[mira_talk] MIRA consensus tags in ace file
- From: Tony Travis <a.travis@xxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Sun, 02 Aug 2009 23:48:28 +0100
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
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