swissprot

[Joerg Schaber]

Hi,

can't load the SWISSPROT- bacteria database 
(ftp://ftp.ebi.ac.uk/pub/databases/swissprot/special_selections/bacteria.seq) 
into EMBOSS. I think EMBOSS is running well because I have no problem 
accessing the test-databases (see showdb below). However, I think 
somehow seqret is using the wrong division file but the PATH-setting 
seem to be correct.

greetings,

joerg
 

 > dbiflat
Index a flat file database
      EMBL : EMBL
     SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew
        GB : Genbank, DDBJ
    REFSEQ : Refseq
Entry format [SWISS]: SWISS
Database directory [.]:
Wildcard database filename [*.dat]: *.seq
Database name: swissbac
Release number [0.0]: 1.0
Index date [00/00/00]: 09/10/02

 > ll
insgesamt 132100
 950883 drwxrwxr-x    2 root     users        4096 Okt  9 18:50 .
 623533 drwxrwxr-x    5 jos      jos          4096 Okt  9 17:50 ..
 950889 -rw-r--r--    1 jos      jos        189028 Okt  9 18:50 acnum.hit
 950888 -rw-r--r--    1 jos      jos        660456 Okt  9 18:50 acnum.trg
 623548 -rw-r--r--    1 jos      jos      133412511 Okt  9 18:25 
bacteria.seq
 950886 -rw-r--r--    1 jos      jos           322 Okt  9 18:50 division.lkp
 950887 -rw-r--r--    1 jos      jos        836840 Okt  9 18:50 entrynam.idx

 > showdb
Displays information on the currently available databases
# Name        Type ID  Qry All Comment
# ====        ==== ==  === === =======
swissbac      P    OK  OK  OK  SWISSPROT sequences of procaryotes 9/10/02
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
buch          N    OK  OK  OK  Buchnera database in DDBJ Format
fbuch         N    OK  OK  OK  Buchnera database in FASTA Format
tembl         N    OK  OK  OK  EMBL in native format with EMBL CD-ROM index
tgb           N    OK  -   -   Genbank IDs
tgenbank      N    OK  OK  OK  GenBank in native format with EMBL CD-ROM 
index

 > head bacteria.seq
ID   120K_RICRI     STANDARD;      PRT;  1300 AA.
AC   P14914;
--snipp

--snipp

 > seqret swissbac:120K_RICRI
Reads and writes (returns) sequences
Warning: Cannot open division file '<null>' for database 'swissbac'
Warning: seqCdQry failed
Error: Unable to read sequence 'swissbac:120K_RICRI'
 >

-- 
----------------------------------------------------------
Joerg Schaber
Instituto Cavanilles de Biodiversidad y Genetica Evolutiva
Universidad de Valencia               Tel.: ++34 96 398 3647
A.C. 22085                            Fax.: ++34 96 398 3670
46071 Valencia, España                email : jos at uv.es