Blast Report from ID
Created: 2011-04-07 22:28:28
Last updated: 2011-04-07 22:39:44
This workflow retrieves a fasta sequence or blast report from an id. Firstly, given some inputs (e.g. ids:EDL10223.1, format:fasta, style:default and db:emblcds), it returns the sequence in fasta format associated to those inputs using the EBI's WSDbfetch web service (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch).
Next, we obtain a Blast report from this fasta sequence and some others parameters. The final result in that case corresponds with the same fasta sequence introduced as input parameter to the "run" processor. However, it could retrieve the blast report in XML format by changing BeanShell "process_ResultTypes" condition from the value "sequence" to "xml".
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Workflow Components
Authors (0)
Titles (0)
Descriptions (0)
Dependencies (0)
Inputs (6)
| Name |
Description |
| ids |
|
| db |
|
| style |
|
| format |
|
| title |
|
| email |
|
Processors (18)
| Name |
Type |
Description |
| fetchBatch |
wsdl |
Wsdlhttp://www.ebi.ac.uk/ws/services/urn:Dbfetch?wsdlWsdl OperationfetchBatch |
| run |
wsdl |
Wsdlhttp://www.ebi.ac.uk/Tools/services/soap/ncbiblast?wsdlWsdl Operationrun |
| run_input |
xmlsplitter |
|
| run_input_2 |
xmlsplitter |
|
| run_output |
xmlsplitter |
|
| program |
stringconstant |
Valueblastp |
| stype |
stringconstant |
Valueprotein |
| database |
stringconstant |
Valueuniprotkb_swissprot |
| seqrange_value |
stringconstant |
ValueSTART-END |
| Merge_List_to_String |
beanshell |
ScriptString seperatorString = "\n";
if (seperator != void) {
seperatorString = seperator;
}
StringBuffer sb = new StringBuffer();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
String item = (String) i.next();
sb.append(item);
if (i.hasNext()) {
sb.append(seperatorString);
}
}
concatenated = sb.toString(); |
| getResultTypes |
wsdl |
Wsdlhttp://www.ebi.ac.uk/Tools/services/soap/ncbiblast?wsdlWsdl OperationgetResultTypes |
| getResultTypes_input |
xmlsplitter |
|
| getResultTypes_output |
xmlsplitter |
|
| Status_Check |
workflow |
|
| getResult |
wsdl |
Wsdlhttp://www.ebi.ac.uk/Tools/services/soap/ncbiblast?wsdlWsdl OperationgetResult |
| getResult_input |
xmlsplitter |
|
| getResult_output |
xmlsplitter |
|
| process_ResultTypes |
beanshell |
Scriptimport javax.xml.parsers.*;
import org.xml.sax.InputSource;
import org.w3c.dom.*;
import java.io.*;
String xml = (String) listType.get(0);
DocumentBuilderFactory dbf =
DocumentBuilderFactory.newInstance();
DocumentBuilder db = dbf.newDocumentBuilder();
InputSource is = new InputSource();
is.setCharacterStream(new StringReader(xml));
Document doc = db.parse(is);
NodeList nodes = doc.getElementsByTagName("type");
// iterate the employees
for (int i = 0; i < nodes.getLength(); i++) {
Element element = (Element) nodes.item(i);
NodeList name = element.getElementsByTagName("identifier");
Element line = (Element) name.item(0);
Node child = line.getFirstChild();
if (child instanceof CharacterData) {
CharacterData cd = (CharacterData) child;
String nameValue = cd.getData();
if(nameValue.equals("sequence"))
identifier=nameValue;
}
}
|
Beanshells (2)
| Name |
Description |
Inputs |
Outputs |
| Merge_List_to_String |
|
stringlist
separator
|
concatenated
|
| process_ResultTypes |
|
listType
|
identifier
|
Outputs (2)
| Name |
Description |
| result |
|
| job_status |
|
Datalinks (26)
| Source |
Sink |
| format |
fetchBatch:format |
| style |
fetchBatch:style |
| db |
fetchBatch:db |
| ids |
fetchBatch:ids |
| run_input:output |
run:parameters |
| run_input_2:output |
run_input:parameters |
| title |
run_input:title |
| email |
run_input:email |
| program:value |
run_input_2:program |
| stype:value |
run_input_2:stype |
| database:value |
run_input_2:database |
| seqrange_value:value |
run_input_2:seqrange |
| Merge_List_to_String:concatenated |
run_input_2:sequence |
| run:parameters |
run_output:input |
| fetchBatch:fetchBatchReturn |
Merge_List_to_String:stringlist |
| getResultTypes_input:output |
getResultTypes:parameters |
| run_output:jobId |
getResultTypes_input:jobId |
| getResultTypes:parameters |
getResultTypes_output:input |
| run_output:jobId |
Status_Check:jobID |
| getResult_input:output |
getResult:parameters |
| run_output:jobId |
getResult_input:jobId |
| process_ResultTypes:identifier |
getResult_input:type |
| getResult:parameters |
getResult_output:input |
| getResultTypes_output:resultTypes |
process_ResultTypes:listType |
| getResult_output:output |
result |
| Status_Check:getStatus_output_status |
job_status |
Coordinations (3)
| Controller |
Target |
| Status_Check |
getResultTypes |
| getResultTypes |
getResult |
| fetchBatch |
run |
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