Re: [Taverna-users] Translate DNA, FASTA to Protein

Alan R Williams Thu, 17 Jul 2014 13:25:35 -0700

I think the problem is that the BioJava Cookbook is out of date. I triedwith BioJava version 1.7.1 (which is very old) and a beanshell works -see attached.


Alan

<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow"; version="1" 
producedBy="taverna-biodiversity-2.5.0"><dataflow 
id="993cd091-c014-4acd-b7b2-d7bf5d3e54a2" 
role="top"><name>Old_BioJava_for_tran</name><inputPorts><port><name>sequenceString</name><depth>0</depth><granularDepth>0</granularDepth><annotations><annotation_chain
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      <annotationBean 
class="net.sf.taverna.t2.annotation.annotationbeans.ExampleValue">
        
<text>GGTAGGTACCGCCCTAAGNCTCCTAATCCGAGCAGAACTANGCCAACCCGGAGCCCTTCTGGGAGACGAC
CAAATCTACAACGTAGTCGTTACGGCCCACGCCTTCGTAATAATCTTTTTCATAGTAATGCCAATCATAA
TCGGAGGATTCGGGAACTGACTAGTTCCTCTAATGATTGGGGCCCCAGACATAGCATTCCCTCGAATAAA
CAACATAAGCTTTTGACTACTACCACCATCATTCCTACTCCTAATAGCCTCCTCAACAGTAGAAGCAGGA
GCCGGAACCGGATGAACCGTGTACCCACCACTAGCTGGAAACCTGGCCCACGCCGGAGCCTCAGTAGACC
TAGCTATCTTCTCCCTACACCTAGCAGGTATCTCATCCATCCTGGGGGCAATTAACTTCATTACAACAGC
AATCAACATAAAACCACCCGCCCTCTCACAATACCAAACACCACTATTCGTGTGATCCGTCCTAATTACG
GCCGTACTACTCCTACTATCTCTCCCAGTACTAGCCGCCGGTATCACCATGCTACTCACAGACCGCAACC
TCAACACCACCTTCTTTGACCCAGCAGGAGGAGGAGACCCAGTACTATACCAGCACCTATTCTGATTCTT
CGGACACCCAGAAGTCTACATCCTAATTCTC</text>
      </annotationBean>
      <date>2014-07-17 19:58:43.883 UTC</date>
      <creators />
      <curationEventList />
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  </annotationAssertions>
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain></annotations></port></inputPorts><outputPorts><port><name>out1</name><lastPredictedDepth>0</lastPredictedDepth><annotations
 
/></port><port><name>trimmed</name><lastPredictedDepth>0</lastPredictedDepth><annotations
 
/></port></outputPorts><processors><processor><name>Beanshell</name><inputPorts><port><name>sequenceString</name><depth>0</depth></port></inputPorts><outputPorts><port><name>out1</name><depth>0</depth><granularDepth>0</granularDepth></port><port><name>trimmed</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations
 
/><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>beanshell-activity</artifact><version>1.5</version></raven><class>net.sf.taverna.t2.activities.beanshell.BeanshellActivity</class><inputMap><map
 from="sequenceString" to="sequenceString" /></inputMap><outputMap><map 
from="trimmed" to="trimmed" /><map from="out1" to="out1" 
/></outputMap><configBean 
encoding="xstream"><net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean
 xmlns="">
  <inputs>
    
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
      <name>sequenceString</name>
      <depth>0</depth>
      <mimeTypes>
        <string>text/plain</string>
      </mimeTypes>
      <handledReferenceSchemes />
      <translatedElementType>java.lang.String</translatedElementType>
      <allowsLiteralValues>true</allowsLiteralValues>
    
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean>
  </inputs>
  <outputs>
    
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
      <name>out1</name>
      <depth>0</depth>
      <mimeTypes />
      <granularDepth>0</granularDepth>
    
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
    
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
      <name>trimmed</name>
      <depth>0</depth>
      <mimeTypes />
      <granularDepth>0</granularDepth>
    
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
  </outputs>
  <classLoaderSharing>workflow</classLoaderSharing>
  <localDependencies>
    <string>biojava.jar</string>
  </localDependencies>
  <artifactDependencies />
  <script>import org.biojava.bio.symbol.*;
import org.biojava.bio.seq.*;
 

String out1 = "failed";

String trimmed = "not trimmed";
    try {
trimmed = sequenceString.replaceAll("\\s","");

int trimmedLength = trimmed.length();

while ((trimmed.length() % 3) != 0) {
        trimmed += "X"; 
}
      //create a DNA SymbolList
      SymbolList symL = DNATools.createDNA(trimmed);


 
      //transcribe to RNA (after biojava 1.4 use this method instead)
      symL = DNATools.toRNA(symL);
 
      //translate to protein
      symL = RNATools.translate(symL);


         out1 = symL.seqString();
 
      //prove that it worked
           System.out.println(symL.seqString());
     }catch (Exception ex) {
 
 
      out1 = ex.getMessage();
     }
</script>
  <dependencies />
</net.sf.taverna.t2.activities.beanshell.BeanshellActivityConfigurationBean></configBean><annotations
 
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 xmlns="">
  <maxJobs>1</maxJobs>
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 encoding="xstream"><null xmlns="" 
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 xmlns="">
  <backoffFactor>1.0</backoffFactor>
  <initialDelay>1000</initialDelay>
  <maxDelay>5000</maxDelay>
  <maxRetries>0</maxRetries>
</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.5</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean
 encoding="xstream"><null xmlns="" 
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 name="sequenceString" depth="0" 
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 /><datalinks><datalink><sink 
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Re: [Taverna-users] Translate DNA, FASTA to Protein

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