[Biopython] Bio.Sequencing.Ace
David WInter
winda002 at student.otago.ac.nz
Wed Jul 1 06:22:08 UTC 2009
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
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