[BioPython] Parsing of phd file names in Ace

[Brad Chapman]

Hi Andy;

[Bio.Sequences.Ace problems]
> Something else I noticed.
> 
> If you make an ace file with phd2Ace.perl in the consed package, the
> resulting ace file breaks the parser

Frank just sent me a new version of the Ace parser, which should
work on a wider variety of these Ace files. Here's Frank's mail:

Frank:
> here's the new one. I tested if a variety of contigs, it seems to work
> fine, and these evil rt tags can now be anywhere between the reads. Andy
> pointed out some bug with leading/trailing spaces which I also fixed.

I just checked this into CVS so hopefully it should be available in
anonymous CVS in a bit. Let us know if this fixes your parsing
problems. Thanks for the feedback.

> Also, has someone implimented a python API for Primer3 ? Something that will
> execute and parse the results?

Yup, I did do some work on this. It's located in Bio.Emboss (it
works with the eprimer3 executable from EMBOSS). The parser is not
ideal (I doubt if it will work for all cases) but it does something,
which is nice :-).

There is some documentation about how to use it in this talk:

http://biopython.org/docs/presentations/scripting.pdf

Hope this helps!
Brad