In article <2jjb6g$ju1 at threed.uchc.edu>, richk at mbcg.uchc.edu writes:
...
|> $ FETCH
...
|> FETCH what sequence(s) ? sw:mbp_rat
|>|> Mbp_Rat.Sw
|> *** Sequence "Mbp_Rat.Sw" could not be read or is not in GCG format!
|>...
This might be that you find the entry correctly in the indices (otherwise
it wouldn't come back with the name Mbp_Rat.Sw but failed to extract
it properly. Check
$ show log swissprotdir
and then
$ dir/date swissprotdir:sw*.seq
$ dir/date swissprotdir:sw*.names
The idea is that .names and .offset files are used for retrieving
the entry from the database. The dates of the names and offset
files should be _LATER_ than the .seq and ref files as the indexing
should have happened after the seq and ref file creation (see
below). If the indices are copied from other computers, this
argument might be weak. Then, you could try swissprot:calm_human
(which is an entry in swissprot as well) in order to check whether
swissprot is operable at your site at all.
'yogi > dir/date swissprotdir:sw*.seq
Directory BIOBIG:[BIOZEN.DATA.][GCGSWISSPROT]
SWISS.SEQ;1 12-NOV-1993 18:25:22.41
Total of 1 file.
'yogi > dir/date swissprotdir:sw*.names
Directory BIOBIG:[BIOZEN.DATA.][GCGSWISSPROT]
SWISS.NAMES;3 12-NOV-1993 18:28:22.68
Total of 1 file.
'yogi > dir/date swissprotdir:sw*.offset
Directory BIOBIG:[BIOZEN.DATA.][GCGSWISSPROT]
SWISS.OFFSET;3 12-NOV-1993 18:28:22.45
Total of 1 file.
--------
Forgive me to post the advertismenet in own matters here;
but we have installed the Hierarchical Access System for
Sequence Libraries in Europe (HASSLE) which is a (free) software
package for various tools. If there is a fault at a given database,
or an entry is not found, our fetch behaves as the following
(I have simulated a failure in swissprot due to bad indexing):
'yogi > fetch sw:mbp_rat
FETCH copies GCG sequences or data files from the GCG database
into your directory or displays them on your terminal screen.
... Trying Network ...Support data file is: "Support.Dat".
Checking resources ...
....found database SW at YETI.EMBNET.UNIBAS.CH ..............
HFETCH HASSLE frontend R.Doelz Version 30/08/93 B4-0-0
--- HASSLE version B4-1-0pre4 (94/01/30) (C) Biocomputing Basel 1992-1994
NOTE: YETI.EMBNET.UNIBAS.CH is used as provider.
NOTE: Listening for reply from YETI.EMBNET.UNIBAS.CH on port 15020 for result
NOTE: Answer from host yeti.embnet.unibas.ch [131.152.8.3], port 2285 ...Resultfor service HFETCH
NOTE: Received file fetch.log
NOTE: Received file mbp_rat.sw
NOTE: JOB 15020 completed
This way, we can use a different computer and still get the
correct answers even if the local one is temporarily out of data.
Regards
Reinhard
===============
DISCLAIMER
Note that the software mentioned resembles Computer Program(s) which
require a license in order to be run unless stated otherwise in a state-
ment codistributed with the software. The use of the program(s) was men-
tioned within a specific problem or example and must not be used to con-
clude that other software products cannot possibly do a similar job.
--
+---------------------------+-------------------------------------------+
| Dr. Reinhard Doelz | Tel. x41 61 2672247 Fax x41 61 2672078 |
| Biocomputing | electronic Mail doelz at urz.unibas.ch |
|Biozentrum der Universitaet+-------------------------------------------+
| Klingelbergstrasse 70 | EMBnet embnet at comp.bioz.unibas.ch |
|CH 4056 Basel SWITZERLAND | Switzerland gopher.embnet.unibas.ch |
+---------------------------+------------- http://beta.embnet.unibas.ch/
