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

[Ulrike Kaule]

Dear Peter,

thank you very much for your help. I installed emboss locally now and I 
can specify output 'listfile' for digest. But the following programm 
(pepstats or iep) does not accept that as input (in taverna). I get the 
error message "Unknown input format 'listfile' ". Then I tried to 
specify the input format using the sformat-qualifier, but this doesn't 
work. My question is: is there any possibility to specify the right 
input format in the acd-file. Or do I have to use an other 
input-qualifier to tell pepstats the format?

Thank you in advance

Ulrike Kaule




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



Hello,

I'm a new user to emboss.
Within a Taverna-Workflow I want to digest a protein-sequence first with 
the emboss-program "digest" and to use the output of "digest" - the 
seqtable with the fragments - as an input for further sequence-analysis 
programs. So the resulting fragments should be analysed by pepstats or 
iep. But I have problems with the connection of these programs, because 
the output of "digest" is not accepted by the other programs as input. I 
thougth to solve this problem with using "seqret" between "digest" and 
"pepstats", but this doesn't work.
Is there any solution to extract the protein-fragments produced by 
"digest" and to use them as input for other programs?

Thank you in advance

Ulrike