Thanks Herve, That would be great indeed. Florian On 29/09/14 21:23, "Hervé Pagès" <hpa...@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. > >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]] >> >> >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > >-- >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: hpa...@fhcrc.org >Phone: (206) 667-5791 >Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
