Get Element ID from Gzipped GenBank file

Created: 2011-10-06 03:53:12      Last updated: 2011-10-06 04:12:18

This workflow gunzips a *.gbk.gz file, converts it to XML (via agavewriter) and finds the Element ID.

Does not work on *.gz files larger than 10MB.

I upped the JVM settings on Taverna to:        

<key>VMOptions</key>
        <string>-Xmx4096m -XX:MaxPermSize=1024m</string>

Created my own agave.dtd to get the XPath service to work the XML file generated from the Read_GenBank_File service. You will need to save the 3 dtd files to your Taverna folder for this workflow to work.

This workflows works on *.gb and *.gbk files that are gzipped. It does NOT work with *.seq files, this is the error generated from the Read_GenBank_File service:

"Sourced file: inline evaluation of: ``import org.biojava.bio.seq.Sequence; import org.biojava.bio.seq.SequenceIterator . . . '' : Method Invocation writer.writeSequence : at Line: 36 : in file: inline evaluation of: ``import org.biojava.bio.seq.Sequence; import org.biojava.bio.seq.SequenceIterator . . . '' : writer .writeSequence ( seq , ps )

Target exception: java.lang.IllegalArgumentException: end must not be lower than start: start=561, end=560"

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