[mira_talk] Re: scaffolded contigs
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 22 Jul 2010 00:32:17 +0200
On Mittwoch 21 Juli 2010 Adnan Niazi wrote:
> [...]
> Yes, i will try it, but i am afraid as I read that convert project will
> list the desired coverage contigs in multifasta format and it will not
> insert N's between the contigs. For example: Zero coverage region b/w two
> contigs is 200bp long, so there should be 200 N's b/w contigs in fasta
> file.
Well, I checked and found a few inconsistencies which came in over time. I've
upgraded and checked a couple of routines and the new convert_project should
do what you want. I don't have time to make a full release yet, but if you
want to play with it, here's the binary (x64):
http://www.chevreux.org/tmp/convert_project.bz2
The following changes are important:
- when used on an assembly file with multiple strains (caf or maf),
"convert_project -t fasta" now also creates files with combined output of
all strains
- reversed default and meaning of '-u' in convert_project: per default filling
of strain is off, can be switched on
- '-u' in convert_project now also fills the '@' "base" (which stands for "no
coverage by this strain")
- '-v' in convert_project now works "per strain" and not "per total coverage"
B.
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