[Bioperl-l] Install help errors

snoze pa snoze.pa at gmail.com
Tue Jul 8 11:29:49 EDT 2008

I agree with you. There is no clean installation help of the
bioperl/biosql/bioperl-db available. If you read the biosql INSTALL
file and follow what is written then you will find database name
biosql. However if you read the mysql entry in same page then you will
find the name of the data base is bioseqdb. For new bee in the area it
is not only difficult but also  confusing.

I am trying a clean installation of bioperl/biosql/bioseqdb but still
there is no success. If I assume the installation is done then it
always crash on DBSOURCE entry.  The load_sequencedb.pl crashes every
time when I encounter with sequences like

LOCUS       P27912                   792 aa            linear   VRL 10-JUN-2008
DEFINITION  Genome polyprotein [Contains: Protein C (Core protein) (Capsid
            protein); prM; Peptide pr; Small envelope protein M (Matrix
            protein); Envelope protein E; Non-structural protein 1 (NS1)].
VERSION     P27912.1  GI:130422
DBSOURCE    swissprot: locus POLG_DEN1A, accession P27912;
            class: standard.
            created: Aug 1, 1992.
            sequence updated: Aug 1, 1992.
            annotation updated: Jun 10, 2008.
            xrefs: D00502.1, BAA00394.1, B32401
            xrefs (non-sequence databases): HSSP:Q88653, SMR:P27912,
            GO:0005789, InterPro:IPR011999, InterPro:IPR013754,
            InterPro:IPR001122, InterPro:IPR000069, InterPro:IPR001157,
            InterPro:IPR002535, InterPro:IPR000336, Gene3D:G3DSA:,
            Gene3D:G3DSA:, Pfam:PF01003, Pfam:PF02832, Pfam:PF00869,
            Pfam:PF01004, Pfam:PF00948, Pfam:PF01570
KEYWORDS    Capsid protein; Cleavage on pair of basic residues; Endoplasmic
            reticulum; Envelope protein; Glycoprotein; Membrane; Secreted;
            Transmembrane; Viral nucleoprotein; Virion.

It can not parse the DBSOURCE entry.  May be I am doing something
wrong but It will great if someone can try to load
P27912, entry of genbank to bioseqdb database.  Please let me know if
you can load the this genbank file.

Thank you all for your Help.
Best S

On Mon, Jul 7, 2008 at 4:20 PM, Sendu Bala <bix at sendu.me.uk> wrote:
> Hilmar Lapp wrote:
>> You may use any name for the database - is there some piece of
>> documentation that prompted you to conclude that this parameter isn't under
>> your control? There should be a command-line parameter (--namespace) in
>> load_seqdatabase.pl
> For what its worth, I was caught out by this as well. It would be a little
> more friendly if the documentation for biosql and bioperl-db were consistent
> in their suggestions for what to call the database.
> When you don't really have any idea what's going on, you at least want to be
> able to copy/paste the suggested commands/code ;)
>> On Jul 7, 2008, at 12:23 PM, snoze pa wrote:
>>> Dear Users,
>>> Thank you very much for you timely support. I highly appreciate your
>>> help in installing the software.  Meanwhile during the  installation
>>> of  bioperl-db and  loading load_seqdatabase.pl, it ask me to use the
>>> dbname "biosql" while the database created in during  bioperl
>>> installation is "bioseqdb". Shall I use bioseqdb instead of biosql as
>>> dbname.

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