[Bioperl-l] Install help errors

snoze pa snoze.pa at gmail.com
Tue Jul 8 15:00:05 EDT 2008


 I really had tough time dealing with bioperl-db and then loading the
sequences. As we discussed earlier(long back) that DBSOURCE is
crashing every time so I removed the gen bank installation. Currently
I am loading uniprot_sprot.dat file which I downloaded from swissprot
site. Based on the guideline in bio-perl website I am able to manage
the bioperl/biosql/bioperl-db/ installation and then try to load the
swissprot file,  uniprot_sprot.dat,  officially uniprot_sprot.dat.gz
latest release july 7th 2008. It always give me a warning

"insert in Bio::DB::BioSQL::SeqFeatureAdaptor (driver) failed,"

which I think okie as long the loading seq is fine. I can see it from
SELECT * FROM biosequence

but now it also crashes after loading 214 sequence from uniprot_sprot.dat file.

Here is the error message

Could not store P21215:
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: The supplied lineage does not start near 'Clostridium sp.' (I was
supplied 'sp. ATCC29733 | Clostridium | Clostridiaceae | Clostridiales
| Clostridia |Firmicutes | Bacteria')
STACK: Error::throw
STACK: Bio::Root::Root::throw
STACK: Bio::Species::classification
STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
STACK: Bio::DB::Persistent::PersistentObject::create
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
STACK: Bio::DB::Persistent::PersistentObject::store
STACK: /usr/local/bioperl-db/scripts/biosql/load_seqdatabase.pl:630

 at /usr/local/bioperl-db/scripts/biosql/load_seqdatabase.pl line 643

If I remove this entry from uniprot_sprot.dat file then it gives
similar error in other IDs

Any Idea,

 Thanks a lot for your reply and help

On Tue, Jul 8, 2008 at 1:35 PM, Hilmar Lapp <hlapp at gmx.net> wrote:
> 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:,
>>           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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>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> --
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================

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