Query EVS by chromosomal position

Created: 2013-07-26 10:42:18 Last updated: 2013-07-26 10:44:00

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The workflow takes a list of chromosomal positions (in the format chr:pos e.g. 2:139574) and returns a selection of data in the Exome Variant Server (http://evs.gs.washington.edu/EVS/).

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Workflow Components

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Titles (1)

Descriptions (0)

Dependencies (0)

Inputs (1)

Name	Description
Location_list

Processors (19)

Name	Type	Description
Text_constant	stringconstant	Value \n
Split	localworker	Script List split = new ArrayList(); if (!string.equals("")) { String regexString = ","; if (regex != void) { regexString = regex; } String[] result = string.split(regexString); for (int i = 0; i < result.length; i++) { split.add(result[i]); } }
getEvsData	wsdl	Wsdl http://evs.gs.washington.edu/wsEVS/EVSDataQueryService?wsdl Wsdl Operation getEvsData
getEvsData_input	xmlsplitter
getEvsData_output	xmlsplitter
XPath_alleles	localworker	Script import org.dom4j.Document; import org.dom4j.Node; import org.dom4j.io.SAXReader; SAXReader reader = new SAXReader(false); reader.setIncludeInternalDTDDeclarations(false); reader.setIncludeExternalDTDDeclarations(false); Document document = reader.read(new StringReader(xmltext)); List nodelist = document.selectNodes(xpath); // Process the elements in the nodelist ArrayList outputList = new ArrayList(); ArrayList outputXmlList = new ArrayList(); String val = null; String xmlVal = null; for (Iterator iter = nodelist.iterator(); iter.hasNext();) { Node element = (Node) iter.next(); xmlVal = element.asXML(); val = element.getStringValue(); if (val != null && !val.equals("")) { outputList.add(val); outputXmlList.add(xmlVal); } } List nodelist=outputList; List nodelistAsXML=outputXmlList;
XPath_strand	localworker	Script import org.dom4j.Document; import org.dom4j.Node; import org.dom4j.io.SAXReader; SAXReader reader = new SAXReader(false); reader.setIncludeInternalDTDDeclarations(false); reader.setIncludeExternalDTDDeclarations(false); Document document = reader.read(new StringReader(xmltext)); List nodelist = document.selectNodes(xpath); // Process the elements in the nodelist ArrayList outputList = new ArrayList(); ArrayList outputXmlList = new ArrayList(); String val = null; String xmlVal = null; for (Iterator iter = nodelist.iterator(); iter.hasNext();) { Node element = (Node) iter.next(); xmlVal = element.asXML(); val = element.getStringValue(); if (val != null && !val.equals("")) { outputList.add(val); outputXmlList.add(xmlVal); } } List nodelist=outputList; List nodelistAsXML=outputXmlList;
xpath_value	stringconstant	Value /return/snpList/alleles
xpath_value_1	stringconstant	Value /return/strand
XPath_protein	localworker	Script import org.dom4j.Document; import org.dom4j.Node; import org.dom4j.io.SAXReader; SAXReader reader = new SAXReader(false); reader.setIncludeInternalDTDDeclarations(false); reader.setIncludeExternalDTDDeclarations(false); Document document = reader.read(new StringReader(xmltext)); List nodelist = document.selectNodes(xpath); // Process the elements in the nodelist ArrayList outputList = new ArrayList(); ArrayList outputXmlList = new ArrayList(); String val = null; String xmlVal = null; for (Iterator iter = nodelist.iterator(); iter.hasNext();) { Node element = (Node) iter.next(); xmlVal = element.asXML(); val = element.getStringValue(); if (val != null && !val.equals("")) { outputList.add(val); outputXmlList.add(xmlVal); } } List nodelist=outputList; List nodelistAsXML=outputXmlList;
XPath_cdna	localworker	Script import org.dom4j.Document; import org.dom4j.Node; import org.dom4j.io.SAXReader; SAXReader reader = new SAXReader(false); reader.setIncludeInternalDTDDeclarations(false); reader.setIncludeExternalDTDDeclarations(false); Document document = reader.read(new StringReader(xmltext)); List nodelist = document.selectNodes(xpath); // Process the elements in the nodelist ArrayList outputList = new ArrayList(); ArrayList outputXmlList = new ArrayList(); String val = null; String xmlVal = null; for (Iterator iter = nodelist.iterator(); iter.hasNext();) { Node element = (Node) iter.next(); xmlVal = element.asXML(); val = element.getStringValue(); if (val != null && !val.equals("")) { outputList.add(val); outputXmlList.add(xmlVal); } } List nodelist=outputList; List nodelistAsXML=outputXmlList;
XPath_ua	localworker	Script import org.dom4j.Document; import org.dom4j.Node; import org.dom4j.io.SAXReader; SAXReader reader = new SAXReader(false); reader.setIncludeInternalDTDDeclarations(false); reader.setIncludeExternalDTDDeclarations(false); Document document = reader.read(new StringReader(xmltext)); List nodelist = document.selectNodes(xpath); // Process the elements in the nodelist ArrayList outputList = new ArrayList(); ArrayList outputXmlList = new ArrayList(); String val = null; String xmlVal = null; for (Iterator iter = nodelist.iterator(); iter.hasNext();) { Node element = (Node) iter.next(); xmlVal = element.asXML(); val = element.getStringValue(); if (val != null && !val.equals("")) { outputList.add(val); outputXmlList.add(xmlVal); } } List nodelist=outputList; List nodelistAsXML=outputXmlList;
XPath_aa	localworker	Script import org.dom4j.Document; import org.dom4j.Node; import org.dom4j.io.SAXReader; SAXReader reader = new SAXReader(false); reader.setIncludeInternalDTDDeclarations(false); reader.setIncludeExternalDTDDeclarations(false); Document document = reader.read(new StringReader(xmltext)); List nodelist = document.selectNodes(xpath); // Process the elements in the nodelist ArrayList outputList = new ArrayList(); ArrayList outputXmlList = new ArrayList(); String val = null; String xmlVal = null; for (Iterator iter = nodelist.iterator(); iter.hasNext();) { Node element = (Node) iter.next(); xmlVal = element.asXML(); val = element.getStringValue(); if (val != null && !val.equals("")) { outputList.add(val); outputXmlList.add(xmlVal); } } List nodelist=outputList; List nodelistAsXML=outputXmlList;
XPath_mrna	localworker	Script import org.dom4j.Document; import org.dom4j.Node; import org.dom4j.io.SAXReader; SAXReader reader = new SAXReader(false); reader.setIncludeInternalDTDDeclarations(false); reader.setIncludeExternalDTDDeclarations(false); Document document = reader.read(new StringReader(xmltext)); List nodelist = document.selectNodes(xpath); // Process the elements in the nodelist ArrayList outputList = new ArrayList(); ArrayList outputXmlList = new ArrayList(); String val = null; String xmlVal = null; for (Iterator iter = nodelist.iterator(); iter.hasNext();) { Node element = (Node) iter.next(); xmlVal = element.asXML(); val = element.getStringValue(); if (val != null && !val.equals("")) { outputList.add(val); outputXmlList.add(xmlVal); } } List nodelist=outputList; List nodelistAsXML=outputXmlList;
xpath_value_2	stringconstant	Value /return/snpList/snpFunction/snpFxnList/hgvsProteinVar
xpath_value_3	stringconstant	Value /return/snpList/snpFunction/snpFxnList/hgvsCdnaVar
xpath_value_4	stringconstant	Value /return/genesInChrRegion/mrnaAccession
xpath_value_5	stringconstant	Value /return/snpList/aaAlleleCounts
xpath_value_6	stringconstant	Value /return/snpList/uaAlleleCounts

Beanshells (0)

Outputs (8)

Name	Description
Results
alleles
strand
protein
cdna
ua
aa
mrna

Datalinks (27)

Source	Sink
Location_list	Split:string
Text_constant:value	Split:regex
getEvsData_input:output	getEvsData:parameters
Split:split	getEvsData_input:arg0
getEvsData:parameters	getEvsData_output:input
xpath_value:value	XPath_alleles:xpath
getEvsData_output:return	XPath_alleles:xml-text
xpath_value_1:value	XPath_strand:xpath
getEvsData_output:return	XPath_strand:xml-text
xpath_value_2:value	XPath_protein:xpath
getEvsData_output:return	XPath_protein:xml-text
xpath_value_3:value	XPath_cdna:xpath
getEvsData_output:return	XPath_cdna:xml-text
getEvsData_output:return	XPath_ua:xml-text
xpath_value_6:value	XPath_ua:xpath
getEvsData_output:return	XPath_aa:xml-text
xpath_value_5:value	XPath_aa:xpath
xpath_value_4:value	XPath_mrna:xpath
getEvsData_output:return	XPath_mrna:xml-text
getEvsData_output:return	Results
XPath_alleles:nodelistAsXML	alleles
XPath_strand:nodelist	strand
XPath_protein:nodelist	protein
XPath_cdna:nodelist	cdna
XPath_ua:nodelist	ua
XPath_aa:nodelist	aa
XPath_mrna:nodelist	mrna