[Bioperl-l] GenBank ASN.1 SeqIO parser

Chris Fields cjfields at uiuc.edu
Thu Feb 7 20:32:18 EST 2008


It's possible that has been fixed in bioperl-live.  However, just in  
case, if you are getting errors could you file a bug report along with  
the relevant code demonstrating it?

chris

On Feb 7, 2008, at 5:59 PM, Ryan Golhar wrote:

> 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
>>>>>> 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
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
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>>>> _______________________________________________
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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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