[mira_talk] Re: difficulty with convert_project
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sun, 2 Jan 2011 21:29:23 +0100
On Jan 2, 2011, at 21:06 , Jeremy Volkening wrote:
> To investigate I used convert_project to
> create a FASTA consensus file from the CAF file and compared this to the
> one generated by gap4. There were indeed differences (though small)
> between the two.
>
> The only conclusion I can draw from this is that convert_project is
> recalculating the consensus, even though I haven't asked it to.
Hmmmm ... I'll have to have a look at when exactly the recalc kicks in.
> I checked the differences in the consensus files, and the gap4 consensus
> appears "correct" while mira is miscalculating the consensus in a few
> relatively clean, uncomplicated places. I don't have a problem with this
> - I'm just using the gap4 consensus - but I'm wondering ...
But I have a problem with miscalculations in clean and uncomplicated places :-)
Would it be possible to get the gap4 database of that project and you pointing
me to the places you have checked? I'd have a look at the consensus routines to
see what goes wrong.
> if there is a
> way to prevent convert_project from re-calculating it, or if there's
> something else going on here that I'm not realizing.
No way until now, perhaps I should implement a no-recalc flag (should be easy).
Could you please put that as a feature request to Trac? (so that I don't loose
track of it)
B.
--
You have received this mail because you are subscribed to the mira_talk mailing
list. For information on how to subscribe or unsubscribe, please visit
http://www.chevreux.org/mira_mailinglists.html
Other related posts:
