[EMBOSS] output of program "digest" as input for program "pepstats" ?
Peter Rice
pmr at ebi.ac.uk
Fri Sep 2 14:58:25 UTC 2005
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
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