[Bioc-devel] BSgenome forge file input file restrictions

[Hervé Pagès]

Hi Florian,

True. These restrictions don't make much sense these days anymore!
Some of them are gone in the devel version of BSgenome. The
BSgenomeForge vignette in devel now says:

   The sequence data must be in a single twoBit file (e.g. musFur1.2bit)
   or in a collection of FASTA files (possibly gzip-compressed).

I guess I should also support a single FASTA file.

H.

On 09/29/2014 01:36 AM, Hahne, Florian wrote:
> Hi all,
> I was wondering whether some of the rather arbitrary restrictions on input files for the process of forging as new Bsgenome package could be liftet. In particular:
>
> Why do we need all chromosomes in individual files? Couldn�t the function be smart enough to just extract the relevant bits from a single file containing all chromosomes? Or even from several such files?
>
> Why are gzipped files not allowed? Pretty much all tools in Biostrings seem to be able to deal with gzipped fasta files these days.
>
> Thanks,
> Florian
>
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-- 
Hervé Pagès

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