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WSCensor

Description

NB: On Tuesday 4th December 2012 the WSCensor web service was deprecated. New development should use the replacement CENSOR (REST) and/or CENSOR (SOAP) services instead.

CENSOR 1) screens sequences against a reference collection of sequence repeats, “censors” (masks) homologous portions with masking symbols and generates a report classifying all found repeats.

For more information about this tool see:

Web service registry entries:

Important

We kindly ask all users of EMBL-EBI Web Services to submit tool jobs in batches of up to 25 at a time and to not submit more until the results and processing has completed for these. This enables users as well as the service maintainers to deal more easily with local and remote network outages as well as scheduled or unscheduled downtime.

Service provision happens on a fair-share basis. Overzealous usage of a particular resource will be dealt with in accordance to the EMBL-EBI's Terms of Use.

Clients

Sample clients are provided for a number of programming languages. For details of how to use these clients, download the client and run the program without any arguments.

Language Download Requirements
C# .NET Executable: wscensor.exe; Source: wscensor.cs A .NET runtime environment. If building from source development tools are also required. See the .NET tutorial for details.
Java Executable jar: WSCensor.jar; Source: WSCensorClient.java Axis 1.4; All dependencies, including Axis 1.4 and Commons-CLI, are available in lib-1.4.zip.
Perl censor.pl SOAP::Lite
Taverna 1.x EBI_CENSOR Taverna

For further details see WSCensor Clients.

Workflows

In addition to these sample clients users have submitted workflows using these services to the myExperiment workflow repository. See workflows using the WSCensor Web Service for a list.

WSDL

Service API

runCensor(params, content)

Submits a CENSOR job to the service.

Arguments:

  • params an instance of the inputParams data structure.
  • content a list of data data structures describing the query sequence data.

Returns: a string containing the job ID (jobid).

getSupportedLibs()

Get a list of available repeat library names.

Arguments: none

Returns: a string containing a list of newline separated repeat library names.

checkStatus(jobId)

Get the status of a job.

Arguments:

  • jobid the job identifier of the job to check status of.

Returns: a string indicating the status of the job. Current values are:

  • DONE: job has finished, and the results can then be retrieved.
  • ERROR: the job failed or no results where found
  • NOT_FOUND: the job id is no longer available (job results are deleted after 24 h)
  • PENDING: the job is in a queue waiting processing
  • RUNNING: the job is currently being processed

getResults(jobid)

Get details of the result types available.

Arguments:

  • jobid the job identifier of the job to get result types for.

Returns: an array of WSFile structures describing the available result types for the job.

poll(jobid, type)

Wait until the job has finished and get the specified type of result data.

Arguments:

  • jobid the job identifier of the job to get result from.
  • type a string specifying the type of result to retrieve. See getResults(jobid) and WSFile for details of how to obtain valid values.

Returns: a base64 encoded string containing the result data. Depending on the SOAP library and programming language used the result may be returned in decoded form.

data

Structure containing the input data for the job

Attribute Type Description Default
type string Type of content being used. Valid values are: 'sequence' and 'dbfetch' required
content string A sequence entry identifier in db:id format or a formatted sequence (fasta recommended) required

For example to specify an input sequence in Java:

Data inSeq = new Data();
inSeq.setType = "sequence";
inSeq.setContent = ">TestSequence\nASAMPLESEQ\n";

inputParams

A structure containing the parameters required to run the job.

Attribute Type Description Default
lib string Repeat library to search. See getSupportedLibs(). required
mode string Stringency of search. Values are: 'rough', 'norm', 'sens' 'norm'
identity boolean Limit to identical matches. false
maskpseudo boolean Mask pseudogenes false
translate boolean Perform a translated search false
showsimple boolean Show simple repeats false
async boolean Asynchronous submission false
email string Valid email address. See Why do you need my e-mail address? required

WSFile

Structure describing a result type. Returned by the getResults(jobid) method.

Attribute Type Description
type string Symbolic name of the result type. Used with the poll(jobid, type) method.
ext string Recommended file extension for this result type.

Contact

If you have any questions or comments, or you plan to use this service as part of a course or for a high number of submissions, please contact us EMBL-EBI Support.

1) Kohany O., Gentles A.J., Hankus L. and Jurka J. (2006)
Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor.
BMC Bioinformatics 7:474
PMID: 17064419
DOI: 10.1186/1471-2105-7-474
 
services/archive/so/wscensor.txt · Last modified: 2013/04/23 16:33 by hpm
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