[EMBOSS] 30 entries only

[Rodrigo Lopez]

Hi,

I suspect this is related to the default view used in SRS. It is 
returning the first page of results that contains 30 sequences (the 
default). To overcome this problem, the call need to have the following 
parameters:

http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?[uniprot-des:kinase]+-vn+1+-lv+100

-vn <int> is the view to use (1=names, 2=complete entries)
-lv <int> is the number of entries to be used in one go

It is important to realize that downloading a lot of entries, although 
possible, take a while and results in high loads for the servers.

The way in which I use to download a large set of entries is by 
generating a list (using -vn 1) and then using the list
with seqret in the following way:

% seqret @listname -out mykinases

and making sure this time that -vn 2 is used to retrieve complete 
entries. This requires the addition of other EMBOSS database definitions 
(one for lists and another for complete entry retrieval).

Hope this helps,

R:)


Marlena Roszczyk wrote:
> Does anybody know how to solve this problem:
> 
> I use Emboss via srswww method and everything seems to work fine until I
> ask seqret or infoseq (or any other application that searches the
> database) for many sequences  (for example typing: "seqret
> database-des:kinase"). The output consists only of 30 entries even
> though the same query on srs.ebi.ac.uk results in a 6-digit number of
> entries. What shall I do to get all the entries I want? Is it a problem
> with Emboss or rather srs policy of sending data?
> 
> 
> Just in case you would like to see my emboss.default:
> 
> DB zuniprot [ 
> methodquery: srswww
> format: swiss
> type: P
> fields: "id acc sv des key org"
> dbalias: uniprot
> url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz"
> comment: "uniprot/swiss via srswww"
> ]
> 
> DB zswiss [
> methodquery: srswww
> format: swiss
> type: P
> fields: "id acc sv des key org"
> dbalias: swissprot
> url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz"
> comment: "swissprot via srswww"
> ]
> 
> DB zembl [
> type: N
> methodquery: srswww
> format: embl
> fields: "id acc key sv des org"
> dbalias: embl
> url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz"
> comment: "embl via srswww"
> ]
> 
> 
> Thanks in advance, 
> Marlena Roszczyk
> 
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