[Bioperl-l] Bio::DB::GenPept , Bio::SeqIO::genbank

Hilmar Lapp hlapp@gmx.net
Sun, 13 Aug 2000 23:16:31 +0200

I noticed that Bio::DB::GenPept had the same limitation as GenBank,
namely retrieving sequences only in Fasta format. I've added now the same
capability as for GenBank, and default format is now also Genbank instead
of Fasta.

BTW is seems as if GenBank.pm and GenPept.pm in Bio/DB are almost
identical apart from the database specification for NCBI (db=n versus
db=p). It may be advantageous from a maintenance point of view to
introduce a method db_spec() to GenBank.pm and make GenPept.pm inherit
from GenBank.pm, with the only method (overridden) being db_spec().
Anything that would be broken by this?

Interestingly, this revealed that the Genbank parser was not capable of
dealing with protein (i.e. GenPept) sequences at various places. It's now

(All changes only in the main trunk.)

Hilmar Lapp                                email: hlapp@gmx.net
NFI Vienna, IFD/Bioinformatics             phone: +43 1 86634 631
A-1235 Vienna                                fax: +43 1 86634 727