[BioPython] Parsing ACE files

[Peter]

On Fri, Nov 7, 2008 at 5:02 PM, dr goettel <biopythonlist at gmail.com> wrote:
> Thank you!
>
>> Yes.  Depending on what information you want from the ACE files, you
>> might be better off using Bio.Sequencing.Ace directly.
>
> Any example or tutorial for this solution?
>

The bad news is I don't think this is covered in the Biopython
Tutorial.  However, there are some quite detailed built-in docstrings.

>From within python, you can access the documentation via the python
help function:
>>> from Bio.Sequencing import Ace
>>> help(Ace)
...

These are also available online on our API pages (for the current release):
http://biopython.org/DIST/docs/api/
http://biopython.org/DIST/docs/api/Bio.Sequencing.Ace-module.html

However, you'll see this is quite a low level parser and it helps to
know what the two letter line types mean (consult the ACE
documentation).

>>  Using Bio.SeqIO may not expose all the details you want (I'd have to check
>> the details - its not fresh in my mind).
>
> You are right, it's not all the information I need.

I wrote the Bio.SeqIO wrapper for the ACE parser, so it might be
possible to extend this to capture more information.  What in
particular do you want to extract?

> Cheers!

Sure!

By the way - make sure you are using Biopython 1.48 or later, as
Bio.Sequencing.Ace was switched to a more modern python iterator style
then.

Peter