[mira_talk] Re: miraconvert FASTA output files?
- From: Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Fri, 8 Nov 2013 11:03:54 +0000
On Thu, Nov 7, 2013 at 6:22 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:
> 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.
OK
>> (B) Can I ask miraconvert to produce just FASTA files, without sister
>> QUAL files?
>
> I don’t think so, no.
OK
>> (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) :-)
OK
>> Can I specify for which strains FASTA files are wanted?
>
> No.
>
>> (D) Can I specify if padded or unpadded (or both) is wanted?
>
> No.
Thanks - the good news is the documentation wasn't missing
any hidden options ;)
Peter
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