[EMBOSS] output of program "digest" as input for program "pepstats" ?

[Peter Rice]

Guy Bottu wrote:

> 	Dear Ulrike,
> 
> You can ask digest for a "Report Format" of type "List File", which you 
> can give as input to pepstats or iep (the peptides will be analyzed as 
> individual sequences and the results given the one aftert the other, they 
> are not merged).
> 
> I have no experience with Taverna and hence cannot tell you exactly how 
> to. I know that at the command line you would have to :
> digest mysequence -rformat=listfile -outfile=myreport
> iep list::myreport

In taverna, using the EBI SoapLab services to run EMBOSS you will not be able 
to use the -rformat qualifier - that will be added in a future release of 
SoapLab later this year. The current SoapLab has the EMBOSS qualifiers, but is 
missing some "associated qualifiers" including -rformat for reports and 
-aformat fopr alignments.

If you have your own soaplab server running, one solution that has been tried 
is to change the rformat value in the digest.acd file to "listfile" - digest 
will then always produce the listfile version of the output.

Hope that helps

Peter