[Bioperl-l] Install help errors
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')
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
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?
>> LOCUS P27912 792 aa linear VRL
>> 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:188.8.131.52,
>> Gene3D:G3DSA:184.108.40.2060, Pfam:PF01003, Pfam:PF02832,
>> Pfam:PF01004, Pfam:PF00948, Pfam:PF01570
>> KEYWORDS Capsid protein; Cleavage on pair of basic residues;
>> 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
>>>> 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
>>> 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
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
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