[Biopython] Bio.Sequencing.Ace

[David WInter]

Fungazid wrote:
> 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
>   
Hi again Avi,

I took me a while to get to grips with the difference, the 'bs' list is 
a mapping of the contig's consensus to the particular read that was used 
to as the 'base segment' in that region. If you have a monospaced font 
in your email client this might help:

             consensus             

|===================================|              
+---read3---x
             +---read5--x
                         +--read1---x


(which would give a contig.bs list with 3 bs instances)

I'm not sure that this is particularly important information for a 454 assembly ;) 

I've updated the examples on the wiki page a little, if you find anything else that you think should 
be there feel free to add to it


Cheers,
David