[EMBOSS] sreformat: problems with parameter

Marc Logghe Marc.Logghe at DEVGEN.com
Tue Sep 20 20:31:57 UTC 2005 

Hi Ulrike,
EMBOSS seqret is perfectly suited to perform sequence conversion. You can pass it any standard format of sequence and de default output is fasta. But you can also specify the input and output formats if you want, using the options -sformat and -osformat respectively. Check out the docs for all possible formats at http://emboss.sourceforge.net/apps/seqret.html
It's really useful as a kind of filter in taverna.
HTH,
Marc

-----Oorspronkelijk bericht-----
Van: emboss-bounces at emboss.open-bio.org namens Ulrike Kaule
Verzonden: di 20/09/2005 22:03
Aan: emboss at emboss.open-bio.org
Onderwerp: [EMBOSS] sreformat: problems with parameter
 
Hello,

I want to develop a workflow in Taverna, which accepts a sequence in 
fasta-format and does some analysis with it. But a demand is also, that 
the user could input some other formats than fasta - so I have to 
convert them internally to fasta. The only programm I found for this 
purpose was sreformat from HMMER. At the moment this programm is not 
included in EMBOSS, so I wrote a new acd-file and deployed it as a 
web-service.
The acd-file is as follows:

-----------------------------------------------------
application: sreformat [
  documentation: "Converts sequence file to different format"
  groups: "Utils"
]

section: input [
  information: "Input section"
  type: "page"
]

string: format  [
  parameter: "Y"
  information: "Output format"
]

sequence: seqfile  [
  parameter: "Y"
  information: "Input sequence"
]

endsection: input

section: output [
  information: "Output section"
  type: "page"
]

seqout: outfile  [
  parameter: "Y"
]

endsection: output
-----------------------------------------------------


To ensure, that the output-format of sreformat is 'fasta', I coded it 
hard in a string-constant and gave it to parameter 'osformat' of sreformat.
But the error-message I got was:

----------------------------------------------------------------------------------------
Task failed due to problem invoking soaplab service
    SoaplabTask.execute(..) : line 201 <SoaplabTask.java>
    ProcessorTask.runAndGenerateTemplates(..) : line 444 
<ProcessorTask.java>
    ProcessorTask.doInvocationWithRetryLogic(..) : line 397 
<ProcessorTask.java>
    ProcessorTask.invokeOnce(..) : line 319 <ProcessorTask.java>   
    ProcessorTask.invokeWithoutIteration(..) : line 503<ProcessorTask.java>
    ProcessorTask.invoke(..) : line 251 <ProcessorTask.java>   
    ProcessorTask.handleRun(..) : line 199 <ProcessorTask.java>   
    NewState$1.run(..) : line 67 <NewState.java>
    
    org.embl.ebi.SoaplabShare.SoaplabException: CONFLICTING_INPUT. 
format * (Parameter (Output format): Cannot remain empty.)
    
    SOAPFaultBuilder.createFault(..) : line 221 <SOAPFaultBuilder.java>
    SOAPFaultBuilder.endElement(..) : line 128 <SOAPFaultBuilder.java>
    DeserializationContext.endElement(..) : line 1087 
<DeserializationContext.java>
    AbstractSAXParser.endElement(..) : line -1 <Unknown filename>
    XMLNSDocumentScannerImpl.scanEndElement(..) : line -1 <Unknown filename>
   
 XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(..) : 
line -1 <Unknown filename>
    XMLDocumentFragmentScannerImpl.scanDocument(..) : line -1 <Unknown 
filename>
    XML11Configuration.parse(..) : line -1 <Unknown filename>
    XML11Configuration.parse(..) : line -1 <Unknown filename>
    XMLParser.parse(..) : line -1 <Unknown filename>
    AbstractSAXParser.parse(..) : line -1 <Unknown filename>
    SAXParser.parse(..) : line 345 <SAXParser.java>
    DeserializationContext.parse(..) : line 227 
<DeserializationContext.java>
    SOAPPart.getAsSOAPEnvelope(..) : line 696 <SOAPPart.java>
    Message.getSOAPEnvelope(..) : line 424 <Message.java>
    MustUnderstandChecker.invoke(..) : line 62 <MustUnderstandChecker.java>
    AxisClient.invoke(..) : line 206 <AxisClient.java>
    Call.invokeEngine(..) : line 2754 <Call.java>
    Call.invoke(..) : line 2737 <Call.java&>
    Call.invoke(..) : line 2413 <Call.java>
    Call.invoke(..) : line 2336 <Call.java>
    Call.invoke(..) : line 1793 <Call.java>
    SoaplabTask.execute(..) : line 98 <SoaplabTask.java>
    ProcessorTask.runAndGenerateTemplates(..) : line 444 
<ProcessorTask.java>
    ProcessorTask.doInvocationWithRetryLogic(..) : line 397 
<ProcessorTask.java>
    ProcessorTask.invokeOnce(..) : line 319 <ProcessorTask.java>
    ProcessorTask.invokeWithoutIteration(..) : line 503 <ProcessorTask.java>
    ProcessorTask.invoke(..) : line 251 <ProcessorTask.java>
    ProcessorTask.handleRun(..) : line 199 <ProcessorTask.java>
    NewState$1.run(..) : line 67 <NewState.java>
----------------------------------------------------------------------------------------
So it seems, that the string-constant is not recognized. Therefore I 
changed in the acd-file, the default-value for format to "fasta" :
...
string: format  [
  parameter: "Y"
  information: "Output format"
  default: "fasta"
  standard: "N"
]
...
but I got an error-message too.

Soaplab call returned an error : Summary:
    Completed: Erroneously
    Termination status: 256
    Platform: Linux linux 2.6.4-52-default #1 Wed Apr 7 02:08:30 UTC 
2004 i686 i686 i386 GNU/Linux
    Started: 20.09.2005 20:22:43 (Europe/Berlin)
    Ended: 20.09.2005 20:22:43 (Europe/Berlin)
Report:
Name: sreformat
Started: 05-09-20 20:22:43
Program and parameters:
sreformat
/usr/local/analysis-interfaces/a/unknown/Projects/default/Data/in1127240561172
/usr/local/analysis-interfaces/a/unknown/Projects/default/Data/out1127240561314
--- end of parameters

Completed: 05-09-20 20:22:43

Exit: 1


FATAL: Unknown output format 
/usr/local/analysis-interfaces/a/unknown/Projects/default/Data/in1127240561172
Usage: sreformat [-options] <format> <seqfile>
  Output format choices: Unaligned      Aligned
                         -----------    -------
                         fasta          stockholm
                         embl           msf
                         genbank        a2m
                         gcg            phylip
                         gcgdata        clustal
                         pir            selex
                         raw            eps

  Available options are:
    -h : help; print brief help on version and usage
    -d : force DNA alphabet for nucleic acid sequence
    -r : force RNA alphabet for nucleic acid sequence
    -l : force lower case
    -u : force upper case
    -x : convert non-IUPAC chars in DNA to N's for IUPAC/BLAST compatibility


SoaplabTask.execute(..) : line 151 <SoaplabTask.java>
   ProcessorTask.runAndGenerateTemplates(..) : line 444 <ProcessorTask.java>
   ProcessorTask.doInvocationWithRetryLogic(..) : line 397 
<ProcessorTask.java>
   ProcessorTask.invokeOnce(..) : line 319 <ProcessorTask.java>
   ProcessorTask.invokeWithoutIteration(..) : line 503 <ProcessorTask.java>
   ProcessorTask.invoke(..) : line 251 <ProcessorTask.java>
   ProcessorTask.handleRun(..) : line 199 <ProcessorTask.java>
   NewState$1.run(..) : line 67 <NewState.java>
-----------------------------------------------------------------------------------
My questions are:
1) Is there another programm in emboos, what does the same like 
sreformat - until now I couldn't found some.
2) Is the error-message due to a problem in acd-file or is it a problem 
in soaplab? (At the moment the acd-file is in soaplab-directory 
(analysis-interfaces/metadata/))
3) Is there another way to tell sreformat in acd-file, that the 
output-format should be 'fasta ?

Thank you in advance

Ulrike Kaule


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