Antwort: [EMBOSS] EMBOSS and SRS

[Stefanie Lager]

Thank you David,

I think I can solve it, calling an external script as you suggests.

Stefanie

> Stefanie,
> 
> in emboss.default I have:
> ##################################################
> DB gb [ type: N method: app format: genbank
> app: "/usr/local/bin/cgdb_getz_n %s"
> comment: "GenBank, RefSeq, RefSeqP" ]
> ##################################################
> And the script contains:
> ###################################################
> #!/usr/local/bin/perl
> use LWP::UserAgent;
> use URI::URL;
> 
> $id=$ARGV[0];
> $id=~s/\.\d+//;
> $url=new
> URI::URL("http://bes270.schering.de:7777/srs7bin/cgi-bin/wgetz?
> -ascii+-
> e+[{GENBANK%20REFSEQ%20REFSEQP}-id:$id]|[{GENBANK%20REFSEQ%20REFSE
> QP} -acc:$id]"); $req=new HTTP::Request(GET,$url);
> $ua=new LWP::UserAgent;
> $resp=$ua->request($req);
> $seq=$resp->content;
> print $seq;
> ###########################################################
> 
> Hope this helps.
> 
> Cheers,
> David.
> 
> 
> 
> 
> "Stefanie Lager"
> <stefanielager at fa
> stmail.ca>               An:     emboss at embnet.org
> Gesendet von:            Kopie:
> owner-emboss at hgmp        Thema:  [EMBOSS] EMBOSS and SRS
> .mrc.ac.uk
> 
> 
> 03.09.03 18:09
> 
> 
> 
> 
> 
> 
> I have some problem to set up SRS indexed databases and to make
> them available in EMBOSS. It's OK when I run EMBOSS on commandline
> and the user have SRS set up so getz is in the users path. But for
> users who don't have SRS set up or through web-interface I get
> problems. In the (fairly) new SRS 7.1.1 I have to have SRS setup
> to run getz, previously I only had to have the full path to getz
> to run it. Is it possible to have the SRS setup in the
> emboss.default file, so SRS is set up automatically?
> 
> Stefanie
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