On Mon, Apr 5, 2010 at 21:39, Rinku Saha <[email protected]> wrote:
> I am trying to create a workflow where i am trying to write the output into
> a txt file.Its not giving any error.But i am unable to find the txt file in
> the location i gave (as file:///C:/jiangtaverna). Ineeded some suggestions on
> where i am doing something wrong.Also wanted to ask how am i going to name
> the output file.
> My inputs were:
> file:file:///C:/jiangtaverna
> PDBid:1J47
You've run into a few issues here, I'm afraid..
* The Write_Text_File local worker takes a filename as an argument, not a URI.
* "file:" is included twice in your URI, so it was not a valid URI
* You would not normally be allowed to write to C:\ unless you are a
system administrator
* The Write_text_file takes a single value as an input, but you want
to write the full list of items to the file
* The BioMart query hsapiens_gene_ensembl returns 0 entries
* You have configured the Biomart to filter by EMBL ID instead of Pubmed ID
* BioMart expects the Pubmed ID witout the "PDBid:" prefix.
Try instead:
C:\Users\rinku\Desktop\jiangtaverna.txt as the file parameter (Adjust
for path to your Desktop)
You can inspect the intermediate values from hsapiens_gene_ensembl, in
Taverna 1 select the processor in the Status list, and then inspect
Intermediate Outputs. In Taverna 2.1.2, double-click the service in
the diagram, and a pop-up should show the intermediate outputs.
Alternatively you can also connect the output port of the service to a
second workflow output port to inspect the values returned.
To avoid Taverna overwriting the same file for each value returned
(Taverna does an iteration in cases of list cardinality mismatches),
you will need to join the output list to a single string. One way to
do this is to use the Local Worker "Merge string list to string". If
you don't connect anything to "seperator" (sic) it will add line feeds
between each string in the input. In your case I believe you would
only get a single result back from BioMart, so this is less of an
issue for you unless you feed a list of IDs to the 'emblid' input.
To change your workflow to accept pubmed IDs, configure the Biomart
query for hsapiens_gene_emsembl and set the Filter to have a Gene ID
list selected from "PDB IDs". You can either hardcode the IDs in that
box, or override this by connecting to the filter input poer. (like
you've done). BioMart has a web version called 'MartView' [2] which
you might find useful to experiment with to get a feel about different
filters and columns that can be retrieved.
See the attached workflow were I've added these changes, running with:
file: C:\Users\stain\Desktop\ids.txt
pdbid: 1J47
you will get the output 6736 stored to ids.txt.
(Note that the line feed inserted by Merge is \n, not \r\n as is
common on Windows. You might want to inspect the output file with a
text editor other than Notepad)
Is there any particular reason why you are using Taverna 1? For most
users we recommend to try Taverna 2.1 [1] as it has many improvements
to the user interface and workflow engine. We are however also very
interested in feedback on reasons users are not transitioning to
Taverna 2.
[1] http://www.taverna.org.uk/download/taverna-2-1/
[2] http://www.biomart.org/biomart/martview/
--
Stian Soiland-Reyes, myGrid team
School of Computer Science
The University of Manchester
<?xml version="1.0" encoding="UTF-8"?>
<s:scufl xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"; version="0.2" log="0">
<s:workflowdescription lsid="urn:lsid:net.sf.taverna:wfDefinition:6569c373-43cf-4539-b24f-88a4fdc7a5b3" author="" title="writingtextfile" />
<s:processor name="Write_Text_File">
<s:local>net.sourceforge.taverna.scuflworkers.io.TextFileWriter</s:local>
</s:processor>
<s:processor name="hsapiens_gene_ensembl">
<s:description>Homo sapiens genes (GRCh37)</s:description>
<s:biomart>
<biomart:MartQuery xmlns:biomart="http://org.embl.ebi.escience/xscufl-biomart/0.1alpha";>
<biomart:MartService location="http://www.biomart.org/biomart/martservice"; />
<biomart:MartDataset displayName="Homo sapiens genes (GRCh37)" name="hsapiens_gene_ensembl" type="TableSet" initialBatchSize="200" maximumBatchSize="50000" visible="false" interface="default" modified="2010-03-08 14:50:08">
<biomart:MartURLLocation database="ensembl_mart_57" default="1" displayName="ENSEMBL GENES 57 (SANGER UK)" host="www.biomart.org" includeDatasets="" martUser="" name="ensembl" path="/biomart/martservice" port="80" serverVirtualSchema="default" virtualSchema="default" visible="1" redirect="0" />
</biomart:MartDataset>
<biomart:Query virtualSchemaName="default" count="0" uniqueRows="0" softwareVersion="0.7" requestId="taverna">
<biomart:Dataset name="hsapiens_gene_ensembl">
<biomart:Attribute name="entrezgene" />
<biomart:Filter name="pdb" value="" list="true" />
</biomart:Dataset>
</biomart:Query>
</biomart:MartQuery>
</s:biomart>
</s:processor>
<s:processor name="Merge_string_list_to_string">
<s:local>org.embl.ebi.escience.scuflworkers.java.StringListMerge</s:local>
</s:processor>
<s:link source="file" sink="Write_Text_File:outputFile" />
<s:link source="Write_Text_File:outputFile" sink="out" />
<s:link source="hsapiens_gene_ensembl:hsapiens_gene_ensembl.entrezgene" sink="Merge_string_list_to_string:stringlist" />
<s:link source="pdbid" sink="hsapiens_gene_ensembl:hsapiens_gene_ensembl.pdb_filter" />
<s:link source="Merge_string_list_to_string:concatenated" sink="Write_Text_File:filecontents" />
<s:source name="file">
<s:metadata>
<s:description>File path of where to store the fetched IDs, like C:\Users\johndoe\Desktop\ids.txt</s:description>
</s:metadata>
</s:source>
<s:source name="pdbid">
<s:metadata>
<s:description>PDB id, for instance: 1J47</s:description>
</s:metadata>
</s:source>
<s:sink name="out" />
</s:scufl>
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