Parser for ASN.1 or GenBank?

microbe at CHOLLIAN.NET microbe at CHOLLIAN.NET
Tue Aug 24 20:28:23 EST 1999


Why not Bio-Perl?
http://bio.perl.org/


On 24 Aug 1999, Joe Ryan wrote:

> > > 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/
> > 
> > 
> 

===============================================================================
Science is the game we play with God to find out what his rules are.
-------------------------------------------------------------------------------
Doo Suk Yang
Research Scientist                              Voice: 82-42-866-2222 
LG Chemical Ltd. Research Park
Biotech Research Institute I                    FAX:   82-42-861-2566
-------------------------------------------------------------------------------
A fool hath no delight in understanding, but that his heart may discover itself.
(Proverbs 18:2)
===============================================================================





More information about the Bio-soft mailing list