[EMBOSS] dbiflat and entret...

[Ted Chiang]

Thanks, but that doesn't seem to work.  Here is a record of what I did.


$dbiflat -fields=taxon
Index a flat file database
      EMBL : EMBL
     SWISS : Swiss-Prot, SpTrEMBL, TrEMBLnew
        GB : Genbank, DDBJ
    REFSEQ : Refseq
Entry format [SWISS]:
Database directory [.]:
Wildcard database filename [*.dat]: *.test
Database name: swtest
Release number [0.0]:
Index date [00/00/00]:


$ls -l
-rw-r--r--           322 Mar  5 15:46 division.lkp
-rw-r--r--         12920 Mar  5 15:46 entrynam.idx
-rw-r--r--       2081272 Mar  5 12:27 sw.test
-rw-r--r--         29176 Mar  5 15:46 taxon.hit
-rw-r--r--         64411 Mar  5 15:46 taxon.trg


$showdb -database swtest
Displays information on the currently available databases
# Name        Type ID  Qry All Comment
# ====        ==== ==  === === =======
swtest        P    OK  OK  OK  Swissprot indexed by field <taxon>


$entret swtest-taxon:homo\*
Reads and writes (returns) flatfile entries
Error: USA 'swtest-taxon:homo*' query field 'taxon' not defined for
database 'swtest'
Error: Unable to read sequence 'swtest-taxon:homo*'


$entret swtest:*
Reads and writes (returns) flatfile entries
Output file [hs11_arath.entret]: all_entries

$ls -l
-rw-r--r--    1 tchiang  jamie       2081272 Mar  5 15:51 all_entries
-rw-r--r--    1 tchiang  jamie           322 Mar  5 15:46 division.lkp
-rw-r--r--    1 tchiang  jamie         12920 Mar  5 15:46 entrynam.idx
-rw-r--r--    1 tchiang  jamie       2081272 Mar  5 12:27 sw.test
-rw-r--r--    1 tchiang  jamie         29176 Mar  5 15:46 taxon.hit
-rw-r--r--    1 tchiang  jamie         64411 Mar  5 15:46 taxon.trg


----------------------------------------------


-Ted


=====================================
Ted Chiang, Analyst
Centre for Computational Biology 
Hospital for Sick Children, Toronto
416.813.7028
tchiang at bioinfo.sickkids.on.ca
=====================================


On Fri, 5 Mar 2004, [ISO-8859-1] Jérôme Laroche wrote:

> Try this:
> 
> entret swtest-taxon:homo
> 
> If you want to use wildcard, you type :
> 
> entret swtest-taxon:homo\*
> 
> 
> Jérôme
> 
> Centre de bioinformatique
> Pavillon Charles-Eugène-Marchand
> Bureau 4233d
> tél: 418-656-2131 poste 6184
> fax: 418-656-7176
> www.bioinfo.ulaval.ca
> Le 04-03-05, à 13:36, Ted Chiang a écrit :
> 
> >
> > Hi,
> >
> > I ran dbiflat on a swissprot flatfile with the option '-fields taxon' 
> > in
> > order to index the db by species.  All went well, and there were files:
> >
> > taxon.hit
> > taxon.trg
> >
> > produced in addition to the division.lkp and entrynam.idx.
> >
> > My question is how do I now retrieve only the records that are for a 
> > given
> > species, ie.
> >
> > $ entret swtest:HOMO
> > Reads and writes (returns) flatfiles entries
> > Error: Database Entry 'HOMO' not found
> > Error: Unable to read sequence 'swtest:HOMO'
> >
> >
> >
> > I know the dbiflat worked, because when I run
> >
> > $ entret swtest:*
> >
> > I get all the files in the database.
> >
> >
> > Thanks for the help.
> >
> >
> >
> > -Ted
> >
> >
> > =====================================
> > Ted Chiang, Analyst
> > Centre for Computational Biology
> > Hospital for Sick Children, Toronto
> > 416.813.7028
> > tchiang at bioinfo.sickkids.on.ca
> > =====================================
> >
> 
>