[Bioc-devel] BSgenome forge file input file restrictions

Hahne, Florian florian.hahne at novartis.com
Tue Sep 30 15:31:43 CEST 2014

Thanks Herve,
That would be great indeed.

On 29/09/14 21:23, "Hervé Pagès" <hpages at fhcrc.org> wrote:

>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.
>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
>> 	[[alternative HTML version deleted]]
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>Hervé Pagès
>Program in Computational Biology
>Division of Public Health Sciences
>Fred Hutchinson Cancer Research Center
>1100 Fairview Ave. N, M1-B514
>P.O. Box 19024
>Seattle, WA 98109-1024
>E-mail: hpages at fhcrc.org
>Phone:  (206) 667-5791
>Fax:    (206) 667-1319

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