[mira_talk] Re: edited assembly: reassembly
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 11 Dec 2009 19:55:51 +0100
On Freitag 11 Dezember 2009 Stefano Ghignone wrote:
> and sorry if I bother again the mailing list with my issues.
> I need to reassemble an assembly (a mapping, precisely), which I edited
> using consed, working on the ACE output.
Hi Stefano,
I have no good idea there I must say. One thing you could try: the caf tools
from the Sanger Centre contain a number of programs which read and eventually
sanitize CAFs. One idea could be to put them through these.
An especially ugly workaround could be to convert this CAF to a gap4 database
(with caf2gap) and immediately convert it back to a CAF (with gap2caf). You
might want to try this.
As last resort: if you make the CAF available to me, I could have a look at it
to find out what the CAF parser does not like. Then one could think of taking
countermeasures (if possible), either in the ace2caf script or in the CAF
parser of MIRA. In any way, this would probably not happen before January as
I'm pretty busy at the moment.
Regards,
Bastien
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