[Biopython] Bio.Sequencing.Ace

[David Winter]

Hi Avi,

It's Sunday where I am so I'll give you a quick answer that might point
you in the right direction now and provide some more details if I get a
chance tomorrow ;)

Quoting Fungazid <fungazid at yahoo.com>:


> I am trying to parse a large Ace file produced by newbler on 454 cDNAs
> assemly. I followed the Bio.Sequencing.Ace cookbook here:
> http://biopython.org/wiki/ACE_contig_to_alignment
> and indeed, I can now fetch several properties of my contigs (alignment
> of reads to consensus, contigs name, reads name).

Good.

> Yet,I would like to know if and how to perform the following tasks:
> * retrieving the quality of specific nucleotides in the read.
> * getting the consensus sequence.

The cookbook example isn't meant to be complete documentation for the Ace
module - just an example of something you might want to do with it. At the
moment there is no tutorial chapter on the module but you can read the doc
strings here:

http://www.biopython.org/DIST/docs/api/Bio.Sequencing.Ace-pysrc.html

Most of the tags you want to play with are in the Contig and Reads classes
in that (and have the same names as the ACE format specification

http://bozeman.mbt.washington.edu/consed/distributions/README.14.0.txt

> * fetching specific contigs with no need to visit all contigs.

Sounds like fun... it's possible to dump a whole ACE file into memory with
ace.read(...) but for big files with millions of reads that's likely to be
a 'sub-optimal' solution. There has been a discussion about indexing large
sequencing files here which may (or may not, I didn't follow the thread
very closely ;) ) be useful:

http://lists.open-bio.org/pipermail/biopython/2009-June/thread.html#5263

> * are there other important undocumented tasks ?
>

Almost certainly. I'm sure the devs would like to hear how you get on with
the module. (you might also consider contributing some documentation as
you learn how to use it)

Hope that sets you on the right path,

Cheers,
David