[EMBOSS] retrieving entries from public database

[Peter Rice]

Dear Hanquan,

On 08/08/2010 23:49, Hanquan Liang wrote:
> Georgios,
>
> Thanks for your reply.
>
> I added your lines into the emboss.default.  It works.
> But not for my own lines (I tried before subscribing this mailing list
> for help) like:

Ah, the new user's worst fear. More than one problem.

> DB embl [  type: N method: srswww format: embl release: "EBI"
>    url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?%s"
>    comment: "EMBL from the EBI" ]

The "?%s" at the end of the URL is the problem. "%s" is used for method: 
url to include the sequence ID in the search. Srswww and othe rmethods 
know how to build specific SRS webserver queries.

> DB swissprot [  type: P method: srswww format: swiss release: "EBI"
>    url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz";
>    comment: "SWISSPROT from the EBI" ]

This time the problem is the stray ';' at tghe end of the url: ... this 
stops EMBOSS finding the trailing '"' and so tghe comment has been 
included in the URL.

> DB sw [  type: P method: srswww format: swiss release: "EBI"
>    url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz";
>    dbalias: "SWISSPROT"
>    comment: "SWISSPROT from the EBI" ]

That ';' again ... well done for gettig the dbalias right. dbalias: is 
required when the database name you choose is not the same as the name 
on the SRS server (embl and swissprot both exist on the server)

> DB uniprot [  type: P method: srswww format: swiss release: "EBI"
>    url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz";
>    comment: "UNIPROT from the EBI" ]

The ';' again. Uniprot exists so again no dbalias is needed.


We will try to improve our error messages in these cases so you can see 
more detail on why the query fails. We should be able to find some SRS 
error message where the entries are not found, and return more detail 
where the query fails completely.

Hope this helps, and please do ask again if you have more questions. The 
direct address for the emboss team is emboss-bug at emboss.open-bio.org

Peter Rice