[mira_talk] Re: miraconvert FASTA output files?
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 7 Nov 2013 19:22:48 +0100
On 07 Nov 2013, at 18:54 , Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx> wrote:
> (A) Is there a reason for the empty files project.fasta and
> project.fasta.qual from a command like this? It seems like a bug:
Yes and no. CAF and MAF formats can contain both contigs and unattached-reads.
The empty files you see are created for those and if there are none, they
remain empty. It’s a minor annoyance which I did not have time to fix.
> (B) Can I ask miraconvert to produce just FASTA files, without sister
> QUAL files?
I don’t think so, no.
> (C) In addition to the empty files (and the QUAL files), this also produces:
>
> project_AllStrains.padded.fasta
> project_AllStrains.unpadded.fasta
> project_StrainX.padded.fasta
> project_StrainX.unpadded.fasta
>
> When I only have one strain, the StrainX and AllStrains files are
> identifical, and this duplication is confusing and wasteful.
It is. Reason: similar to A, CAF and MAF do not need to specify all strains
included at the beginning of the file and therefore MIRA outputs an
“AllStrains” as preventive measure in case this changes. Reason for no fix yet:
see A) :-)
> Can I specify for which strains FASTA files are wanted?
No.
> (D) Can I specify if padded or unpadded (or both) is wanted?
No.
B.
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