[mira_talk] Re: scaffolded contigs

  • From: Dan Depledge <d.depledge@xxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Wed, 21 Jul 2010 14:06:08 +0100


Ungapped sequence as Fasta would do me nicely



On 21/07/2010 14:03, Peter wrote:
On Wed, Jul 21, 2010 at 1:49 PM, Davide Scaglione<gianza@xxxxxxxxxx>  wrote:
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?


Daniel Depledge PhD
Research Associate
Division of Infection&  Immunity
University College London
Windeyer Building
46 Cleveland St

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