAGCATTGCCAATGTCGGCCACATCAACAGATCCCCAAAATCTGCAGCATTCTGTTCGCGCAGCAAACTCTGGTAACGACCATACAACTCAACCACATAGCGCCAGCCCGCATCGTCCATAAAACGTTTCTGGGCATGTGCTCGCGCTATCATGGCTTCAACATGATGCCCTGCCATCTCAGGCGTCACCAGATCTTCCTTCAAACGAGATGGGGTGGTTGCCGTCCTCCCCGCACGGCATCGCAATGTGCCAGAATGGTCGTTGGAAGAAACGACTGCGCGAAAGGACGGCAGATGAAGGATACAGTGATAGGCGTTGATCTGGCAAAGAACATTTTCCAGGTTCATGGAGCTTCGCGTGCGGGCGAGGTGATGTTTCGCAAAAAGCTGCGTCGTCAGCAGTTTATGCAGTTCATGGCCACGCAGCCGCCTGCTCTGGTCGTTCTTGAAGCGTGCGGGAGCGCGCATTACTGGGCTCGCGAACTGGCAGGAGCTGGTCACGAGGTCAGACTGATCGCTCCGCAGTATGTGAAGCCTTTCGTGAAGCGCCAGAAGAACGATGCTGCTGATGCGGAAGCGATCGTCATTGCGGCCCGTCAGCCGGAAATGCGCTTTGTCGAACCACGCACTGAAGCGCAGCAGGCGCGTGGCGTTCTTTTCCGGGCCCGGCAGCGTCTGGTGCACCAGCGCACGGAACTGGTGAATGCCCTGCGTGCCGTTCTGTATGAATTCGGTCTCGTCGTGCCACAGGGGATTGCGCATATCAGACACATTGAAGCCATGCTGGATGAGGCGGTTCTGCCAGAGGCTGTGAAGCAGGAATGCCTTGATCTGCTGCGACAGATTTCGGAGCAGAGTGTGCGGATTGATGTCAGAACAAAGAAGATCAGGATGCTTGCCCAGGAAAGTGAAAACACCTGCAGATTGCAGAGCATGCCTGGAGTGGGTCCTCTGACCGCTCTTGCGATTGAAGCTTTTGCGCCTGACCTGCAGAGCTTCCGGCGCGGGCGCGACTTTGCTGCGTGGCTGGGGCTGGTGCCCCGTCAGTTCTCATCTGGCGGAAAGGAAAGGCTGGGGAAGATATCAAAAGCCGGGCAGGCTGATATCCGCAGGCTTCTCATCATGGGCGCCATGACCCAGGTGAACTGGGCCAGCCGTAAGGCCCCTGCACCGGGAAGCTGGCTGGCACGGATGCTGGCCCGCAAGCCCCGTATGCTGGTAGCCATTGCGCTGGCCAACAGGATGGCACGAGCCATCTGGGCCATGGCAACAAAACAGGAGGATTATCGGGATCCGGCCCTGTCCGTGGCAGCCTGAGCGATGGCTCGGCTCCCGCGGATGGAACCGGTAGGGGTGTGAGAGGGCGATGACCTGAATGGGCGCATGATCGTCTGATCCGGATCGGAAAAACCAGTGGATTTCTCTGTGCTTTAAAGCACGCCTGTGAGATTTGGATCTGATCCGCTGATCACCATACTGGCCAGTGGCTTCTGAAAGGCCACATCAACAGGCCTTACAGAAGACCGCACACGATCACACGTCAATATGGGTCAGAAAACTCTTGCATAACGGACGGCAACCATATGTGGACGGCTCCCCCTTGCAAGAGGCTAGGCAAGAAAATGATCGGATCTTTGCTTCCATATGTCCGGCCTGTTGATGCGGCCATAGGGTCGCTGGCCAAGATGGCTTCCGCAGCGTGAGCCCCAAACACAGAAGCGGTCTTTGATGACCACTGGTTGCCACGGGTTTTCTCACGCCATGGATCGATCGATCACACCATCTGCTCTATTACTTGCAAGCCACGACCTCAGCTCGGCACGAGAGCGTCAAATGTCAGCGCATCGTGCCAGGCTAAGCTCAAACAGCAGCTGCGCCGGGTTGCTGCAGAAGGCGCTTATAGTGTTCGCCGCTGACCATCAGTTTCCAAGCAATCCGCGCAATCTTATTGGCAAGGGCCACCGCTGCGAGTTTCGGTTTTTTGCGCTCCAGCAATTCACGTAACCAAGATGAGGCATTCTTCCCATTGGTCCGCCGGGCATGCGACACGACTGCGGTCGCGCCAACCACCAGCGTGCTTCGCAAGACCTCATCGCCAGCGCGTGTGATTCTGCCAAGCCTTGTTTTTCCACCGGTTGAGTGATCCCTGGGCGTCAATCCGATCCAGGCCGCAAAGGC'..b'GGAACGACGTTGCCAGACTGATCAACCACATCCTCTGATTGCTCACGCGTGCAACCGACCCTAAGCCGGGCGATCTCATTGCTCCGAAGGCCTGCATGTGTCCACACCACGGCGATTGCCTGCAACAAGGCGAATGGATAGAAACAGTCAGGAGAAAGGTCGTCTGGTTCGATGTTGAGGCTGGCCCAGGTCAGTTTCAGCCAAGAAGCATCATCTATGGTCCTAGGATTTACGCCAAGATATTTCGCAATATTCTTCGGTGTCGAGAGATGATATCGCGGATTACACCTGAGCCGCGCCCATTCCCAACTCTGAATATCAGATAAAAACCGGCGCATAACCTGATAATAAGCAACTTTCGTTGGAGCCTGCAGAGGCTGGCCAACTGTTGGGATCAGACGATAATCAAAGGTGGAACCGCCCCAATCGCCAACACGTAACCTGTCGACGGCGGCGAGATAGTCGGCACATACCGATACCGTCCATTGCTCTGGTCCAGTGACCTCAGGGTGCTCGCGACCCAACCAGATTCCGATACGGGTTAGAGTGTTGTAAACTGCTCGCCTCGACCCTTCTCGCAACGTTGTTGTTTCCAACCAACGTCGGCACCATGTCATCCACTCAGGATTGATATTATCAGTTTCAGTTCCGTGACGAGGTGGATATGCCCGAAAATGGATAACCTTTGATGTTAATCCCATTGCCGCCAAACCGTTTGACAATATTCCAATCCGCTTGGCGATATGATTTCCTGTGTAACACTCTCGTGTATGTTCCAGTATCTTCCTATCAAAACTTTCAAGTTTTGGATTCTCGCCTTGTAATGCAACTGCAGCAAATACTGATGGTACGAGGGGCCGAACGGTCTGACAGACGAAGCCGACACGGGTTAGGGCCGAGAACAGACGCTCACATTCTGTATCAACAATCTCCGCTCCAAAAACCAATCGGGCAACGACAGCCGTCGCCACATTGCGTTGAATTTTGTACACGCTTCGAAAACCACACAGAAGATAAGCGACTGCAATCAACTGCGGTACCATTCCGGTTTTTTTCAGAACAGGACTATTATTGATAATCTCAACCCACAGGTCTTCACTCCACCCCCAGTAGGGTTTTTCCTGGTGTGCGACCGTCAGAAGCAAATACTTCAAAGCACGATGGCTGTTAGCGCGGTCGAGATTGCTGCGATACAGGATGTCCGTCAGAGGCTTATGAAGACGCGGAGCCTGCCGTTTCGTAATAACAAGATTTTCTTCTTTCCAACGTCTGACAACTTTTAATTCGTCTGCAGACAATGTCGCCCGTCTGTCGTATTCATCGAGATTAATGTGGAATTTGTATTCGGGCTGGATGTGAGAAACCTGAGATTCTACCACTTTTCTATCCTCCGAAGACCCTGTGACCAAGCTTCATATCCATCTGTTCGACTGAGTTTGCGATCTTGCGAAGCAGATCTTCACCGGAAAGATGGATATAGAGTGTCGTGCTTTGAACATTGCGATGCCCGGCATACGTCGCAATATCGTGTAGACGCCAGCCAGCACGGGCCAGATGCGTCAATCTCAGGTGACGCAAAGTGTGCGTACTGAACAATGGCATATCAGCCTGGAGAGCAAGACGTCTGACAGTTTTGCTCCATGACCACTTCGTAATAGGCTGCCGAAAGTTCCGATCTGACTCAGAGAGAAACAGGGCCGCTGAATGAGTCGCTGCGTTGCGCCTTTGATGCAGATATACCGCCAACACAGGACAGAGCGCCGCTGAATAACAAACCACACGAGGGCGAGCGCTTTTACTTGTTTCGGCCCGAATGGTGAGCAAACGTCTCGCAGGGTCGATATCCGAGACGCGCAAATTTACTACGGCGTGTCGTCAGTTAAGCCCTGAGAGTGGCACGTGAGGGTTGTACTTTGTGTCTGCGTGTGCTGACTGTTTTCCCATTTTTTGGGGAGACAGACAGATGCGGCGCTATAGTTTACGCGATGACCAGTGGGAGCGGATAAAGGATCTTCTTCCTGGTCGAGAAGGCTATGTCGGCGGCACTGCGGTGAACAACCGTCTGTTCGTGGAGGCGGTGCTGTATCGCTATCGCGCGGGTATTCCATGGCGCGACCTTCCTGCCCGTTTCGGTGACTGGAAAAACGTGCACCGGCGTCTGCGCCGCTGGTGTGAAAGCGGCGTCATCGAACGGATATTTCGTTATCTGGCCGCTGATTACGACAACGAATACATGATGATCGACAGCACAATTGTCCGAGCGCATCAGCATAGTGCCGGAGCTCTCAAAAAAGGGGCACGGATCAGGCCATCGGACGATCACGGGCGGGCTAACTACAAAGATCCATGCCATCTGCGACGCTCTGGGCAATCCAGTGGAACTCGGCATCACACCGGGACAGGATGCCGATATCACCCAGGCAGAACCACTTCTGGAAAACATCGAACCGGATGCTTTCCTTGCTGACAAGGCGTATGACGCGGACAGGTTGATCGATCGGCTGATACAGCGCGGGATTACCCCGGTCATCCCGCCAAAACGCAACAGAACGACACGACGGGTAATCCCCCCATAAAAAGAGTGACTTTTGAATGAGAATTTTCTCAGCGTAAGAATTGAGGAGATTCTGATGAAGAGTGATCGCTTTAGTGACGCCCAGATCATGGGTGTGATCCGCCAGGCTGAGGGCGGTGTCCCGGTTCCTGACCTGTGCCGGGAGCATGGGATCAGCAACGCCACGTTTTACCGGTGGCGCGCGAAATATGGCGGCATGGATGCTTCGATGATCAGTCAGATGAAGGCTTTGGAAGAGGAGAACCGTCGGCTGAAGCGCATGTATGCGGATTTGAGCATGCAGACGGATATCCTGAAGGAAGCCCTTGGAAAAAAATGAAGCGGCCAGCCCAGCGCCGGGAACTGGCCGCACAGGCTGTGGCGCATCATGGGGTCAGCATTGCGCTGGCCTGTCGGATTTTTGGGATATCCGAGACCTGCTTTCGCTATCGTCCGCGACTGGCAGCGGAGAATGACAGGATTGCCGCTCTTCTGGTGGGACTGACCCAGGCTCACAGGAGATGGGGATTTGGTCTGTGTTTCCTGTATCTGCGCAATGTGCAGGGACAGCTCTGGAATCATAAGCGGGTTTATCGGATCTATCGGGAACTGGAGTTCAACCTGCGGATTAAACCCCGCAGGCGTCTGGTTCGCGAAAAGCCTGAAAAGCTGTCGGTTCCGGCCCTTCCCAACACGGTCTGGTCCATGGATTTCATGGCGGACAGGCTTTTGGATGGACGCGCTTTTCGGCTCCTGAACATCCTGGATGAGTTCAATCGTGAAGGACTGGCGATCGAGGTTGATTTTTCCCTGCCGGCCTGTCGGGTTGTCCGCTGGTAATCCCCCCATTTTTAGTGGGGCATTGAATGAGAATTCAGGCAGCTGTTTTTAGTTTCTGGGCGGGGGTTAGCCCGCTGTTCCCCATGTTGGGTCTGTCATTGTTATATGTCCAGAGCCATTGTGTTGCGACCTCCTGTACGTCCTGAATGCTTTCAAACAAATACTGCTCTAGCCATTCCTGCCGGACAGTTCTGTTGTAGCGTTCAATATAGGCGTTCTGCTGCGGATTGCCCGGTTGTGTATAGATCAGGGTAATCCCCTGCTTTTCGGCCCATGAAACCAACGTATGACTGACATATTCAGGGCCATTGTCCATTCGGATAGCCTCTGGCCTGCCACGCCACTCCATAACCTGTTCCAGACAGCGAACAACCCGACAGGCTGGCAGGGAAAAATCAACCTCAATCGCCAGTCCTTCACGATTGAAATCATCCAGAATGTTCAGGAGCCGAAAAGCACGTCCATCCATCAGCCTGTCCGCCATAAAATCCATGGACCAGACCCTGTTGGGAAGGGCCGGAACCGACAGCTTTTCAGGCTTTTCGCGAACCAGACGCCTGCGGGGTTTAATC" ;\n- ssb:sourcedb "SAPP" .\n-\n'

diff -r f1255292e929 -r 6a858e304888 genetic_elements/aragorn/tool_dependencies.xml
--- a/genetic_elements/aragorn/tool_dependencies.xml Sat Feb 21 22:35:02 2015 +0100
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -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>

diff -r f1255292e929 -r 6a858e304888 protein2rdf/protein_to_ttl.py
--- a/protein2rdf/protein_to_ttl.py Sat Feb 21 22:35:02 2015 +0100
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

diff -r f1255292e929 -r 6a858e304888 protein2rdf/protein_to_ttl.xml
--- a/protein2rdf/protein_to_ttl.xml Sat Feb 21 22:35:02 2015 +0100
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

diff -r f1255292e929 -r 6a858e304888 protein2rdf/test-data/NC_017117.faa
--- a/protein2rdf/test-data/NC_017117.faa Sat Feb 21 22:35:02 2015 +0100
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[