[Bioperl-l] Install help errors

[Hilmar Lapp]

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?

	-hilmar

>
>
> 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)].
> 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: 
> 2.60.98.10,
>            Gene3D:G3DSA:2.60.40.350, 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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-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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