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_COLLA TE=en_US.ISO8859-1;LC_MONETARY=en_US.ISO8859-1;LC_MESSAGES=en_US.ISO88 59-1;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

Hi Mayra, Mayra Eduardoff wrote: > 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_COL LATE=en_US.ISO8859-1;LC_MONETARY=en_US.ISO8859-1;LC_MESSAGES=en_US.ISO 8859-1;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 You need to use write.BStringViews() instead. readFASTA() and writeFASTA() work in a symmetric manner: since the former loads the FASTA file into a list, then the latter writes a list to a FASTA file. read.BStringViews() and write.BStringViews() also work in a symemtric manner. > > My other question is whether the BStringViews object is only thought > to be used for different views on the same BString ? Yes, on the same string. > 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 ? Yes you are doing something that is not natural (i.e. putting unrelated DNAStrings into a BStringViews object) to take advantage of the vectorized feature of complement(). You can't be blamed for this because it's actually the most efficient way to complement or reverse-complement a big collection of sequences... but it's not natural ;-) The reason why the BStringViews container has this constraint that it must contain views on the same string is that it was originally designed to store the result of a call to matchPattern(). For this use case it was natural to return a set of views on the subject of the search. But it feels wrong to use it for storing a set of unrelated BString objects. The problem is that the Biostrings package was lacking a container for doing this. I've added one recently in the devel version of the package: the BStringSet container (there is also a DNAStringSet, RNAStringSet and a AAStringSet container). It has some limitations too (e.g. you can't append new strings to it) but it will not represent a set of views on the same string anymore. This is still a work in progress but it should be ready for the next BioC release. Like for BStringViews objects, there will be a read.BStringSet() and a write.BStringSet() function. Also most of the functions that work for a single BString object will also work in a parallelized fashion for a BStringSet object. For example, if 'x' is a DNAStringSet object, complement(x) will return the DNAStringSet object made of the complements of each sequence in 'x'. Cheers, H. > > thanks, > > Mayra > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor