Query EVS by chromosomal position
Created: 2013-07-26 10:42:18
Last updated: 2013-07-26 10:44:00
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
Authors (0)
Titles (1)
| Query EVS by chromosomal position |
Descriptions (0)
Dependencies (0)
Inputs (1)
| Name |
Description |
| Location_list |
|
Processors (19)
| Name |
Type |
Description |
| Text_constant |
stringconstant |
Value\n |
| Split |
localworker |
ScriptList 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 |
Wsdlhttp://evs.gs.washington.edu/wsEVS/EVSDataQueryService?wsdlWsdl OperationgetEvsData |
| getEvsData_input |
xmlsplitter |
|
| getEvsData_output |
xmlsplitter |
|
| XPath_alleles |
localworker |
Scriptimport 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 |
Scriptimport 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 |
Scriptimport 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 |
Scriptimport 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 |
Scriptimport 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 |
Scriptimport 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 |
Scriptimport 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 |
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 |
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