Re: [Bioc-devel] BSgenome forge file input file restrictions
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
[Bioc-devel] BSgenome forge file input file restrictions
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
Re: [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]] ___ 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
