[Bioperl-l] acquiring a local refseq + index

Chris Fields cjfields at uiuc.edu
Sun Dec 31 14:36:47 EST 2006


As a followup, I have committed the fix Erik had in Bugzilla.  I  
don't know if this helps with the below issue Erik describes (they  
sound unrelated).

chris

On Dec 30, 2006, at 8:33 PM, Chris Fields wrote:

> Agree with Hilmar, in that we need examples.  If you are referring to
> your submitted bug:
>
> http://bugzilla.open-bio.org/show_bug.cgi?id=2167
>
> we could add this in as long as it passes (I'll try giving it a
> workout with my local bacterial seqs tonight or tomorrow).  However,
> in the not-too-distant future your patch would likely be rendered
> obsolete, as any parsing in Bio::SeqIO modules pertaining to
> Bio::Species-related matters will be deprecated in favor of simple
> parsing (more foolproof, less uncertainty) and Bio::Taxon (which has
> optional db lookups using NCBI Taxonomy).  Bio::Species and anything
> related to it are considered marked for deprecation.  Fair warning...
>
> chris
>
> On Dec 30, 2006, at 7:48 PM, Hilmar Lapp wrote:
>
>> Can you send examples and the resulting error messages? Also, I'm
>> assuming you running the 1.5.2 release of Bioperl; if not that's what
>> I would try first.
>>
>> 	-hilmar
>>
>> On Dec 30, 2006, at 7:05 PM, Erik wrote:
>>
>>> Hi all,
>>>
>>> I downloaded the refseq files (.gbff) and want to index the lot with
>>> Bio::DB::Flat.
>>>
>>> It turns out that there are many cases where the SOURCE and
>>> ORGANISM lines
>>> are messed up, sometimes to a degree where the indexing fails on a
>>> Bio::SeqIO::genbank error.
>>>
>>> I'd like to change Bio::SeqIO::genbank to let this parsing go at
>>> least so
>>> far as to make the indexing of the refseq files possible, and
>>> hopefully
>>> improving the taxonomic output ($seq->species->binomial is often
>>> mutilated
>>> at the moment).
>>>
>>> Is it still worthwhile to change parsing modules like
>>> Bio::SeqIO::genbank?
>>>  Is anyone already working on a rewrite? Because if this is the
>>> case I may
>>> be better off writing my own indexing scheme?
>>>
>>> Below is (outline of) my indexing program, which uses
>>> Bio::DB::Flat::DBD.
>>> If anyone knows of a better way to get a locally searchable refseq
>>> flat
>>> file index, I would be very interested.
>>>
>>> Thanks for your help,
>>>
>>> Erikjan
>>>
>>>
>>> -------------
>>> use Bio::DB::Flat;
>>>
>>> my $refseq_dir = '/data/ftp.ncbi.nih.gov/refseq/release/complete';
>>> my $db=Bio::DB::Flat->new(
>>>    -directory  => $refseq_dir,
>>>    -dbname     => 'refseq',
>>>    -format     => 'genbank',
>>>    -index      => 'bdb',
>>>    -write_flag => 1,
>>> );
>>> my @files = getfiles($refseq_dir);
>>> for my $f (@files) {
>>>         db->build_index($f);
>>> }
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> 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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>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
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> Bioperl-l at lists.open-bio.org
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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