Parser for ASN.1 or GenBank?

Joe Ryan jfryan at NHGRI.NIH.GOV
Tue Aug 24 13:43:08 EST 1999


> > I'm looking for some free software to parse GenBank flat file format or
> > better ASN.1 format. 

>   perl -MCPAN install Bundle::Convert::BER

I have looked at Bundle::Convert::BER and I think it only converts
ASN.1 TO and FROM its binary format.  I had heard that there was a 
Perl ASN.1 module in the works from NCBI within the SEALS project

    http://www.ncbi.nlm.nih.gov/Walker/SEALS/

Haven't heard of a finished product though.  Please post if you have 
good news.

Joe
--
Joseph Ryan
Programmer
National Human Genome Research
 

On Tue, Aug 24, 1999 at 01:48:16PM -0500, Jonathan Epstein wrote:
> Try:
>   perl -MCPAN install Bundle::Convert::BER
> 
> Haven't tried it myself.  Please let me know if you have any success.
> 
> - Jonathan
> 
> 
> Arne Mueller wrote:
> 
> > Hi All,
> >
> > I'm looking for some free software to parse GenBank flat file format or
> > better ASN.1 format. Is there any perl or better python module available
> > to read in an ASN.1 file and to presnet all the information in a
> > datastructure (hashes, lists, objects whatever ...)?
> >
> > I'm interested in genomic ORFs but flat FASTA amino acid files do not
> > provide enough information for my purpose, also I'd like (have) to
> > automize most of the dataprocessing. I know there must be a parser
> > (written in C) included in the NCBI toolkit but I'd like to have
> > something written in perl or python.
> >
> >         Any suggestions,
> >         Thanks alot,
> >
> >         Arne
> >
> > --
> > Arne Mueller
> > Biomolecular Modelling Laboratory
> > Imperial Cancer Research Fund
> > 44 Lincoln's Inn Fields
> > London WC2A 3PX, U.K.
> > phone : +44-(0)171 2693405      | fax :+44-(0)171-269-3534
> > email : a.mueller at icrf.icnet.uk | http://www.icnet.uk/bmm/
> 
> 




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