[Bioperl-l] Writing genbank files

[Ewan Birney]

David -

you can get control of how to write the GenBank line by using the "id
generation function" hook inside of the bioperl parser. You need to pass
in a function that generates the correct string from the bioperl sequence
object. This gives complete control of the LOCUS line. Ensembl has to
output strictly correct EMBL and GenBank so all the necessary hooks are
there for this.


Probably in general we should output with the DATE line by default. The
only problem is that there is an obvious thing to use when we are coming
from a format that doesn't have a date.


I've put this in as a bug report and hope to fix it for 1.0



BTW - Andrew's suggestion of writing out the header portion is almost
certainly a bad idea. A format definition is a mixture of the precise
definition and its common usage. Also the old adage rings true "be
permissive in what you accept but strict in what you output".



e.