[Bioperl-l] ASN.1 and BioPerl ?

Pierre Rioux pierre_rioux at yahoo.com
Thu Feb 10 18:28:03 EST 2005

Hello BioPerl users and coders,

I haven't seen much (or any) support for parsing ASN.1
documents in BioPerl; I assume it's either because the
community doesn't need it much, or there are already some
Perl ASN.1 libraries available elsewhere (but I've not
looked very hard, I have to admit). There's some code I
could contribute about that, but before I do anything
I'd like to know what other developers think. The
code I have is basically a pure Perl text parser that
can read ASN.1 text (in .prt format, like NCBI publishes)
and builds a data structure (a hierarchy of hash tables)
to represent it. The object model is quite primitive right
now, but eventually it could be extended into a nice API.
My questions are:

    1) Would this be useful to anyone?
    2) If so, where (roughly) in the BioPerl code
       tree would such a thing go?
    3) Any other comments or recommendations welcome.

I am using this library in my applications to read the file
'gc.prt' as published regularly by NCBI; this file describes
a set of genetic codes, and NCBI updates it from time to time.
In BioPerl, I noticed that the same information is hardcoded
in the class Bio::Tootls::CodonTable, which means that whenever
NCBI updates the gc.prt file the bioperl class also needs
to be modified. An alternative I suggest is that if gc.prt
can be found on the local system (using the NCBI environment
variable) then Bio::Tootls::CodonTable could read it and keep up
to date automatically (otherwise, it could keep using the
hardcoded codon tables it currently has).

I am sure other parts of BioPerl could probably benefit
a little from being able to read NCBI's ASN.1 data files,
unless there's some kind of philosophical opposition to
the idea?

I'm willing to do all the work, AND design a proper and
clean OO interface for the code, provided the answer to
question #1 above is 'yes'...

Pierre Rioux

pierre_rioux {round symbol} yahoo {smallest char} com

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