Actually, now I also remember what problems I encountered with that strategy: not all my FASTA records are limited to 2 lines. Some sequences are long and span 6 lines. So, I can't take advantage of the elegant solution sread <- DNAStringSet(all[c(FALSE, TRUE)]) I'll have to think about a strategy where I read the file one line at a time while I identify the start of a new record every time the character ">" is found at the beginning of the line. Still, thank you. Ivan On 14 Feb 2013 22:50, "Ivan Gregoretti" <ivangreg@gmail.com> wrote: > Thank you Martin. I realize now that I have faced this problem before and > that I can work around it with the ShortRead constructor. > > I appreciate it. > > Ivan > On 14 Feb 2013 21:24, "Martin Morgan" <mtmorgan@fhcrc.org> wrote: > >> On 2/14/2013 12:32 PM, Ivan Gregoretti wrote: >> >>> Hello everybody, >>> >>> The library ShortRead includes two very useful functions: readFastq() >>> and readFasta() >>> >>> While readFastq() can open FASTQ files as either plain text or gzipped >>> files, readFasta() can only open files in plain text. >>> >>> For example: >>> >>> # FASTQ: success >>> >>>> readFastq("t01213R0QU.fq.gz") >>>> >>> class: ShortReadQ >>> length: 43608 reads; width: 178..486 cycles >>> >>> # FASTA: failure >>> >>>> readFasta("t01213R0QU.P.fa.gz"**) >>>> >>> Error in .normargInputFilepath(**filepath) : >>> file "t01213R0QU.P.fa.gz" has unsupported type: gzfile >>> >>> >>> Is this the current status or it's time for me to update my BioC? >>> >>> Can someone offer a work around that does not involve decompressing >>> the FASTA file to disc? I tried, yet unsuccessfully: >>> >> >> readFasta is just an alias for readDNAStringSet, which does not support >> compressed files. >> >> Not sure exactly what is in your fasta file, but Rsamtools::FaFile might >> be what you are looking for (typically, relatively few long sequences; you >> need to create an index (using indexFa) if one does not already exist then >> something along the lines of >> >> fa = FaFile("some.fa.gz") ## index is some.fa.gz. >> scanFa(fa, param=scanFaIndex(fa)) >> >> would read the whole file, or a more selective GRanges to go after >> particular sub-sequences. >> >> A workaround might also involve >> >> http://comments.gmane.org/**gmane.comp.lang.r.sequencing/**1981<htt p:="" comments.gmane.org="" gmane.comp.lang.r.sequencing="" 1981=""> >> >> all <- readLines("s_1.fa.gz") >> sread <- DNAStringSet(all[c(FALSE, TRUE)]) >> id <- BStringSet(all[c(TRUE, FALSE)]) >> fas <- ShortRead(sread=sread, id=id) >> >> >> >>> readFasta(gzfile("t01213R0QU.**P.fa.gz","r")) >>> Error in function (classes, fdef, mtable) : >>> unable to find an inherited method for function ‘readFasta’ for >>> signature ‘"gzfile"’ >>> >>> >>> Thank you, >>> >>> Ivan >>> >>> >>> sessionInfo() >>>> >>> R Under development (unstable) (2012-11-30 r61184) >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >>> [7] LC_PAPER=C LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] parallel stats graphics grDevices utils datasets methods >>> [8] base >>> >>> other attached packages: >>> [1] Rsamtools_1.11.16 Biostrings_2.27.11 GenomicRanges_1.11.29 >>> [4] IRanges_1.17.32 BiocGenerics_0.5.6 >>> >>> loaded via a namespace (and not attached): >>> [1] bitops_1.0-5 stats4_2.16.0 tools_2.16.0 zlibbioc_1.5.0 >>> >>> ______________________________**_________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org >>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.="" ethz.ch="" mailman="" listinfo="" bioconductor=""> >>> Search the archives: http://news.gmane.org/gmane.** >>> science.biology.informatics.**conductor<http: news.gmane.org="" gman="" e.science.biology.informatics.conductor=""> >>> >>> >> >> -- >> Dr. Martin Morgan, PhD >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N. >> PO Box 19024 Seattle, WA 98109 >> > [[alternative HTML version deleted]]