[mira_talk] Re: MIRA consensus tags in ace file
- From: Sven Klages <sir.svencelot@xxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 3 Aug 2009 08:08:02 +0200
Hi Travis, Bastien,
the real problem is the closing brace of the CT tag being on the same line
as the closing brace for the COMMENT.
Tags with comments look like this:
CT{
Contig1 polymorphism consed 1308 1315 080819:132640
COMMENT{
this is comment line 1
this is comment line 2
C}
}
(taken from the same consed doku).
btw. you should switch to consed v19; there is no need to stick to v18
(unless you need to pay for it).
There should be some bugs fixed ...
hth,
Sven
2009/8/3 Tony Travis <a.travis@xxxxxxxxxx>
> Hello, Bastien.
>
> I've just tried reading the 'ace' format output by MIRA 3 into Consed 18.0,
> but it fails to parse the file correctly because of errors in the MIRA CT
> (Consensus Tag) format
>
> This is an example from my ace file created by MIRA 3 today:
>
> CT{
> R_hominis_c1 MIRA MIRA 1 5 020202:121212 NoTrans
> COMMENT{
> Assembled with MIRA
> C}}
>
> CT{
> R_hominis_c1 DGPc MIRA 22 22 020202:121212 NoTrans
> COMMENT{
> *: 1 C: 1 - 50%
> C}}
>
> I don't think ace file comments can be nested '{}' or read in this format -
> An example from the Consed 18.0 documentation looks like:
>
> CT{
> Contig1 comment consed 996 1007 971218:180623
> This is line 1 of a comment
> There may be any number of lines
> }
>
> Maybe my ace output should look more like this?
>
> CT{
> R_hominis_c1 MIRA MIRA 1 5 020202:121212 NoTrans
> }
>
> CT{
> R_hominis_c1 comment MIRA 1 5 020202:121212 NoTrans
> Assembled with MIRA
> }
>
> CT{
> R_hominis_c1 DGPc MIRA 22 22 020202:121212 NoTrans
> }
>
> CT{
> R_hominis_c1 comment MIRA 22 22 020202:121212 NoTrans
> *: 1 C: 1 - 50%
> }
>
> Bye,
>
> Tony.
> --
> Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
> and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
> tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk
> mailto:a.travis@xxxxxxxxxx,
> http://bioinformatics.rri.sari.ac.uk/~ajt<http://bioinformatics.rri.sari.ac.uk/%7Eajt>
>
> --
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