DAS_sequence_retrieval_and_parsing_with_JDASIDs00O35502,P999992011-05-30 04:01:34.907 CESTYou can input more than one ID using comma-separated values. You can use different types of IDs depending on the DAS coordinate system (http://www.dasregistry.org/help_coordsys.jsp) you decided to use. If you selected a DAS source of type "Protein Sequence" and authority "UniProt" you could use UniProt (TrEMBL and SwissProt) accessions. For instance "P37173". If you selected a DAS source of type "Chromosome", authority "GRCh_37" and organism "Homo sapiens" you could use a chromosome ID. For instance "1".2011-05-30 04:01:22.608 CESTDasSource00Input a DAS reference source following this format "http://www.server.com/das/source/". Find a public list of available DAS reference sources providing sequence information in the DAS registry … http://www.dasregistry.org/listSources.jsp … or create your own DAS source with easyDAS … http://www.ebi.ac.uk/panda-srv/easydas/2011-05-30 04:01:54.364 CESThttp://www.ebi.ac.uk/das-srv/uniprot/das/uniprot/2011-05-30 02:29:17.129 CESTstart00The start and stop attributes indicate the range of the segment to query. In this workflow is optional. Set an empty value to get the whole sequence.2011-05-30 04:02:13.175 CEST112011-05-30 04:02:18.694 CESTstop00322011-05-30 04:02:39.38 CESTThe start and stop attributes indicate the range of the segment to query. In this workflow is optional. Set an empty value to get the whole sequence.2011-05-30 04:02:22.298 CESTSequence_Custom_FormatThis output was achieved using the JDAS library …
http://code.google.com/p/jdas/
To be able to use this workflow with JDAS copy this file …
http://www.ebi.ac.uk/~maven/m2repo/uk/ac/ebi/das/jdas/1.0.3/jdas-1.0.3.jar
… to the lib folder inside the Taverna application. This jar file is a dependency needed to parse DAS outputs.2011-05-30 04:07:04.130 CESTSequence_DAS_formatHave a look to the specification to know more about the DAS format ... http://www.biodas.org/documents/spec-1.6.html#sequence2011-05-30 04:04:25.201 CESTService_status2002011-05-30 04:03:56.367 CESTHTTP response status codes ... http://en.wikipedia.org/wiki/List_of_HTTP_status_codes 2011-05-30 04:03:51.296 CESTDAS_sequence_retrievalDasSource0start0stop0ID0Sequence_DAS_format00Service_status00net.sf.taverna.t2.activitiesdataflow-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeJDASsequenceXML0sequenceText00net.sf.taverna.t2.activitiesbeanshell-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.beanshell.BeanshellActivitysequenceXML0text/plainjava.lang.StringtruesequenceText00workflownet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokesplit_by_regexstring0regex0split11net.sf.taverna.t2.activitieslocalworker-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.localworker.LocalworkerActivitystring0'text/plain'java.lang.Stringtrueregex0'text/plain'java.lang.Stringtruesplit11workfloworg.embl.ebi.escience.scuflworkers.java.SplitByRegexUserNameHere2011-05-30 03:58:05.622 CESTnet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeregex_valuevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.stringconstant.StringConstantActivity,net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeDAS_sequence_retrievalDasSourceDAS_sequence_retrievalstartDAS_sequence_retrievalstopDAS_sequence_retrievalIDJDASsequenceXMLsplit_by_regexstringsplit_by_regexregexSequence_Custom_FormatSequence_DAS_formatService_statusRetrieve Protein or Genome sequences using the Distributed Annotation System (DAS) and create your own text output by modifying the JDAS component. To be able to use this workflow with JDAS copy this file …
http://www.ebi.ac.uk/~maven/m2repo/uk/ac/ebi/das/jdas/1.0.3/jdas-1.0.3.jar
… to the lib folder inside the Taverna application. This jar file is a dependency needed to parse DAS outputs.2011-05-30 04:10:18.475 CESTc8c59c76-0444-4a87-965c-100b1233efea2011-05-30 03:39:25.578 CESTa1708814-616b-42b3-9486-98014544eb482011-05-30 03:34:49.44 CEST87adc1b2-2043-4a77-9d88-fe4b2aed17e72011-05-30 03:20:22.554 CEST076007bb-74d1-4ba5-b581-64618dd0c8972011-05-30 03:25:43.94 CESTba998355-bec5-4575-a66f-676391e68f332011-05-30 03:44:57.378 CESTf15449de-8120-43a2-97fa-9c2d90eb94742011-05-30 02:51:35.544 CESTaf896ceb-6fa5-45a0-806f-db8a2430bf722011-05-30 03:36:12.651 CEST8bf845ff-13c9-408c-a47a-f18f1df2e0a82011-05-30 03:58:59.698 CEST4dcda7cd-4679-4df6-b557-350488e980f62011-05-30 02:53:31.861 CESTDAS sequence retrieval and parsing with JDAS2011-05-30 04:10:24.871 CEST816d6ae4-580f-406e-a837-7d16c1a3717d2011-05-30 03:55:19.696 CEST9b8849d8-a1d3-4a7d-8106-2e37c0d5d2c92011-05-30 03:33:28.950 CEST87c07b0a-bc75-49d6-b490-0c1b896f54cb2011-05-30 03:37:59.703 CESTe7a97f0d-7f82-451d-bde5-ef8f5f5f17ec2011-05-30 04:11:00.444 CEST564e88c0-046e-4781-90ea-3ec4d69842412011-05-30 02:56:05.576 CESTc5ec8b42-23e2-40cb-b7ee-83aa3cc460f62011-05-30 02:47:40.436 CEST0a47eda6-25d1-4832-99e9-54ffcb3f53722011-05-30 02:57:50.895 CEST77093bcd-f2fa-400d-918c-26fbe2c6cff62011-05-30 03:51:39.304 CESTDAS_sequence_retrievalID00You can use different types of IDs depending on the DAS coordinate system (http://www.dasregistry.org/help_coordsys.jsp) you decided to use. If you selected a DAS source of type "Protein Sequence" and authority "UniProt" you could use UniProt (TrEMBL and SwissProt) accessions. For instance "P37173". If you selected a DAS source of type "Chromosome", authority "GRCh_37" and organism "Homo sapiens" you could use a chromosome ID. For instance "1".2011-05-30 01:52:17.550 CESTP371732011-05-30 01:52:18.805 CESTDasSource00http://www.ebi.ac.uk/das-srv/uniprot/das/uniprot/2011-05-30 01:28:16.88 CESTInput a DAS reference source following this format "http://www.server.com/das/source/". Find a public list of available DAS reference sources providing sequence information in the DAS registry … http://www.dasregistry.org/listSources.jsp … or create your own DAS source with easyDAS … http://www.ebi.ac.uk/panda-srv/easydas/2011-05-30 02:15:09.967 CESTstart00112011-05-30 01:55:19.329 CESTThe start and stop attributes indicate the range of the segment to query. In this workflow is optional. Set an empty value to get the whole sequence.2011-05-30 02:17:50.251 CESTstop00The start and stop attributes indicate the range of the segment to query. In this workflow is optional. Set an empty value to get the whole sequence.2011-05-30 02:18:12.559 CEST342011-05-30 01:55:40.282 CESTSequence_DAS_formatHave a look to the specification to know more about the DAS format ... http://www.biodas.org/documents/spec-1.6.html#sequence2011-05-30 02:23:33.888 CESTService_statusHTTP response status codes ... http://en.wikipedia.org/wiki/List_of_HTTP_status_codes 2011-05-30 02:22:21.891 CEST2002011-05-30 02:22:25.299 CESTGet_SequenceID0range0DasSource0responseBody00status00net.sf.taverna.t2.activitiesrest-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.rest.RESTActivityGET{DasSource}sequence?segment={ID}{range}text/plainapplication/xmlStringfalsefalsefalserangejava.lang.StringIDjava.lang.StringDasSourcejava.lang.Stringnet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokecreate_rangestart0stop0range00net.sf.taverna.t2.activitiesbeanshell-activity1.3-SNAPSHOTnet.sf.taverna.t2.activities.beanshell.BeanshellActivitystart0text/plainjava.lang.Stringtruestop0text/plainjava.lang.Stringtruerange00workflownet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.3-SNAPSHOTnet.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeGet_SequenceIDGet_SequencerangeGet_SequenceDasSourcecreate_rangestartcreate_rangestopSequence_DAS_formatService_status9644404d-5f8d-492a-b3d8-c745997f3aa02011-05-30 02:13:55.383 CESTa8bada53-c671-4e50-ade0-8e34c32901e62011-05-30 02:18:01.306 CEST733432d7-c241-4e41-a456-7a66a34d8d9b2011-05-30 01:58:53.465 CEST93e3904a-0744-418f-a528-a56516e0c7462011-05-30 01:59:54.881 CESTfc528ec7-bb47-49dc-81ee-c39d697fff3d2011-05-30 02:11:31.834 CEST1666f142-70c6-49a3-b19b-c833bc6a22a82011-05-30 02:01:31.744 CEST5ac5004d-9ed3-4196-9388-c6a66dfe1ad62011-05-30 02:09:39.158 CEST730c1649-36b7-4a8f-9243-1bc86b91803a2011-05-30 02:06:27.364 CESTedf775f1-683a-4fbe-a7c2-dfa731ca84b52011-05-30 01:34:56.825 CEST79201635-7ebc-4498-aa96-286c5e6279b42011-05-30 02:16:24.682 CESTRetrieve Protein or Genome sequences using the Distributed Annotation System (DAS).2011-05-30 02:16:33.776 CEST73bbadd7-3fb6-4f7c-abe3-3da636e96b342011-05-30 02:23:53.286 CEST92ff601d-9ad6-4731-b9a7-6e3d292b2be72011-05-30 01:57:19.424 CESTRafael C. Jimenez2011-05-30 01:51:35.732 CESTDAS sequence retrieval2011-05-30 01:52:03.426 CEST2b8cbaeb-375e-40c9-ad77-7e4ab49c057f2011-05-30 02:03:47.677 CESTb1b262e0-bddb-47d9-80f8-507b989561132011-05-30 02:08:08.718 CEST