[Bioc-devel] BSgenome forge file input file restrictions

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

	[[alternative HTML version deleted]]

-- 
Herv? Pag?s

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