[Biopython] Bio.Sequencing.Ace

[Fungazid]

David hi,

Many many thanks for the diagram.
I'm not sure I understand the differences between contig.af[readn].padded_start,  and contig.bs[readn].padded_start, and other unknown parameters. I'll try to compare to the Ace format

Avi

--- On Mon, 6/29/09, Peter <biopython at maubp.freeserve.co.uk> wrote:

> From: Peter <biopython at maubp.freeserve.co.uk>
> Subject: Re: [Biopython] Bio.Sequencing.Ace
> To: "David Winter" <winda002 at student.otago.ac.nz>
> Cc: biopython at lists.open-bio.org
> Date: Monday, June 29, 2009, 10:26 AM
> On Mon, Jun 29, 2009 at 6:19 AM,
> David
> Winter<winda002 at student.otago.ac.nz>
> wrote:
> > Quoting Peter <biopython at maubp.freeserve.co.uk>:
> >>
> >> There top level properties are simple enough - but
> I find drilling
> >> down into the reads a bit more tricky. In general
> the Ace parser is
> >> a bit non-obvious without knowing the Ace format.
> Having some
> >> __str__ and __repr__ methods defined on the
> objects returned
> >> would be very nice - I may get time to work on
> this later this year.
> >> Anyone else interested in this drop us an email.
> >>
> >> Peter
> >
> > I had a scrawled diagram of the contig class next to
> me when I was using
> > it more frequently - it was easy enough to reproduce
> digitally
> >
> > http://biopython.org/wiki/Ace_contig_class
> >
> > Hopefully it helps make sese of where all the data is.
> I've added a couple
> > of very brief examples there for now - will expand it
> when I get a chance.
> >
> > David
> 
> This could get turned in docstring/doctest for the Ace
> parser :)
> 
> Peter
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