[Bioc-devel] export() to 2bit file

Hervé Pagès Fri, 09 May 2014 16:09:07 -0700

Hi Michael,

  library(rtracklayer)
  library(Biostrings)
  x <- DNAStringSet("AAA-CCC-GGG-TTT-NNN-KKK")


Then:

  > x
    A DNAStringSet instance of length 1
      width seq
  [1]    23 AAA-CCC-GGG-TTT-NNN-KKK

  > export(x, "x.2bit")

  > import("x.2bit")
    A DNAStringSet instance of length 1

width seq names

  [1]    23 AAATCCCTGGGTTTTTNNNTTTT                           1

What about having the "export" method for TwoBitFile raise an error
(or at least issue a warning) instead of silently turning everything
that is not A, C, G, T, or N into a T?

Thanks,
H.

--
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] export() to 2bit file

Reply via email to