[mira_talk] Re: scaffolded contigs
- From: "Bastien Chevreux" <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 21 Jul 2010 15:57:30 +0200 (MEST)
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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