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

Hervé Pagès hpages at fhcrc.org
Sat May 10 01:07:54 CEST 2014

Hi Michael,

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


   > 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?


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
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