Why program yourself if it's already present?
Adnan: if you used strain information for your reads, try
convert_project -f (maf or caf) -t fasta ...
which will output different FASTAs for each strain present in the assembly.
Then grep the FASTAs for the '@' sign ... these are the places where no read
from a given strain covers the place.
Peter: convert_project also has "-v" as parameter ... is this what you wanted
by parsing the ACE by hand?
B.
----- original message --------
Subject: [mira_talk] Re: scaffolded contigs
Sent: Wed, 21 Jul 2010
From: Peter<peter@xxxxxxxxxxxxxxxxxxxxx>
On Wed, Jul 21, 2010 at 1:49 PM, Davide Scaglione <gianza@xxxxxxxxxx>
wrote:
Fourth!
Wow - I wasn't expecting such interest.
I've just looked at the code and I'm afraid there is a catch: It was
using Biopython
with some experimental stuff that isn't in the main release (and may never
be).
In order to be useful to you guys, I'd have to re-write it to use the basic
ACE
parsing in standard Biopython... but that shouldn't take too long.
What output file format would suit you all? Just the ungapped sequence as
FASTA?
Peter
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