| Previous changeset 29:d854b21ada0c (2019-08-07) |
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Commit message:
planemo upload commit f74fd52b330cc7460d98121b9bb78c08ca915d1e |
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modified:
toolOptBioDes.py |
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added:
out/out.sbol test/diag.csv test/out.csv |
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removed:
optbiodes.xml |
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| diff -r d854b21ada0c -r 0ad6fda90f41 optbiodes.xml --- a/optbiodes.xml Wed Aug 07 05:13:27 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,33 +0,0 @@ -<tool id="optbiodes" name="OptBioDes" version="0.1.0"> - <description>optimal synbio design</description> - <requirements> - <requirement type="package" version="2">requests</requirement> - </requirements> - <command detect_errors="exit_code"><![CDATA[ - python $__tool_directory__/toolOptBioDes.py $input1 $input2 $output1 $output2 -server $server - ]]></command> - <inputs> - <param type="data" name="input1" format="csv" /> - <param type="integer" name="input2" value="48" label="Library size" help="Library size" /> - <param name="server" type="text" label="OptBioDes RES server" value="http://optbiodes.synbiochem.co.uk/REST" help="OptBioDes REST server" /> - </inputs> - <outputs> - <data name="output1" format="csv" from_work_dir="out1.csv" /> - <data name="output2" format="csv" from_work_dir="out2.csv" /> - </outputs> - <help><![CDATA[ - usage: toolOptBioDes.py [-h] [-server SERVER] infile outfile diagfile - -toolOptBioDes: Optimal SynBio Design. Pablo Carbonell, SYNBIOCHEM, 2019 - -positional arguments: - infile Input xlsx file (DoE specificiations). - outfile Output csv design file. - diagfile Output csv diagnostics file. - -optional arguments: - -h, --help show this help message and exit - -server SERVER OptBioDes server. - - ]]></help> -</tool> \ No newline at end of file |
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| diff -r d854b21ada0c -r 0ad6fda90f41 out/out.sbol --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/out/out.sbol Thu Aug 29 06:59:58 2019 -0400 |
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| b'@@ -0,0 +1,8334 @@\n+<?xml version="1.0" encoding="utf-8"?>\n+<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/"\n+ xmlns:prov="http://www.w3.org/ns/prov#"\n+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"\n+ xmlns:sbol="http://sbols.org/v2#"\n+ xmlns:sys-bio="http://sys-bio.org#">\n+ <sbol:ComponentDefinition rdf:about="http://synbiochem.co.uk/ComponentDefinition/AtCHI1/1">\n+ <dcterms:description>P41088</dcterms:description>\n+ <sbol:displayId>AtCHI1</sbol:displayId>\n+ <sbol:persistentIdentity rdf:resource="http://synbiochem.co.uk/ComponentDefinition/AtCHI1"/>\n+ <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>\n+ <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n+ <sbol:version>1</sbol:version>\n+ </sbol:ComponentDefinition>\n+ <sbol:ComponentDefinition rdf:about="http://synbiochem.co.uk/ComponentDefinition/BBR1/1">\n+ <dcterms:description>https://synbiohub.org/public/igem/BBa_I50041/1</dcterms:description>\n+ <sbol:displayId>BBR1</sbol:displayId>\n+ <sbol:persistentIdentity rdf:resource="http://synbiochem.co.uk/ComponentDefinition/BBR1"/>\n+ <sbol:role rdf:resource="http://identifiers.org/so/SO:0000296"/>\n+ <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n+ <sbol:version>1</sbol:version>\n+ </sbol:ComponentDefinition>\n+ <sbol:ComponentDefinition rdf:about="http://synbiochem.co.uk/ComponentDefinition/ColE1/1">\n+ <dcterms:description>https://synbiohub.org/public/igem/BBa_J64101/1</dcterms:description>\n+ <sbol:displayId>ColE1</sbol:displayId>\n+ <sbol:persistentIdentity rdf:resource="http://synbiochem.co.uk/ComponentDefinition/ColE1"/>\n+ <sbol:role rdf:resource="http://identifiers.org/so/SO:0000296"/>\n+ <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n+ <sbol:version>1</sbol:version>\n+ </sbol:ComponentDefinition>\n+ <sbol:ComponentDefinition rdf:about="http://synbiochem.co.uk/ComponentDefinition/MsCHI1/1">\n+ <dcterms:description>P28012</dcterms:description>\n+ <sbol:displayId>MsCHI1</sbol:displayId>\n+ <sbol:persistentIdentity rdf:resource="http://synbiochem.co.uk/ComponentDefinition/MsCHI1"/>\n+ <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>\n+ <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n+ <sbol:version>1</sbol:version>\n+ </sbol:ComponentDefinition>\n+ <sbol:ComponentDefinition rdf:about="http://synbiochem.co.uk/ComponentDefinition/Os4CL/1">\n+ <dcterms:description>Q6ETN3</dcterms:description>\n+ <sbol:displayId>Os4CL</sbol:displayId>\n+ <sbol:persistentIdentity rdf:resource="http://synbiochem.co.uk/ComponentDefinition/Os4CL"/>\n+ <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>\n+ <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n+ <sbol:version>1</sbol:version>\n+ </sbol:ComponentDefinition>\n+ <sbol:ComponentDefinition rdf:about="http://synbiochem.co.uk/ComponentDefinition/PcFNSI/1">\n+ <dcterms:description>Q7XZQ8</dcterms:description>\n+ <sbol:displayId>PcFNSI</sbol:displayId>\n+ <sbol:persistentIdentity rdf:resource="http://synbiochem.co.uk/ComponentDefinition/PcFNSI"/>\n+ <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>\n+ <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n+ <sbol:version>1</sbol:version>\n+ </sbol:ComponentDefinition>\n+ <sbol:ComponentDefinition rdf:about="http://synbiochem.co.uk/ComponentDefinition/PdCHSX/1">\n+ <dcterms:description>Q9MBF0</dcterms:description>\n+ <sbol:displayId>PdCHSX</sbol:displayId>\n+ <sbol:persistentIdentity rdf:resource="http://synbiochem.co.uk/ComponentDefinition/PdCHSX"/>\n+ <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>\n+ <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n+ <sbol:version>1</sbol:version>\n+ </sbol:ComponentDe'..b'urce="http://synbiochem.co.uk/ComponentDefinition/plasmid32/Ptrc_1/1"/>\n+ <sbol:persistentIdentity rdf:resource="http://synbiochem.co.uk/ComponentDefinition/plasmid32/constraint5"/>\n+ <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>\n+ <sbol:subject rdf:resource="http://synbiochem.co.uk/ComponentDefinition/plasmid32/Ter_0/1"/>\n+ <sbol:version>1</sbol:version>\n+ </sbol:SequenceConstraint>\n+ </sbol:sequenceConstraint>\n+ <sbol:sequenceConstraint>\n+ <sbol:SequenceConstraint rdf:about="http://synbiochem.co.uk/ComponentDefinition/plasmid32/constraint6/1">\n+ <sbol:displayId>constraint6</sbol:displayId>\n+ <sbol:object rdf:resource="http://synbiochem.co.uk/ComponentDefinition/plasmid32/Os4CL_0/1"/>\n+ <sbol:persistentIdentity rdf:resource="http://synbiochem.co.uk/ComponentDefinition/plasmid32/constraint6"/>\n+ <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>\n+ <sbol:subject rdf:resource="http://synbiochem.co.uk/ComponentDefinition/plasmid32/Ptrc_1/1"/>\n+ <sbol:version>1</sbol:version>\n+ </sbol:SequenceConstraint>\n+ </sbol:sequenceConstraint>\n+ <sbol:sequenceConstraint>\n+ <sbol:SequenceConstraint rdf:about="http://synbiochem.co.uk/ComponentDefinition/plasmid32/constraint7/1">\n+ <sbol:displayId>constraint7</sbol:displayId>\n+ <sbol:object rdf:resource="http://synbiochem.co.uk/ComponentDefinition/plasmid32/Ter_1/1"/>\n+ <sbol:persistentIdentity rdf:resource="http://synbiochem.co.uk/ComponentDefinition/plasmid32/constraint7"/>\n+ <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>\n+ <sbol:subject rdf:resource="http://synbiochem.co.uk/ComponentDefinition/plasmid32/Os4CL_0/1"/>\n+ <sbol:version>1</sbol:version>\n+ </sbol:SequenceConstraint>\n+ </sbol:sequenceConstraint>\n+ <sbol:sequenceConstraint>\n+ <sbol:SequenceConstraint rdf:about="http://synbiochem.co.uk/ComponentDefinition/plasmid32/constraint8/1">\n+ <sbol:displayId>constraint8</sbol:displayId>\n+ <sbol:object rdf:resource="http://synbiochem.co.uk/ComponentDefinition/plasmid32/PlacUV5_0/1"/>\n+ <sbol:persistentIdentity rdf:resource="http://synbiochem.co.uk/ComponentDefinition/plasmid32/constraint8"/>\n+ <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>\n+ <sbol:subject rdf:resource="http://synbiochem.co.uk/ComponentDefinition/plasmid32/Ter_1/1"/>\n+ <sbol:version>1</sbol:version>\n+ </sbol:SequenceConstraint>\n+ </sbol:sequenceConstraint>\n+ <sbol:sequenceConstraint>\n+ <sbol:SequenceConstraint rdf:about="http://synbiochem.co.uk/ComponentDefinition/plasmid32/constraint9/1">\n+ <sbol:displayId>constraint9</sbol:displayId>\n+ <sbol:object rdf:resource="http://synbiochem.co.uk/ComponentDefinition/plasmid32/PdCHSX_0/1"/>\n+ <sbol:persistentIdentity rdf:resource="http://synbiochem.co.uk/ComponentDefinition/plasmid32/constraint9"/>\n+ <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>\n+ <sbol:subject rdf:resource="http://synbiochem.co.uk/ComponentDefinition/plasmid32/PlacUV5_0/1"/>\n+ <sbol:version>1</sbol:version>\n+ </sbol:SequenceConstraint>\n+ </sbol:sequenceConstraint>\n+ <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n+ <sbol:version>1</sbol:version>\n+ </sbol:ComponentDefinition>\n+ <sbol:ComponentDefinition rdf:about="http://synbiochem.co.uk/ComponentDefinition/res1/1">\n+ <dcterms:description>https://synbiohub.org/public/igem/BBa_I13800/1</dcterms:description>\n+ <sbol:displayId>res1</sbol:displayId>\n+ <sbol:persistentIdentity rdf:resource="http://synbiochem.co.uk/ComponentDefinition/res1"/>\n+ <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>\n+ <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n+ <sbol:version>1</sbol:version>\n+ </sbol:ComponentDefinition>\n+</rdf:RDF>\n' |
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| diff -r d854b21ada0c -r 0ad6fda90f41 test/diag.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test/diag.csv Thu Aug 29 06:59:58 2019 -0400 |
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| @@ -0,0 +1,2 @@ +Size,Efficiency +32,98.03845888071827 |
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| diff -r d854b21ada0c -r 0ad6fda90f41 test/out.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test/out.csv Thu Aug 29 06:59:58 2019 -0400 |
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| @@ -0,0 +1,33 @@ +origin1,promoter3,promoter5,promoter7,promoter9,gene10,promoter11 +0,1,0,1,1,1,1 +1,0,1,3,1,1,0 +2,1,2,1,3,0,3 +2,1,3,0,1,1,3 +1,1,1,2,3,0,1 +2,1,2,3,2,1,1 +2,0,0,1,3,0,2 +2,0,1,3,0,0,3 +1,1,2,3,1,0,2 +1,0,2,2,3,1,1 +1,0,2,0,0,0,0 +0,0,0,3,3,1,0 +2,0,3,1,2,0,0 +0,1,2,0,3,1,2 +0,0,1,1,1,0,1 +0,0,3,2,1,0,2 +2,1,0,2,0,1,0 +1,1,1,1,0,1,2 +2,0,1,0,2,1,2 +0,0,2,2,2,0,3 +1,1,0,2,0,0,2 +1,0,0,0,2,0,1 +2,1,2,2,1,0,0 +1,0,0,0,1,1,3 +0,0,2,1,0,1,3 +0,1,1,2,2,1,3 +0,1,0,3,2,0,2 +2,0,3,3,0,1,1 +1,1,3,3,3,0,3 +0,1,3,0,0,0,1 +1,1,3,1,2,1,0 +0,1,1,0,3,0,0 |
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| diff -r d854b21ada0c -r 0ad6fda90f41 toolOptBioDes.py --- a/toolOptBioDes.py Wed Aug 07 05:13:27 2019 -0400 +++ b/toolOptBioDes.py Thu Aug 29 06:59:58 2019 -0400 |
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| @@ -55,7 +55,7 @@ cw.writerow( [res['data']['libsize'], res['data']['J']] ) print( 'Size:', res['data']['libsize'], 'Efficiency:', res['data']['J'] ) -def partsUploadSbol( partsfile, genesfile, size, outfile, diagfile, sbolOut, server ): +def partsUploadSbol( partsfile, genesfile, size, outfile, diagfile, sbolOut, url ): files = { 'parts': open(partsfile, 'rb' ), 'genes': open(genesfile, 'rb') @@ -80,8 +80,8 @@ if __name__ == "__main__": parser = arguments() arg = parser.parse_args() - assert os.path.exists(arg.infile) if arg.sbolOut is None: sheetUpload( arg.infile, arg.size, arg.outfile, arg.diagfile, arg.server ) else: - partsUploadSbol( arg.partsfile, arg.genesfile, arg.size, arg.outfile, arg.diagfile, arg.sbolOut, arg.server ) + partsUploadSbol( arg.partsfile, arg.genesfile, arg.size, + arg.outfile, arg.diagfile, arg.sbolOut, arg.server ) |