The CENSOR tool identifies and masks simple and complex sequence repeats found in nucleotide and protein sequences. This workflow uses the EBI's WSCensor web service (see http://www.ebi.ac.uk/Tools/webservices/services/censor) to access the tool.
Unpack the byte[] from the service into a string.
org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
Wrap the input data in a list.
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
Parameters structure for the job.
1
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
Add type information to the input data.
sequence
org.embl.ebi.escience.scuflworkers.java.XMLInputSplitter
Unpack the byte[] from the service into a string.
org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
Unpack the byte[] from the service into a string.
org.embl.ebi.escience.scuflworkers.java.ByteArrayToString
Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/censor#poll_jobid_type)
toolmap
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSCensor.wsdl
poll
Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/censor#poll_jobid_type)
toolaln
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSCensor.wsdl
poll
Submit a CENSOR analysis job (see http://www.ebi.ac.uk/Tools/webservices/services/censor#runcensor_params_content)
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSCensor.wsdl
runCensor
Check status of a WSCensor job.
Check status of a WSCensor job.
Fail if the job has not finished.
org.embl.ebi.escience.scuflworkers.java.FailIfFalse
Map the job status code into a true/false value.
if(job_status.equals("DONE")) {
is_done = "true";
} else {
is_done = "false";
}
job_status
is_done
Get the status of a submited job (see http://www.ebi.ac.uk/Tools/webservices/services/censor#checkstatus_jobid)
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSCensor.wsdl
checkStatus
EBI job identifer for a WSCensor job.
Job status code.
Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/censor#poll_jobid_type)
tooloutput
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSCensor.wsdl
poll
User e-mail address.
Input sequence. Either an actual sequence (fasta format recommended) or an entry identifier in database:identifier format (e.g. embl:AJ608703).
Library of complex repeats to search against (e.g. Fungi).
EBI job identifer for the job.
Repeat masked sequence in fasta format.
Alignments of the repeat signature sequences with the masked regions.
Table describing masked regions and identified repeats.
Completed
EBI_CENSOR_poll_job
Get_masked_sequence
Scheduled
Running
Completed
EBI_CENSOR_poll_job
Get_alignment
Scheduled
Running
Completed
EBI_CENSOR_poll_job
Get_table
Scheduled
Running