library(ShortRead) fastadata <- readFasta("fastafolder", "fa$") file <- tempfile() writeFasta(fastadata, file) var1 <- readLines(file) while(countlength(tmp <- readLines(file, n = -1)) > 0) { #do something } I want the while loop to run till the end of file is reached, but the while statement dosent work. Thanks for help. Regards Jack -- output of sessionInfo(): > sessionInfo() R version 2.15.1 (2012-06-22) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] ShortRead_1.14.4 latticeExtra_0.6-24 RColorBrewer_1.0-5 Rsamtools_1.8.6 lattice_0.20-10 Biostrings_2.24.1 GenomicRanges_1.8.13 [8] IRanges_1.14.4 BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] Biobase_2.16.0 bitops_1.0-4.1 grid_2.15.1 hwriter_1.3 stats4_2.15.1 tools_2.15.1 zlibbioc_1.2.0 -- Sent via the guest posting facility at bioconductor.org.

On 09/13/2012 01:42 AM, Jack [guest] wrote: > > library(ShortRead) > fastadata <- readFasta("fastafolder", "fa$") > file <- tempfile() > writeFasta(fastadata, file) > var1 <- readLines(file) > while(countlength(tmp <- readLines(file, n = -1)) > 0) { > #do something > } > > I want the while loop to run till the end of file is reached, but the while statement dosent work. Thanks for help. Hi Jack -- if the goal is to read the fasta file in chunks, use a 'connection' that can remember the current location. After running the following to get a reproducible example fasta file library(ShortRead) example(readFasta) fl = dir(analysisPath(sp), "s_1_sequence.txt", full=TRUE) we can create a connection and open it, and the do our loop reading 500 lines at a time con <- file(fl); open(con) while(length(res <- readLines(con, n=500))) cat(length(res), "\n") close(con) which prints out 500 500 24 Unfortunately, readFasta doesn't work on connections (that would be a worthwhile feature request). There is also FaFile in Rsamtools, try example(FaFile) FaFile is most useful when the fasta file would benefit from being indexed, e.g., hundreds of contigs, but might also be useful for your purposes. Martin > Regards > Jack > > > -- output of sessionInfo(): > >> sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] ShortRead_1.14.4 latticeExtra_0.6-24 RColorBrewer_1.0-5 Rsamtools_1.8.6 lattice_0.20-10 Biostrings_2.24.1 GenomicRanges_1.8.13 > [8] IRanges_1.14.4 BiocGenerics_0.2.0 > > loaded via a namespace (and not attached): > [1] Biobase_2.16.0 bitops_1.0-4.1 grid_2.15.1 hwriter_1.3 stats4_2.15.1 tools_2.15.1 zlibbioc_1.2.0 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793