[Bioperl-l] Install help errors
hlapp at gmx.net
Tue Jul 8 14:35:38 EDT 2008
On Jul 8, 2008, at 11:29 AM, snoze pa wrote:
> 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.
That's useful feedback. In fact it sounds like there is a
documentation bug (inconsistent documentation is a bug, IMHO). Would
you mind filing a bug report (BioSQL has its own queue now)?
> 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
Could you post the error message? The entry you quote in reality is a
Swissprot (or Uniprot) entry sucked up into GenPept, so it's possible
that it's the BioPerl genbank parser that's failing, not bioperl-db. I
recall that we've had issues with these records before, though I don't
recall what the actual cause was, nor the recommended fix. Is there a
requirement that prevents you from loading these entries in their
native Uniprot format?
> LOCUS P27912 792 aa linear VRL
> DEFINITION Genome polyprotein [Contains: Protein C (Core protein)
> protein); prM; Peptide pr; Small envelope protein M (Matrix
> protein); Envelope protein E; Non-structural protein 1
> ACCESSION P27912
> 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:22.214.171.1240, Pfam:PF01003, Pfam:PF02832,
> Pfam:PF01004, Pfam:PF00948, Pfam:PF01570
> KEYWORDS Capsid protein; Cleavage on pair of basic residues;
> reticulum; Envelope protein; Glycoprotein; Membrane;
> 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
>> For what its worth, I was caught out by this as well. It would be a
>> more friendly if the documentation for biosql and bioperl-db were
>> 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
>>>> help in installing the software. Meanwhile during the
>>>> of bioperl-db and loading load_seqdatabase.pl, it ask me to use
>>>> dbname "biosql" while the database created in during bioperl
>>>> installation is "bioseqdb". Shall I use bioseqdb instead of
>>>> biosql as
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: Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
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