[mira_talk] Re: Sample MIRA output?
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sun, 21 Aug 2011 19:09:09 +0200
On Thursday 18 August 2011 21:03:57 Peter Cock wrote:
> I was wondering if there are any public datasets of MIRA output?
> That would be useful for things like testing ACE or MAF parsers,
> and also assembly viewing tools.
Hello Peter,
no, nothing "official", though the data sets present in the minidemo directory
could perhaps be used for this. Care to flesh out what you need?
That being said ... be careful: MIRA 3.4.0 (and maybe hotfixes leading to .1,
.2, etc.) will be the last MIRA with the current way MIRA encodes annotation
tags.
Some major changes are underway.
I've got a development in testing (and already my first eukaryote resequenced
with that) which implements full GFF3 input and output. With that the coding
of annotation stored in the commment of tags will also switch to GFF3
(backward compatibility to read old data sets written by MIRA should be
retained though).
I am tempted to release that quite soon as development version for preview and
shortly after as MIRA 3.5 (change in version number because it breaks said
annotation scheme).
Furthermore: MIRA already uses some kind of read group scheme internally.
However, implementating full I/O support for that requires also a couple of
changes which I need to consider very, very carefully. For MAF things will be
"easy": I'll update it (and rename it to something else, current favourite is
SMF) to be able to store everything needed. But I still want to retain
compatibility with CAF (and perhaps ACE) and need to find out how to hide some
MIRA information in those things. Discussion what to implement (and what not)
welcome.
At the latest there, MIRA will jump to 3.6 as with the "new MAF" I'll break
again a few things.
Best,
Bastien
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