[Bioperl-l] GenBank ASN.1 SeqIO parser

Ryan Golhar golharam at umdnj.edu
Thu Feb 7 18:59:52 EST 2008


That's what I thought too.  However, I'm getting errors with a parser.

I found Bio::ASN1::EntrezGene online and am using that module outside of 
Bioperl as it works well for what I'm doing.

I've already changed my code and don't want to deal with tracking down 
the errors I had with BioPerl (I've already spend enough time on this) 
but they were easy enough to reproduce.

Ryan


Chris Fields wrote:
> Bio::SeqIO::entrezgene should do this.  Any dbxrefs (including GO IDs) 
> should be stored in the annotation collection, but I'm not sure how it 
> is parsed; you'll have to test it out.
> 
> I agree with Jason; ASN.1 isn't a very friendly format.  Don't know why 
> NCBI sticks with it, but I'm sure they have their reasons (I think this 
> may have been discussed before on the list).
> 
> chris
> 
> On Feb 7, 2008, at 5:04 PM, Ryan Golhar wrote:
> 
>> Let me re-phrase then - I want to parse an entry such as this:
>>
>> http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=11258 
>>
>>
>> to retrieve the text of the Gene Ontology entries and the associated 
>> GO IDs for those entries.  Is this possible with BioPerl?  If so, how 
>> can I do this with BioPerl?
>>
>> Ryan
>>
>>
>>
>> Jason Stajich wrote:
>>> ugh - why parse ASN.1? NCBI provides converter application in the 
>>> ncbi toolkit to many formats : genbank, XML, etc.
>>> On Feb 7, 2008, at 1:48 PM, Chris Fields wrote:
>>>> No.  The only ASN.1 parser is entrezgene.  You could probably try 
>>>> building one using the same ASN.1 parser that SeqIO::entrezgene uses 
>>>> (Bio::ASN1::EntrezGene); it includes a parser for sequences:
>>>>
>>>> http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/Bio/ASN1/Sequence.pm 
>>>>
>>>>
>>>> chris
>>>>
>>>> On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote:
>>>>
>>>>> Is there a SeqIO parser module for GenBank ASN.1 format?  I thought 
>>>>> it would have been genbank or entrezgene, but neither of them work.
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
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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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> 
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
> 
> 
> 
> 
> 



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