[mira_talk] Re: MIRA consensus tags in ace file
- From: Tony Travis <a.travis@xxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Mon, 03 Aug 2009 18:59:24 +0100
Bastien Chevreux wrote:
On Montag 03 August 2009 Tony Travis wrote:
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
Hello Tony,
oww ... bad bug. As Sven already noted, the ACE file allows for multiline
comments. I've fixed the error and the fix will be rolled out with the next
release.
In the mean time, you can fix the ACE with this:
sed -e 's/^C}}/C}\n}/' infile.ace >outfile.ace
Hello, Bastien.
I tried doing that after reading Sven's message, and created tags like this:
CT{
R_hominis_c1 MIRA MIRA 1 5 020202:121212 NoTrans
COMMENT{
Assembled with MIRA
C}
}
I also upgraded to Consed 19.0 as he suggested, and this fixes the
problem with the comments, but consed still fails to parse the RT tags
in the (edited) ace file created by MIRA:
exception thrown: ace file error detected from source file parseAceFile.cpp at
1077
Error in file temp.ace at line 12213273. Line:
FI7H5NB02G5BZ7 HAF5 MIRA 5 5 020202:121212
RT tag line should be:
<readname> <tag type> <tag source> <padded read pos start> <padded read pos end>
<date YYMMDD:HH24MISS>
where the padded read pos's are from the left end and tag type must be
recognized by consed but tag type is not recognized
ace file: temp.ace
Version 19.0 (090206)
ace file error detected from source file parseAceFile.cpp at 1077
Error in file temp.ace at line 12213273. Line:
FI7H5NB02G5BZ7 HAF5 MIRA 5 5 020202:121212
RT tag line should be:
<readname> <tag type> <tag source> <padded read pos start> <padded read pos end>
<date YYMMDD:HH24MISS>
where the padded read pos's are from the left end and tag type must be
recognized by consed but tag type is not recognized
Version 19.0 (090206)
ace file: temp.ace
unrecognized line: }
This is the relevant part of the ace file with line numbers:
12213272 RT{
12213273 FI7H5NB02G5BZ7 HAF5 MIRA 5 5 020202:121212
12213274 }
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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