[BioC] BioStrings - BStringViews Object

[Mayra Eduardoff]

Hi ,

I am now using R version 2.6.0 (2007-10-03)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.ISO8859-1;LC_NUMERIC=C;LC_TIME=en_US.ISO8859-1;LC_COLLATE=en_US.ISO8859-1;LC_MONETARY=en_US.ISO8859-1;LC_MESSAGES=en_US.ISO8859-1;LC_PAPER=en_US.ISO8859-1;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.ISO8859-1;LC_IDENTIFICATION=C

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] Biobase_1.16.1   Biostrings_2.6.4 RMySQL_0.6-0     DBI_0.2-4
[5] biomaRt_1.12.2   RCurl_0.8-3

loaded via a namespace (and not attached):
[1] rcompgen_0.1-15 XML_1.93-2


I was wondering whether the writeFASTA() function is not reading in
BStringViews object anymore ? It only seems to work with a list.

class(bsv)
[1] "BStringViews"
attr(,"package")
[1] "Biostrings"

writeFASTA(bsv, "Doc/tables/pta-seq.fasta")
Error in writeFASTA(bsv, "Doc/tables/pta-seq.fasta") :
  invalid type/length (S4/1) in vector allocation

My other question is whether the BStringViews object is only thought
to be used for different views on the same BString ? I kept using it
for different BString-objects to i.e use the function complement(),
but I guess I shoud have sapplied the function to a vector of
DNAStrings or something like that ?

thanks,

Mayra