Mercurial > repos > tduigou > sbol_converter
changeset 0:38a0feb2e79d draft
planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
| author | tduigou |
|---|---|
| date | Thu, 15 Sep 2022 13:40:15 +0000 |
| parents | |
| children | 529ee7dc1be9 |
| files | sbol_converter.xml test-data/BASIC_construct_A1_sbol2_input.xml test-data/BASIC_construct_A1_sbol3_output.nt test-data/BBa_J23101.gb test-data/BBa_J23101.nt |
| diffstat | 5 files changed, 762 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sbol_converter.xml Thu Sep 15 13:40:15 2022 +0000 @@ -0,0 +1,144 @@ +<tool id="sbol_converter" name="SBOL Converter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"> + <description>Convert between SBOL3 and other genetic design formats</description> + <macros> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@TOOL_VERSION@">1.0a16</token> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">sbol-utilities</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + #if str($convert_type.type) == "SBOL2 to SBOL3" + ln -sv '$sbol2_input' 'input.$sbol2_input.ext' && + sbol2to3 -o '$output' 'input.$sbol2_input.ext' + #elif str($convert_type.type) == "SBOL3 to SBOL2" + ln -sv '$sbol3_input' 'input.$sbol3_input.ext' && + sbol3to2 -o '$output' 'input.$sbol3_input.ext' + #elif str($convert_type.type) == "SBOL3 to GENBANK" + ln -sv '$sbol3_input' 'input.$sbol3_input.ext' && + sbol2genbank -o '$output' 'input.$sbol3_input.ext' + #elif str($convert_type.type) == "GENBANK to SBOL3" + ln -sv '$genbank_input' 'input.$genbank_input.ext' && + genbank2sbol -o '$output' 'input.$genbank_input.ext' --namespace '$convert_type.namespace' + #elif str($convert_type.type) == "SBOL3 to FASTA" + ln -sv '$sbol3_input' 'input.$sbol3_input.ext' && + sbol2fasta -o '$output' 'input.$sbol3_input.ext' + #elif str($convert_type.type) == "FASTA to SBOL3" + ln -sv '$fasta_input' 'input.$fasta_input.ext' && + fasta2sbol -o '$output' 'input.$fasta_input.ext' --namespace '$convert_type.namespace' + #elif str($convert_type.type) == "SBOL2 to FASTA" + ln -sv '$sbol2_input' 'input.$sbol2_input.ext' && + sbol-converter SBOL2 FASTA -o '$output' 'input.$sbol2_input.ext' + #elif str($convert_type.type) == "FASTA to SBOL2" + ln -sv '$fasta_input' 'input.$fasta_input.ext' && + sbol-converter FASTA SBOL2 -o '$output' 'input.$fasta_input.ext' --namespace '$convert_type.namespace' + #end if + ]]></command> + <inputs> + <conditional name="convert_type"> + <param name="type" type="select" label="Converting type" help="Choose the format (input/ouput) for SBOL conversion"> + <option value="SBOL2 to SBOL3" selected="True">From SBOL2 to SBOL3</option> + <option value="SBOL2 to FASTA" >From SBOL2 to FASTA</option> + <option value="SBOL3 to SBOL2" >From SBOL3 to SBOL2</option> + <option value="SBOL3 to FASTA" >From SBOL3 to FASTA</option> + <option value="SBOL3 to GENBANK" >From SBOL3 to GENBANK</option> + <option value="GENBANK to SBOL3" >From GENBANK to SBOL3</option> + <option value="FASTA to SBOL3" >From FASTA to SBOL3</option> + <option value="FASTA to SBOL2" >From FASTA to SBOL2</option> + </param> + <when value="SBOL2 to SBOL3"> + <param name="sbol2_input" type="data" format="xml,rdf,nt" label="SBOL2 input" help="SBOL2 file in XML or RDF or NT format"/> + </when> + <when value="SBOL3 to SBOL2"> + <param name="sbol3_input" type="data" format="xml,rdf,nt" label="SBOL3 input" help="SBOL3 file in XML or RDF or NT format"/> + </when> + <when value="SBOL3 to GENBANK"> + <param name="sbol3_input" type="data" format="xml,rdf,nt" label="SBOL3 input" help="SBOL3 file in XML or RDF or NT format"/> + </when> + <when value="GENBANK to SBOL3"> + <param name="genbank_input" type="data" format="gb" label="Genbank input" help="Genbank file in GB format"/> + <param argument="--namespace" type="text" value="https://synbiohub.org/public/igem" label="Namespace URL" help="Namespace URL, required for conversions from GenBank. Default=https://synbiohub.org/public/igem" /> + </when> + <when value="SBOL3 to FASTA"> + <param name="sbol3_input" type="data" format="xml,rdf,nt" label="SBOL3 input" help="SBOL3 file in XML or RDF or NT format"/> + </when> + <when value="FASTA to SBOL3"> + <param name="fasta_input" type="data" format="fasta" label="FASTA input" help="FASTA input file"/> + <param argument="--namespace" type="text" value="https://synbiohub.org/public/igem" label="Namespace URL" help="Namespace URL, required for conversions from FASTA. Default=https://synbiohub.org/public/igem" /> + </when> + <when value="SBOL2 to FASTA"> + <param name="sbol2_input" type="data" format="xml,rdf,nt" label="SBOL2 input" help="SBOL2 file in XML or RDF or NT format" /> + </when> + <when value="FASTA to SBOL2"> + <param name="fasta_input" type="data" format="fasta" label="FASTA input" help="FASTA input file"/> + <param argument="--namespace" type="text" value="https://synbiohub.org/public/igem" label="Namespace URL" help="Namespace URL, required for conversions from FASTA. Default=https://synbiohub.org/public/igem" /> + </when> + </conditional> + </inputs> + <outputs> + <data name="output" format="nt" label="${tool.name} on ${on_string}: ${convert_type.type}" > + <change_format> + <when input="convert_type.type" value="SBOL3 to GENBANK" format="gb" /> + <when input="convert_type.type" value="SBOL3 to FASTA" format="fasta" /> + <when input="convert_type.type" value="SBOL2 to FASTA" format="fasta" /> + </change_format> + </data> + </outputs> + <tests> + <test> + <!-- test 1: check if identical outputs are produced sbol2 to sbol3--> + <conditional name="convert_type"> + <param name="type" value="SBOL2 to SBOL3"/> + </conditional> + <param name="sbol2_input" value="BASIC_construct_A1_sbol2_input.xml" /> + <output name="output" file="BASIC_construct_A1_sbol3_output.nt" ftype="nt" compare="diff"/> + </test> + + <test> + <!-- test 2: check if identical outputs are produced sbol3 to genbank--> + <conditional name="convert_type"> + <param name="type" value="SBOL3 to GENBANK"/> + </conditional> + <param name="sbol3_input" value="BBa_J23101.nt" /> + <output name="output" file="BBa_J23101.gb" ftype="gb" compare="diff"/> + </test> + + <test> + <!-- test 2: check if identical outputs are produced sbol3 to fasta--> + <conditional name="convert_type"> + <param name="type" value="SBOL3 to FASTA"/> + </conditional> + <param name="sbol3_input" value="BBa_J23101.nt" /> + <output name="output" > + <assert_contents> + <has_text text=">BBa_J23101 constitutive promoter family member" /> + <has_text text="tttacagctagctcagtcctaggtattatgctagc" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +SBOL Converter +================ + +Convert between SBOL3 and other genetic design formats. + +Input +----- +Required: +* **INPUT_FILE**\ : SBOL2 or SBOL3 or GENBANK or FASTA input file. +* **Namespace URL**\ : Namespace URL, required for conversions from GenBank or from Fasta. Default=https://synbiohub.org/public/igem" + +Output +------ +* **OUTPUT_FILE**\ : SBOL2 or SBOL3 or GENBANK or FASTA output file. + +Project Links +------------------ +* `GitHub <https://github.com/SynBioDex/SBOL-utilities>`_ + +License +------- +* `MIT <https://github.com/SynBioDex/SBOL-utilities/blob/develop/LICENSE.txt>`_ + ]]></help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/BASIC_construct_A1_sbol2_input.xml Thu Sep 15 13:40:15 2022 +0000 @@ -0,0 +1,339 @@ +<rdf:RDF xmlns:brick="https://brickschema.org/schema/Brick#" xmlns:csvw="http://www.w3.org/ns/csvw#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcat="http://www.w3.org/ns/dcat#" xmlns:dcmitype="http://purl.org/dc/dcmitype/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:dcam="http://purl.org/dc/dcam/" xmlns:doap="http://usefulinc.com/ns/doap#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:odrl="http://www.w3.org/ns/odrl/2/" xmlns:org="http://www.w3.org/ns/org#" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:prof="http://www.w3.org/ns/dx/prof/" xmlns:prov="http://www.w3.org/ns/prov#" xmlns:qb="http://purl.org/linked-data/cube#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:schema="https://schema.org/" xmlns:sh="http://www.w3.org/ns/shacl#" xmlns:skos="http://www.w3.org/2004/02/skos/core#" xmlns:sosa="http://www.w3.org/ns/sosa/" xmlns:ssn="http://www.w3.org/ns/ssn/" xmlns:time="http://www.w3.org/2006/time#" xmlns:vann="http://purl.org/vocab/vann/" xmlns:void="http://rdfs.org/ns/void#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:sbol="http://sbols.org/v2#"> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/LMS/1"> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:displayId>LMS</sbol:displayId> + <sbol:version>1</sbol:version> + <sbol:sequence rdf:resource="https://localhost/Sequence/LMS/1"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/LMS"/> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000001"/> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1/1"> + <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1</sbol:displayId> + <sbol:version>1</sbol:version> + <sbol:sequence rdf:resource="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1/1"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1"/> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000988"/> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/LMP/1"> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/LMP"/> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000001"/> + <sbol:version>1</sbol:version> + <sbol:displayId>LMP</sbol:displayId> + <sbol:sequence rdf:resource="https://localhost/Sequence/LMP/1"/> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/PJ23119_BASIC/1"> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/PJ23119_BASIC"/> + <sbol:sequence rdf:resource="https://localhost/Sequence/PJ23119_BASIC/1"/> + <sbol:version>1</sbol:version> + <sbol:displayId>PJ23119_BASIC</sbol:displayId> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U1_RBS1/1"> + <sbol:displayId>U1_RBS1</sbol:displayId> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/> + <sbol:version>1</sbol:version> + <sbol:sequence rdf:resource="https://localhost/Sequence/U1_RBS1/1"/> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U1_RBS1"/> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P21684/1"> + <sbol:version>1</sbol:version> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P21684"/> + <sbol:displayId>P21684</sbol:displayId> + <sbol:sequence rdf:resource="https://localhost/Sequence/P21684/1"/> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U2_RBS1/1"> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U2_RBS1"/> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:displayId>U2_RBS1</sbol:displayId> + <sbol:sequence rdf:resource="https://localhost/Sequence/U2_RBS1/1"/> + <sbol:version>1</sbol:version> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P21683/1"> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/> + <sbol:version>1</sbol:version> + <sbol:sequence rdf:resource="https://localhost/Sequence/P21683/1"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P21683"/> + <sbol:displayId>P21683</sbol:displayId> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U3_RBS2/1"> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/> + <sbol:displayId>U3_RBS2</sbol:displayId> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U3_RBS2"/> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:version>1</sbol:version> + <sbol:sequence rdf:resource="https://localhost/Sequence/U3_RBS2/1"/> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P21685/1"> + <sbol:sequence rdf:resource="https://localhost/Sequence/P21685/1"/> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P21685"/> + <sbol:version>1</sbol:version> + <sbol:displayId>P21685</sbol:displayId> + </sbol:ComponentDefinition> + <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/1"> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1"/> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_2/1"> + <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/LMP_0/1"/> + <sbol:version>1</sbol:version> + <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/PJ23119_BASIC_0/1"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_2"/> + <sbol:displayId>constraint_2</sbol:displayId> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/P21685_0/1"> + <sbol:displayId>P21685_0</sbol:displayId> + <sbol:version>1</sbol:version> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/P21685_0"/> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/P21685/1"/> + </sbol:Component> + </sbol:component> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/BASIC_SEVA_37_CmR_p15A_1_0/1"> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/BASIC_SEVA_37_CmR_p15A_1_0"/> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1/1"/> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:version>1</sbol:version> + <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1_0</sbol:displayId> + </sbol:Component> + </sbol:component> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/LMS_0/1"> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:displayId>LMS_0</sbol:displayId> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/LMS/1"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/LMS_0"/> + <sbol:version>1</sbol:version> + </sbol:Component> + </sbol:component> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/U1_RBS1_0/1"> + <sbol:displayId>U1_RBS1_0</sbol:displayId> + <sbol:version>1</sbol:version> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U1_RBS1_0"/> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U1_RBS1/1"/> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + </sbol:Component> + </sbol:component> + <sbol:version>1</sbol:version> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/P21684_0/1"> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/P21684_0"/> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/P21684/1"/> + <sbol:displayId>P21684_0</sbol:displayId> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:version>1</sbol:version> + </sbol:Component> + </sbol:component> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_7/1"> + <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/P21683_0/1"/> + <sbol:version>1</sbol:version> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_7"/> + <sbol:displayId>constraint_7</sbol:displayId> + <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U3_RBS2_0/1"/> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:type rdf:resource="http://identifiers.org/so/SO:0000987"/> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_0/1"> + <sbol:displayId>constraint_0</sbol:displayId> + <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/LMS_0/1"/> + <sbol:version>1</sbol:version> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_0"/> + <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/BASIC_SEVA_37_CmR_p15A_1_0/1"/> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/U2_RBS1_0/1"> + <sbol:version>1</sbol:version> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U2_RBS1/1"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U2_RBS1_0"/> + <sbol:displayId>U2_RBS1_0</sbol:displayId> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + </sbol:Component> + </sbol:component> + <sbol:displayId>BASIC_construct_A1</sbol:displayId> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/PJ23119_BASIC_0/1"> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/PJ23119_BASIC/1"/> + <sbol:version>1</sbol:version> + <sbol:displayId>PJ23119_BASIC_0</sbol:displayId> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/PJ23119_BASIC_0"/> + </sbol:Component> + </sbol:component> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_1/1"> + <sbol:displayId>constraint_1</sbol:displayId> + <sbol:version>1</sbol:version> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_1"/> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/LMP_0/1"/> + <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/BASIC_SEVA_37_CmR_p15A_1_0/1"/> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_8/1"> + <sbol:displayId>constraint_8</sbol:displayId> + <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U3_RBS2_0/1"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_8"/> + <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/P21685_0/1"/> + <sbol:version>1</sbol:version> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/LMP_0/1"> + <sbol:version>1</sbol:version> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/LMP_0"/> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/LMP/1"/> + <sbol:displayId>LMP_0</sbol:displayId> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + </sbol:Component> + </sbol:component> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/U3_RBS2_0/1"> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/U3_RBS2/1"/> + <sbol:version>1</sbol:version> + <sbol:displayId>U3_RBS2_0</sbol:displayId> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U3_RBS2_0"/> + </sbol:Component> + </sbol:component> + <sbol:component> + <sbol:Component rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/P21683_0/1"> + <sbol:access rdf:resource="http://sbols.org/v2#public"/> + <sbol:definition rdf:resource="https://localhost/ComponentDefinition/P21683/1"/> + <sbol:version>1</sbol:version> + <sbol:displayId>P21683_0</sbol:displayId> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/P21683_0"/> + </sbol:Component> + </sbol:component> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_5/1"> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_5"/> + <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/P21684_0/1"/> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U2_RBS1_0/1"/> + <sbol:displayId>constraint_5</sbol:displayId> + <sbol:version>1</sbol:version> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_3/1"> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/PJ23119_BASIC_0/1"/> + <sbol:displayId>constraint_3</sbol:displayId> + <sbol:version>1</sbol:version> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_3"/> + <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U1_RBS1_0/1"/> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_4/1"> + <sbol:version>1</sbol:version> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U1_RBS1_0/1"/> + <sbol:displayId>constraint_4</sbol:displayId> + <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/P21684_0/1"/> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_4"/> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/> + <sbol:sequenceConstraint> + <sbol:SequenceConstraint rdf:about="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_6/1"> + <sbol:subject rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/U2_RBS1_0/1"/> + <sbol:version>1</sbol:version> + <sbol:object rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/P21683_0/1"/> + <sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/> + <sbol:displayId>constraint_6</sbol:displayId> + <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_A1/constraint_6"/> + </sbol:SequenceConstraint> + </sbol:sequenceConstraint> + </sbol:ComponentDefinition> + <sbol:Sequence rdf:about="https://localhost/Sequence/LMS/1"> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/LMS"/> + <sbol:displayId>LMS</sbol:displayId> + <sbol:version>1</sbol:version> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + <sbol:elements></sbol:elements> + </sbol:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1/1"> + <sbol:elements></sbol:elements> + <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1</sbol:displayId> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1"/> + <sbol:version>1</sbol:version> + </sbol:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/LMP/1"> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/LMP"/> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + <sbol:version>1</sbol:version> + <sbol:displayId>LMP</sbol:displayId> + <sbol:elements></sbol:elements> + </sbol:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/PJ23119_BASIC/1"> + <sbol:version>1</sbol:version> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + <sbol:displayId>PJ23119_BASIC</sbol:displayId> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/PJ23119_BASIC"/> + <sbol:elements></sbol:elements> + </sbol:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/U1_RBS1/1"> + <sbol:displayId>U1_RBS1</sbol:displayId> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U1_RBS1"/> + <sbol:version>1</sbol:version> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + <sbol:elements></sbol:elements> + </sbol:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/P21684/1"> + <sbol:displayId>P21684</sbol:displayId> + <sbol:elements>atgc</sbol:elements> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21684"/> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + <sbol:version>1</sbol:version> + </sbol:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/U2_RBS1/1"> + <sbol:elements></sbol:elements> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U2_RBS1"/> + <sbol:version>1</sbol:version> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + <sbol:displayId>U2_RBS1</sbol:displayId> + </sbol:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/P21683/1"> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + <sbol:displayId>P21683</sbol:displayId> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21683"/> + <sbol:elements>atgc</sbol:elements> + <sbol:version>1</sbol:version> + </sbol:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/U3_RBS2/1"> + <sbol:elements></sbol:elements> + <sbol:displayId>U3_RBS2</sbol:displayId> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + <sbol:version>1</sbol:version> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U3_RBS2"/> + </sbol:Sequence> + <sbol:Sequence rdf:about="https://localhost/Sequence/P21685/1"> + <sbol:displayId>P21685</sbol:displayId> + <sbol:elements>atgc</sbol:elements> + <sbol:version>1</sbol:version> + <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21685"/> + <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/> + </sbol:Sequence> +</rdf:RDF>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/BASIC_construct_A1_sbol3_output.nt Thu Sep 15 13:40:15 2022 +0000 @@ -0,0 +1,207 @@ +<https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1> <http://sbols.org/v3#displayId> "BASIC_SEVA_37_CmR_p15A_1" . +<https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1> <http://sbols.org/v3#hasNamespace> <https://localhost> . +<https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1> <http://sbols.org/v3#hasSequence> <https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1> . +<https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1> <http://sbols.org/v3#role> <http://identifiers.org/so/SO:0000988> . +<https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1> <http://sbols.org/v3#type> <https://identifiers.org/SBO:0000251> . +<https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1> <http://sboltools.org/backport#sbol2type> <http://sbols.org/v2#ComponentDefinition> . +<https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1> <http://sboltools.org/backport#sbol2version> "1" . +<https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Component> . +<https://localhost/ComponentDefinition/BASIC_construct_A1/BASIC_SEVA_37_CmR_p15A_1_0> <http://sbols.org/v3#displayId> "BASIC_SEVA_37_CmR_p15A_1_0" . +<https://localhost/ComponentDefinition/BASIC_construct_A1/BASIC_SEVA_37_CmR_p15A_1_0> <http://sbols.org/v3#instanceOf> <https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1> . +<https://localhost/ComponentDefinition/BASIC_construct_A1/BASIC_SEVA_37_CmR_p15A_1_0> <http://sboltools.org/backport#sbol2type> <http://sbols.org/v2#Component> . +<https://localhost/ComponentDefinition/BASIC_construct_A1/BASIC_SEVA_37_CmR_p15A_1_0> <http://sboltools.org/backport#sbol2version> "1" . +<https://localhost/ComponentDefinition/BASIC_construct_A1/BASIC_SEVA_37_CmR_p15A_1_0> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#SubComponent> . +<https://localhost/ComponentDefinition/BASIC_construct_A1/LMP_0> <http://sbols.org/v3#displayId> "LMP_0" . +<https://localhost/ComponentDefinition/BASIC_construct_A1/LMP_0> <http://sbols.org/v3#instanceOf> <https://localhost/ComponentDefinition/LMP> . +<https://localhost/ComponentDefinition/BASIC_construct_A1/LMP_0> <http://sboltools.org/backport#sbol2type> <http://sbols.org/v2#Component> . +<https://localhost/ComponentDefinition/BASIC_construct_A1/LMP_0> <http://sboltools.org/backport#sbol2version> "1" . +<https://localhost/ComponentDefinition/BASIC_construct_A1/LMP_0> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#SubComponent> . +<https://localhost/ComponentDefinition/BASIC_construct_A1/LMS_0> <http://sbols.org/v3#displayId> "LMS_0" . +<https://localhost/ComponentDefinition/BASIC_construct_A1/LMS_0> <http://sbols.org/v3#instanceOf> <https://localhost/ComponentDefinition/LMS> . +<https://localhost/ComponentDefinition/BASIC_construct_A1/LMS_0> <http://sboltools.org/backport#sbol2type> <http://sbols.org/v2#Component> . +<https://localhost/ComponentDefinition/BASIC_construct_A1/LMS_0> <http://sboltools.org/backport#sbol2version> "1" . +<https://localhost/ComponentDefinition/BASIC_construct_A1/LMS_0> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#SubComponent> . +<https://localhost/ComponentDefinition/BASIC_construct_A1/P21683_0> <http://sbols.org/v3#displayId> "P21683_0" . +<https://localhost/ComponentDefinition/BASIC_construct_A1/P21683_0> <http://sbols.org/v3#instanceOf> <https://localhost/ComponentDefinition/P21683> . +<https://localhost/ComponentDefinition/BASIC_construct_A1/P21683_0> <http://sboltools.org/backport#sbol2type> <http://sbols.org/v2#Component> . +<https://localhost/ComponentDefinition/BASIC_construct_A1/P21683_0> <http://sboltools.org/backport#sbol2version> "1" . +<https://localhost/ComponentDefinition/BASIC_construct_A1/P21683_0> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#SubComponent> . +<https://localhost/ComponentDefinition/BASIC_construct_A1/P21684_0> <http://sbols.org/v3#displayId> "P21684_0" . +<https://localhost/ComponentDefinition/BASIC_construct_A1/P21684_0> <http://sbols.org/v3#instanceOf> <https://localhost/ComponentDefinition/P21684> . +<https://localhost/ComponentDefinition/BASIC_construct_A1/P21684_0> <http://sboltools.org/backport#sbol2type> <http://sbols.org/v2#Component> . +<https://localhost/ComponentDefinition/BASIC_construct_A1/P21684_0> <http://sboltools.org/backport#sbol2version> "1" . +<https://localhost/ComponentDefinition/BASIC_construct_A1/P21684_0> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#SubComponent> . +<https://localhost/ComponentDefinition/BASIC_construct_A1/P21685_0> <http://sbols.org/v3#displayId> "P21685_0" . +<https://localhost/ComponentDefinition/BASIC_construct_A1/P21685_0> <http://sbols.org/v3#instanceOf> <https://localhost/ComponentDefinition/P21685> . +<https://localhost/ComponentDefinition/BASIC_construct_A1/P21685_0> <http://sboltools.org/backport#sbol2type> <http://sbols.org/v2#Component> . +<https://localhost/ComponentDefinition/BASIC_construct_A1/P21685_0> <http://sboltools.org/backport#sbol2version> "1" . +<https://localhost/ComponentDefinition/BASIC_construct_A1/P21685_0> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#SubComponent> . +<https://localhost/ComponentDefinition/BASIC_construct_A1/PJ23119_BASIC_0> <http://sbols.org/v3#displayId> "PJ23119_BASIC_0" . +<https://localhost/ComponentDefinition/BASIC_construct_A1/PJ23119_BASIC_0> <http://sbols.org/v3#instanceOf> <https://localhost/ComponentDefinition/PJ23119_BASIC> . +<https://localhost/ComponentDefinition/BASIC_construct_A1/PJ23119_BASIC_0> <http://sboltools.org/backport#sbol2type> <http://sbols.org/v2#Component> . +<https://localhost/ComponentDefinition/BASIC_construct_A1/PJ23119_BASIC_0> <http://sboltools.org/backport#sbol2version> "1" . +<https://localhost/ComponentDefinition/BASIC_construct_A1/PJ23119_BASIC_0> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#SubComponent> . +<https://localhost/ComponentDefinition/BASIC_construct_A1/U1_RBS1_0> <http://sbols.org/v3#displayId> "U1_RBS1_0" . +<https://localhost/ComponentDefinition/BASIC_construct_A1/U1_RBS1_0> <http://sbols.org/v3#instanceOf> <https://localhost/ComponentDefinition/U1_RBS1> . +<https://localhost/ComponentDefinition/BASIC_construct_A1/U1_RBS1_0> <http://sboltools.org/backport#sbol2type> <http://sbols.org/v2#Component> . +<https://localhost/ComponentDefinition/BASIC_construct_A1/U1_RBS1_0> <http://sboltools.org/backport#sbol2version> "1" . +<https://localhost/ComponentDefinition/BASIC_construct_A1/U1_RBS1_0> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#SubComponent> . +<https://localhost/ComponentDefinition/BASIC_construct_A1/U2_RBS1_0> <http://sbols.org/v3#displayId> "U2_RBS1_0" . +<https://localhost/ComponentDefinition/BASIC_construct_A1/U2_RBS1_0> <http://sbols.org/v3#instanceOf> <https://localhost/ComponentDefinition/U2_RBS1> . +<https://localhost/ComponentDefinition/BASIC_construct_A1/U2_RBS1_0> <http://sboltools.org/backport#sbol2type> <http://sbols.org/v2#Component> . +<https://localhost/ComponentDefinition/BASIC_construct_A1/U2_RBS1_0> <http://sboltools.org/backport#sbol2version> "1" . +<https://localhost/ComponentDefinition/BASIC_construct_A1/U2_RBS1_0> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#SubComponent> . +<https://localhost/ComponentDefinition/BASIC_construct_A1/U3_RBS2_0> <http://sbols.org/v3#displayId> "U3_RBS2_0" . +<https://localhost/ComponentDefinition/BASIC_construct_A1/U3_RBS2_0> <http://sbols.org/v3#instanceOf> <https://localhost/ComponentDefinition/U3_RBS2> . +<https://localhost/ComponentDefinition/BASIC_construct_A1/U3_RBS2_0> <http://sboltools.org/backport#sbol2type> <http://sbols.org/v2#Component> . +<https://localhost/ComponentDefinition/BASIC_construct_A1/U3_RBS2_0> <http://sboltools.org/backport#sbol2version> "1" . +<https://localhost/ComponentDefinition/BASIC_construct_A1/U3_RBS2_0> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#SubComponent> . +<https://localhost/ComponentDefinition/BASIC_construct_A1> <http://sbols.org/v3#displayId> "BASIC_construct_A1" . +<https://localhost/ComponentDefinition/BASIC_construct_A1> <http://sbols.org/v3#hasFeature> <https://localhost/ComponentDefinition/BASIC_construct_A1/BASIC_SEVA_37_CmR_p15A_1_0> . +<https://localhost/ComponentDefinition/BASIC_construct_A1> <http://sbols.org/v3#hasFeature> <https://localhost/ComponentDefinition/BASIC_construct_A1/LMP_0> . +<https://localhost/ComponentDefinition/BASIC_construct_A1> <http://sbols.org/v3#hasFeature> <https://localhost/ComponentDefinition/BASIC_construct_A1/LMS_0> . +<https://localhost/ComponentDefinition/BASIC_construct_A1> <http://sbols.org/v3#hasFeature> <https://localhost/ComponentDefinition/BASIC_construct_A1/P21683_0> . +<https://localhost/ComponentDefinition/BASIC_construct_A1> <http://sbols.org/v3#hasFeature> <https://localhost/ComponentDefinition/BASIC_construct_A1/P21684_0> . +<https://localhost/ComponentDefinition/BASIC_construct_A1> <http://sbols.org/v3#hasFeature> <https://localhost/ComponentDefinition/BASIC_construct_A1/P21685_0> . +<https://localhost/ComponentDefinition/BASIC_construct_A1> <http://sbols.org/v3#hasFeature> <https://localhost/ComponentDefinition/BASIC_construct_A1/PJ23119_BASIC_0> . +<https://localhost/ComponentDefinition/BASIC_construct_A1> <http://sbols.org/v3#hasFeature> <https://localhost/ComponentDefinition/BASIC_construct_A1/U1_RBS1_0> . +<https://localhost/ComponentDefinition/BASIC_construct_A1> <http://sbols.org/v3#hasFeature> <https://localhost/ComponentDefinition/BASIC_construct_A1/U2_RBS1_0> . +<https://localhost/ComponentDefinition/BASIC_construct_A1> <http://sbols.org/v3#hasFeature> <https://localhost/ComponentDefinition/BASIC_construct_A1/U3_RBS2_0> . +<https://localhost/ComponentDefinition/BASIC_construct_A1> <http://sbols.org/v3#hasNamespace> <https://localhost> . +<https://localhost/ComponentDefinition/BASIC_construct_A1> <http://sbols.org/v3#type> <http://identifiers.org/so/SO:0000987> . +<https://localhost/ComponentDefinition/BASIC_construct_A1> <http://sbols.org/v3#type> <https://identifiers.org/SBO:0000251> . +<https://localhost/ComponentDefinition/BASIC_construct_A1> <http://sboltools.org/backport#sbol2type> <http://sbols.org/v2#ComponentDefinition> . +<https://localhost/ComponentDefinition/BASIC_construct_A1> <http://sboltools.org/backport#sbol2version> "1" . +<https://localhost/ComponentDefinition/BASIC_construct_A1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Component> . +<https://localhost/ComponentDefinition/LMP> <http://sbols.org/v3#displayId> "LMP" . +<https://localhost/ComponentDefinition/LMP> <http://sbols.org/v3#hasNamespace> <https://localhost> . +<https://localhost/ComponentDefinition/LMP> <http://sbols.org/v3#hasSequence> <https://localhost/Sequence/LMP> . +<https://localhost/ComponentDefinition/LMP> <http://sbols.org/v3#role> <http://identifiers.org/so/SO:0000001> . +<https://localhost/ComponentDefinition/LMP> <http://sbols.org/v3#type> <https://identifiers.org/SBO:0000251> . +<https://localhost/ComponentDefinition/LMP> <http://sboltools.org/backport#sbol2type> <http://sbols.org/v2#ComponentDefinition> . +<https://localhost/ComponentDefinition/LMP> <http://sboltools.org/backport#sbol2version> "1" . +<https://localhost/ComponentDefinition/LMP> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Component> . +<https://localhost/ComponentDefinition/LMS> <http://sbols.org/v3#displayId> "LMS" . +<https://localhost/ComponentDefinition/LMS> <http://sbols.org/v3#hasNamespace> <https://localhost> . +<https://localhost/ComponentDefinition/LMS> <http://sbols.org/v3#hasSequence> <https://localhost/Sequence/LMS> . +<https://localhost/ComponentDefinition/LMS> <http://sbols.org/v3#role> <http://identifiers.org/so/SO:0000001> . +<https://localhost/ComponentDefinition/LMS> <http://sbols.org/v3#type> <https://identifiers.org/SBO:0000251> . +<https://localhost/ComponentDefinition/LMS> <http://sboltools.org/backport#sbol2type> <http://sbols.org/v2#ComponentDefinition> . +<https://localhost/ComponentDefinition/LMS> <http://sboltools.org/backport#sbol2version> "1" . +<https://localhost/ComponentDefinition/LMS> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Component> . +<https://localhost/ComponentDefinition/P21683> <http://sbols.org/v3#displayId> "P21683" . +<https://localhost/ComponentDefinition/P21683> <http://sbols.org/v3#hasNamespace> <https://localhost> . 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<https://localhost/Sequence/P21684> . +<https://localhost/ComponentDefinition/P21684> <http://sbols.org/v3#role> <http://identifiers.org/so/SO:0000316> . +<https://localhost/ComponentDefinition/P21684> <http://sbols.org/v3#type> <https://identifiers.org/SBO:0000251> . +<https://localhost/ComponentDefinition/P21684> <http://sboltools.org/backport#sbol2type> <http://sbols.org/v2#ComponentDefinition> . +<https://localhost/ComponentDefinition/P21684> <http://sboltools.org/backport#sbol2version> "1" . +<https://localhost/ComponentDefinition/P21684> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Component> . +<https://localhost/ComponentDefinition/P21685> <http://sbols.org/v3#displayId> "P21685" . +<https://localhost/ComponentDefinition/P21685> <http://sbols.org/v3#hasNamespace> <https://localhost> . +<https://localhost/ComponentDefinition/P21685> <http://sbols.org/v3#hasSequence> <https://localhost/Sequence/P21685> . +<https://localhost/ComponentDefinition/P21685> <http://sbols.org/v3#role> <http://identifiers.org/so/SO:0000316> . +<https://localhost/ComponentDefinition/P21685> <http://sbols.org/v3#type> <https://identifiers.org/SBO:0000251> . +<https://localhost/ComponentDefinition/P21685> <http://sboltools.org/backport#sbol2type> <http://sbols.org/v2#ComponentDefinition> . +<https://localhost/ComponentDefinition/P21685> <http://sboltools.org/backport#sbol2version> "1" . +<https://localhost/ComponentDefinition/P21685> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Component> . +<https://localhost/ComponentDefinition/PJ23119_BASIC> <http://sbols.org/v3#displayId> "PJ23119_BASIC" . +<https://localhost/ComponentDefinition/PJ23119_BASIC> <http://sbols.org/v3#hasNamespace> <https://localhost> . +<https://localhost/ComponentDefinition/PJ23119_BASIC> <http://sbols.org/v3#hasSequence> <https://localhost/Sequence/PJ23119_BASIC> . +<https://localhost/ComponentDefinition/PJ23119_BASIC> <http://sbols.org/v3#role> <http://identifiers.org/so/SO:0000167> . +<https://localhost/ComponentDefinition/PJ23119_BASIC> <http://sbols.org/v3#type> <https://identifiers.org/SBO:0000251> . +<https://localhost/ComponentDefinition/PJ23119_BASIC> <http://sboltools.org/backport#sbol2type> <http://sbols.org/v2#ComponentDefinition> . +<https://localhost/ComponentDefinition/PJ23119_BASIC> <http://sboltools.org/backport#sbol2version> "1" . +<https://localhost/ComponentDefinition/PJ23119_BASIC> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Component> . +<https://localhost/ComponentDefinition/U1_RBS1> <http://sbols.org/v3#displayId> "U1_RBS1" . +<https://localhost/ComponentDefinition/U1_RBS1> <http://sbols.org/v3#hasNamespace> <https://localhost> . +<https://localhost/ComponentDefinition/U1_RBS1> <http://sbols.org/v3#hasSequence> <https://localhost/Sequence/U1_RBS1> . +<https://localhost/ComponentDefinition/U1_RBS1> <http://sbols.org/v3#role> <http://identifiers.org/so/SO:0000139> . 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<https://identifiers.org/SBO:0000251> . +<https://localhost/ComponentDefinition/U2_RBS1> <http://sboltools.org/backport#sbol2type> <http://sbols.org/v2#ComponentDefinition> . +<https://localhost/ComponentDefinition/U2_RBS1> <http://sboltools.org/backport#sbol2version> "1" . +<https://localhost/ComponentDefinition/U2_RBS1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Component> . +<https://localhost/ComponentDefinition/U3_RBS2> <http://sbols.org/v3#displayId> "U3_RBS2" . +<https://localhost/ComponentDefinition/U3_RBS2> <http://sbols.org/v3#hasNamespace> <https://localhost> . +<https://localhost/ComponentDefinition/U3_RBS2> <http://sbols.org/v3#hasSequence> <https://localhost/Sequence/U3_RBS2> . +<https://localhost/ComponentDefinition/U3_RBS2> <http://sbols.org/v3#role> <http://identifiers.org/so/SO:0000139> . +<https://localhost/ComponentDefinition/U3_RBS2> <http://sbols.org/v3#type> <https://identifiers.org/SBO:0000251> . 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<http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Sequence> . +<https://localhost/Sequence/LMP> <http://sbols.org/v3#displayId> "LMP" . +<https://localhost/Sequence/LMP> <http://sbols.org/v3#elements> "" . +<https://localhost/Sequence/LMP> <http://sbols.org/v3#encoding> <https://identifiers.org/edam:format_1207> . +<https://localhost/Sequence/LMP> <http://sbols.org/v3#hasNamespace> <https://localhost> . +<https://localhost/Sequence/LMP> <http://sboltools.org/backport#sbol2version> "1" . +<https://localhost/Sequence/LMP> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Sequence> . +<https://localhost/Sequence/LMS> <http://sbols.org/v3#displayId> "LMS" . +<https://localhost/Sequence/LMS> <http://sbols.org/v3#elements> "" . +<https://localhost/Sequence/LMS> <http://sbols.org/v3#encoding> <https://identifiers.org/edam:format_1207> . +<https://localhost/Sequence/LMS> <http://sbols.org/v3#hasNamespace> <https://localhost> . +<https://localhost/Sequence/LMS> <http://sboltools.org/backport#sbol2version> "1" . +<https://localhost/Sequence/LMS> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Sequence> . +<https://localhost/Sequence/P21683> <http://sbols.org/v3#displayId> "P21683" . +<https://localhost/Sequence/P21683> <http://sbols.org/v3#elements> "atgc" . +<https://localhost/Sequence/P21683> <http://sbols.org/v3#encoding> <https://identifiers.org/edam:format_1207> . +<https://localhost/Sequence/P21683> <http://sbols.org/v3#hasNamespace> <https://localhost> . +<https://localhost/Sequence/P21683> <http://sboltools.org/backport#sbol2version> "1" . +<https://localhost/Sequence/P21683> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Sequence> . +<https://localhost/Sequence/P21684> <http://sbols.org/v3#displayId> "P21684" . +<https://localhost/Sequence/P21684> <http://sbols.org/v3#elements> "atgc" . +<https://localhost/Sequence/P21684> <http://sbols.org/v3#encoding> <https://identifiers.org/edam:format_1207> . +<https://localhost/Sequence/P21684> <http://sbols.org/v3#hasNamespace> <https://localhost> . +<https://localhost/Sequence/P21684> <http://sboltools.org/backport#sbol2version> "1" . +<https://localhost/Sequence/P21684> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Sequence> . +<https://localhost/Sequence/P21685> <http://sbols.org/v3#displayId> "P21685" . +<https://localhost/Sequence/P21685> <http://sbols.org/v3#elements> "atgc" . +<https://localhost/Sequence/P21685> <http://sbols.org/v3#encoding> <https://identifiers.org/edam:format_1207> . +<https://localhost/Sequence/P21685> <http://sbols.org/v3#hasNamespace> <https://localhost> . +<https://localhost/Sequence/P21685> <http://sboltools.org/backport#sbol2version> "1" . +<https://localhost/Sequence/P21685> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Sequence> . +<https://localhost/Sequence/PJ23119_BASIC> <http://sbols.org/v3#displayId> "PJ23119_BASIC" . +<https://localhost/Sequence/PJ23119_BASIC> <http://sbols.org/v3#elements> "" . +<https://localhost/Sequence/PJ23119_BASIC> <http://sbols.org/v3#encoding> <https://identifiers.org/edam:format_1207> . +<https://localhost/Sequence/PJ23119_BASIC> <http://sbols.org/v3#hasNamespace> <https://localhost> . +<https://localhost/Sequence/PJ23119_BASIC> <http://sboltools.org/backport#sbol2version> "1" . +<https://localhost/Sequence/PJ23119_BASIC> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Sequence> . +<https://localhost/Sequence/U1_RBS1> <http://sbols.org/v3#displayId> "U1_RBS1" . +<https://localhost/Sequence/U1_RBS1> <http://sbols.org/v3#elements> "" . +<https://localhost/Sequence/U1_RBS1> <http://sbols.org/v3#encoding> <https://identifiers.org/edam:format_1207> . +<https://localhost/Sequence/U1_RBS1> <http://sbols.org/v3#hasNamespace> <https://localhost> . +<https://localhost/Sequence/U1_RBS1> <http://sboltools.org/backport#sbol2version> "1" . +<https://localhost/Sequence/U1_RBS1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Sequence> . +<https://localhost/Sequence/U2_RBS1> <http://sbols.org/v3#displayId> "U2_RBS1" . +<https://localhost/Sequence/U2_RBS1> <http://sbols.org/v3#elements> "" . +<https://localhost/Sequence/U2_RBS1> <http://sbols.org/v3#encoding> <https://identifiers.org/edam:format_1207> . +<https://localhost/Sequence/U2_RBS1> <http://sbols.org/v3#hasNamespace> <https://localhost> . +<https://localhost/Sequence/U2_RBS1> <http://sboltools.org/backport#sbol2version> "1" . +<https://localhost/Sequence/U2_RBS1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Sequence> . +<https://localhost/Sequence/U3_RBS2> <http://sbols.org/v3#displayId> "U3_RBS2" . +<https://localhost/Sequence/U3_RBS2> <http://sbols.org/v3#elements> "" . +<https://localhost/Sequence/U3_RBS2> <http://sbols.org/v3#encoding> <https://identifiers.org/edam:format_1207> . +<https://localhost/Sequence/U3_RBS2> <http://sbols.org/v3#hasNamespace> <https://localhost> . +<https://localhost/Sequence/U3_RBS2> <http://sboltools.org/backport#sbol2version> "1" . +<https://localhost/Sequence/U3_RBS2> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Sequence> .
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/BBa_J23101.gb Thu Sep 15 13:40:15 2022 +0000 @@ -0,0 +1,12 @@ +LOCUS BBa_J23101 35 bp DNA linear UNK 01-JAN-1980 +DEFINITION constitutive promoter family member. +ACCESSION BBa_J23101 +VERSION BBa_J23101.1 +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers +ORIGIN + 1 tttacagcta gctcagtcct aggtattatg ctagc +//
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/BBa_J23101.nt Thu Sep 15 13:40:15 2022 +0000 @@ -0,0 +1,60 @@ + +<https://synbiohub.org/public/igem/BBa_J23101> <http://purl.org/dc/elements/1.1/creator> "John Anderson" . +<https://synbiohub.org/public/igem/BBa_J23101> <http://purl.org/dc/terms/created> "2006-08-03T11:00:00Z" . +<https://synbiohub.org/public/igem/BBa_J23101> <http://purl.org/dc/terms/modified> "2015-08-31T04:08:40Z" . +<https://synbiohub.org/public/igem/BBa_J23101> <http://sbols.org/v3#description> "constitutive promoter family member" . +<https://synbiohub.org/public/igem/BBa_J23101> <http://sbols.org/v3#displayId> "BBa_J23101" . +<https://synbiohub.org/public/igem/BBa_J23101> <http://sbols.org/v3#hasNamespace> <https://synbiohub.org> . +<https://synbiohub.org/public/igem/BBa_J23101> <http://sbols.org/v3#hasSequence> <https://synbiohub.org/public/igem/BBa_J23101_sequence> . +<https://synbiohub.org/public/igem/BBa_J23101> <http://sbols.org/v3#name> "BBa_J23101" . +<https://synbiohub.org/public/igem/BBa_J23101> <http://sbols.org/v3#role> <http://identifiers.org/so/SO:0000167> . +<https://synbiohub.org/public/igem/BBa_J23101> <http://sbols.org/v3#role> <http://wiki.synbiohub.org/wiki/Terms/igem#partType/Regulatory> . +<https://synbiohub.org/public/igem/BBa_J23101> <http://sbols.org/v3#type> <https://identifiers.org/SBO:0000251> . +<https://synbiohub.org/public/igem/BBa_J23101> <http://sboltools.org/backport#sbol2type> <http://sbols.org/v2#ComponentDefinition> . +<https://synbiohub.org/public/igem/BBa_J23101> <http://sboltools.org/backport#sbol2version> "1" . +<https://synbiohub.org/public/igem/BBa_J23101> <http://wiki.synbiohub.org/wiki/Terms/igem#discontinued> "false" . +<https://synbiohub.org/public/igem/BBa_J23101> <http://wiki.synbiohub.org/wiki/Terms/igem#dominant> "true" . +<https://synbiohub.org/public/igem/BBa_J23101> <http://wiki.synbiohub.org/wiki/Terms/igem#experience> <http://wiki.synbiohub.org/wiki/Terms/igem#experience/Works> . +<https://synbiohub.org/public/igem/BBa_J23101> <http://wiki.synbiohub.org/wiki/Terms/igem#group_u_list> "_52_" . +<https://synbiohub.org/public/igem/BBa_J23101> <http://wiki.synbiohub.org/wiki/Terms/igem#m_user_id> "0" . +<https://synbiohub.org/public/igem/BBa_J23101> <http://wiki.synbiohub.org/wiki/Terms/igem#owner_id> "483" . +<https://synbiohub.org/public/igem/BBa_J23101> <http://wiki.synbiohub.org/wiki/Terms/igem#owning_group_id> "95" . +<https://synbiohub.org/public/igem/BBa_J23101> <http://wiki.synbiohub.org/wiki/Terms/igem#partStatus> "Released HQ 2013" . +<https://synbiohub.org/public/igem/BBa_J23101> <http://wiki.synbiohub.org/wiki/Terms/igem#sampleStatus> "In stock" . +<https://synbiohub.org/public/igem/BBa_J23101> <http://wiki.synbiohub.org/wiki/Terms/igem#status> <http://wiki.synbiohub.org/wiki/Terms/igem#status/Available> . +<https://synbiohub.org/public/igem/BBa_J23101> <http://wiki.synbiohub.org/wiki/Terms/synbiohub#bookmark> "true" . +<https://synbiohub.org/public/igem/BBa_J23101> <http://wiki.synbiohub.org/wiki/Terms/synbiohub#mutableDescription> "later" . +<https://synbiohub.org/public/igem/BBa_J23101> <http://wiki.synbiohub.org/wiki/Terms/synbiohub#mutableNotes> "N/A" . +<https://synbiohub.org/public/igem/BBa_J23101> <http://wiki.synbiohub.org/wiki/Terms/synbiohub#mutableProvenance> "later" . +<https://synbiohub.org/public/igem/BBa_J23101> <http://wiki.synbiohub.org/wiki/Terms/synbiohub#ownedBy> <https://synbiohub.org/user/james> . +<https://synbiohub.org/public/igem/BBa_J23101> <http://wiki.synbiohub.org/wiki/Terms/synbiohub#ownedBy> <https://synbiohub.org/user/myers> . +<https://synbiohub.org/public/igem/BBa_J23101> <http://wiki.synbiohub.org/wiki/Terms/synbiohub#star> "true" . +<https://synbiohub.org/public/igem/BBa_J23101> <http://wiki.synbiohub.org/wiki/Terms/synbiohub#topLevel> <https://synbiohub.org/public/igem/BBa_J23101> . +<https://synbiohub.org/public/igem/BBa_J23101> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Component> . +<https://synbiohub.org/public/igem/BBa_J23101> <http://www.w3.org/ns/prov#wasDerivedFrom> <http://parts.igem.org/Part:BBa_J23101> . +<https://synbiohub.org/public/igem/BBa_J23101> <http://www.w3.org/ns/prov#wasGeneratedBy> <https://synbiohub.org/public/igem/igem2sbol> . +<https://synbiohub.org/public/igem/BBa_J23101_sequence> <http://sbols.org/v3#displayId> "BBa_J23101_sequence" . +<https://synbiohub.org/public/igem/BBa_J23101_sequence> <http://sbols.org/v3#elements> "tttacagctagctcagtcctaggtattatgctagc" . +<https://synbiohub.org/public/igem/BBa_J23101_sequence> <http://sbols.org/v3#encoding> <https://identifiers.org/edam:format_1207> . +<https://synbiohub.org/public/igem/BBa_J23101_sequence> <http://sbols.org/v3#hasNamespace> <https://synbiohub.org> . +<https://synbiohub.org/public/igem/BBa_J23101_sequence> <http://sboltools.org/backport#sbol2version> "1" . +<https://synbiohub.org/public/igem/BBa_J23101_sequence> <http://wiki.synbiohub.org/wiki/Terms/synbiohub#ownedBy> <https://synbiohub.org/user/james> . +<https://synbiohub.org/public/igem/BBa_J23101_sequence> <http://wiki.synbiohub.org/wiki/Terms/synbiohub#ownedBy> <https://synbiohub.org/user/myers> . +<https://synbiohub.org/public/igem/BBa_J23101_sequence> <http://wiki.synbiohub.org/wiki/Terms/synbiohub#topLevel> <https://synbiohub.org/public/igem/BBa_J23101_sequence> . +<https://synbiohub.org/public/igem/BBa_J23101_sequence> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Sequence> . +<https://synbiohub.org/public/igem/BBa_J23101_sequence> <http://www.w3.org/ns/prov#wasDerivedFrom> <http://parts.igem.org/Part:BBa_J23101> . +<https://synbiohub.org/public/igem/BBa_J23101_sequence> <http://www.w3.org/ns/prov#wasGeneratedBy> <https://synbiohub.org/public/igem/igem2sbol> . +<https://synbiohub.org/public/igem/igem2sbol> <http://purl.org/dc/elements/1.1/creator> "Chris J. Myers" . +<https://synbiohub.org/public/igem/igem2sbol> <http://purl.org/dc/elements/1.1/creator> "James Alastair McLaughlin" . +<https://synbiohub.org/public/igem/igem2sbol> <http://purl.org/dc/terms/description> "Conversion of the iGEM parts registry to SBOL2.1" . +<https://synbiohub.org/public/igem/igem2sbol> <http://purl.org/dc/terms/title> "iGEM to SBOL conversion" . +<https://synbiohub.org/public/igem/igem2sbol> <http://sbols.org/v2#persistentIdentity> <https://synbiohub.org/public/igem/igem2sbol> . +<https://synbiohub.org/public/igem/igem2sbol> <http://sbols.org/v3#displayId> "igem2sbol" . +<https://synbiohub.org/public/igem/igem2sbol> <http://sbols.org/v3#hasNamespace> <https://synbiohub.org> . +<https://synbiohub.org/public/igem/igem2sbol> <http://sboltools.org/backport#sbol2version> "1" . +<https://synbiohub.org/public/igem/igem2sbol> <http://wiki.synbiohub.org/wiki/Terms/synbiohub#ownedBy> <https://synbiohub.org/user/james> . +<https://synbiohub.org/public/igem/igem2sbol> <http://wiki.synbiohub.org/wiki/Terms/synbiohub#ownedBy> <https://synbiohub.org/user/myers> . +<https://synbiohub.org/public/igem/igem2sbol> <http://wiki.synbiohub.org/wiki/Terms/synbiohub#topLevel> <https://synbiohub.org/public/igem/igem2sbol> . +<https://synbiohub.org/public/igem/igem2sbol> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#TopLevel> . +<https://synbiohub.org/public/igem/igem2sbol> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/ns/prov#Activity> . +<https://synbiohub.org/public/igem/igem2sbol> <http://www.w3.org/ns/prov#endedAtTime> "2017-03-06T15:00:00+00:00" .