[mira_talk] Re: fasta info line info
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 7 Jul 2010 23:43:51 +0200
On Mittwoch 07 Juli 2010 Walt Lorenz wrote:
> A friend of mine said that in the older versions of mira, the info. line
> for the contig.fasta file gave the name, the length of the contig, and the
> number of reads it contained. Mira 3.0.5 only gives the contig name. I
> realize this info. is available in one of the other output files, but is
> there a switch to output it to the info. line of each sequence? It would
> be very helpful!
Hello Walt,
Uh ... MIRA had that? On second thought (and after looking at the code): yes
... and no. MIRA had the number of sequences contained as additional value,
but nothing else.
The TIGR assembler has some additional output in its pseudo-FASTA output.
I disabled this because IGB (at least version 4.56) did not parse FASTA files
when there was more than the name in the description line.
As this "additional description" is not standardised, I'm a little bit
uncomfortable with putting this information there. Would it be really a
problem to look up the information in the *info_contigstat.txt file?
Bastien
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