[EMBOSS] srs/www madness

[rpg at mrc-lmb.cam.ac.uk]

So I decided to install EMBOSS on my Mac, and went the fink route (2.6.0).

I have a emboss.default file that is being read, I've put in some database
definitions, e.g. 

DB embl [ type: N 
     method: srswww format: embl release: EBI 
     dbalias: embl
     comment: "EMBL from EBI" 
     url: "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[embl-id:'%s']" 
] 

(- and in another iteration

DB embl [ type: N
        format: embl
        method: url
        dbalias: embl
        url:
"http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[embl-id:'%s']"
        comment: "EMBL.  Allegedly."
]
)

and showdb gives

# Name        Type ID  Qry All Comment
# ====        ==== ==  === === =======
tpir          P    OK  OK  OK  PIR using NBRF access for 4 files
tsw           P    OK  OK  OK  Swissprot native format with EMBL CD-ROM
index
tswnew        P    OK  OK  OK  Swissnew as 3 files in native format with
EMBL CD-ROM index
twp           P    OK  OK  OK  EMBL new in native format with EMBL CD-ROM
index
embl          N    OK  -   -   EMBL from EBI


I can construct a query and type it into a browser e.g.

http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[embl-id:'AB07888']

and get an answer.

BUT seqret does not want to play:

% seqret
Reads and writes (returns) sequences
Input sequence(s): embl:AB078884
Error: Unable to read sequence 'embl:AB078884'


So, what am I missing?  I went through the mailing list archives and found
a couple of people had similar trouble, but as far as I can tell I've
covered all the bases covered there (emboss.default is being read, for
example).  I know I don't need a proxy to get out, and as far as I can
tell the request is being made to the server, but either the correct
magic is not being uttered or the server is returning something that
seqret does not like.   David Martin kindly pointed me
at embl-alltext and that does not return anything either.  In fact, using
the alltext database with a very short string results in a very long
delay, so I suspect the problem is in retrieving the answers.  And before
you ask, ports 80 and 427 are open on my machine.

Thanks for any help,

Richard


-- 
Richard P. Grant               http://www2.mrc-lmb.cam.ac.uk/personal/rpg/
MRC-LMB, Cambridge, UK      
PGP:  0x5F9559B1               weblog: http://www.rg-d.com/BioLOG/