[BioPython] Parsing ACE files

[Peter]

On Fri, Nov 7, 2008 at 4:26 PM, dr goettel <biopythonlist at gmail.com> wrote:
> I don't know why but I cannot search in the mailing list using the search
> link (http://search.open-bio.org/).

That's odd - it used to work OK...

> I've seen in the documentation that the Bio.SeqIO can read ace files and
> uses Bio.Sequencing.Ace.

Yes.  Depending on what information you want from the ACE files, you
might be better off using Bio.Sequencing.Ace directly.  Using
Bio.SeqIO may not expose all the details you want (I'd have to check
the details - its not fresh in my mind).

> After reading module Bio.SeqIO.AceIO it remains unclear for me how to use
> it. Could anybody tell me how to parse ACE files? is there a tutorial or
> example to look at?

You would typically use the Bio.SeqIO.parse() function (which will
call Bio.SeqIO.AceIO internally).  See Chapter 4 of the tutorial on
Bio.SeqIO,
http://biopython.org/DIST/docs/tutorial/Tutorial.html
http://biopython.org/DIST/docs/tutorial/Tutorial.pdf

Or the Bio.SeqIO wiki page,
http://biopython.org/wiki/SeqIO

Peter