[Biopython-dev] rebase

[Jeffrey Chang]

>   An alternative to regular expressions, that would work with rebase,
> would be read_and_calls with an lstrip?  The only reason for a regular
> expression is lots of white space before every field.  Except for the
> recognition site.

Well, I've already added in support for regular expressions, so that's an
option now.  If you need to lstrip the string before read_and_call, you
can write a wrapper function that does that.


>   The recognition site may deserve a class of its own, with cutting
> sites, methyl sites, overhange, etc.?

Probably the correct thing to do is to have a SeqFeature class (like
bioperl) to annotate locations in a sequence.


>   Some of the fields in rebase, like enzyme number and source, stay
> the same but some vary or appear only in a few files.  Should I use an
> on-the fly dictionary for the field that only appear in a few files?

What I've been doing is creating classes that can hold every field, and
initializing fields to a reasonable default value.  It seems friendlier
than to require the client to check for the existence in a dictionary.

Jeff