Hi Herve, Thanks for your suggestions and comments.Sorry for my unclear questions.I am learing R as I am trying to build the code. I wrote the code with asper your suggestions.Its working perfectly fine. >source("http://bioconductor.org/biocLite.R") >biocLite(c("BSgenome","BSgenome.Hsapiens.UCSC.hg19")) >library(BSgenome) >library("BSgenome.Hsapiens.UCSC.hg19") > tb<-read.table("test.txt",header=TRUE,sep="\t",colClasses=c('character ','character','integer','integer')) >myseq<- getSeq(Hsapiens,tb$chr,start=tb$Start,end=tb$End) > x <-DNAStringSet(myseq) > names(x)<-tb$Name > write.XStringSet(x,"test_seq1.txt",format="fasta") #my test file looks like this Name chr Start End chr2:10000-10020 chr2 10000 10020 chr19:1560295-1560450 chr19 1560295 1560450 I would be using this to extarct 2000 sequences.So please comment on the efficiency,or other suggestions. Thanks once again, Viritha 2011/8/18 Hervé Pagès <hpages@fhcrc.org> > Viritha, > > > On 11-08-16 10:54 AM, viritha kaza wrote: > >> Hi Herve, >> Thanks for your response. System is considering as characters in the >> dataframe.So I was thinking of using them as vectors.But if I scan as >> seperate elements and convert them to numeric using lapply.It becomes >> atomic numeric.How do I make them as vectors without using combining >> fuction as c(1,2,3)?I am basically new to sequences using R.So will read >> write.XStringSet(). >> > > Your question is particularly unclear and it seems like you would > benefit a lot from reading a little bit about data frames and > read.table(). There are a lot of arguments to this function that > give you a lot of control on how the data will actually be loaded > into the data frame. In particular look at the 'colClasses' arg: > it lets you control the types of the columns of the data frame. > > That will help you solve the first step which is loading the > file into a data frame. I don't think you need any > scan/lappl/combining for this step. > > Once you've solved this, step 2 will be to use getSeq() to extract > your sequences and step 3 will be to write your sequences to a FASTA > file with write.XStringSet(). > > Right now, it's almost impossible to know where you are encountering > difficulties. Please have a look at our posting guide before your > next post: > > http://bioconductor.org/help/**mailing-list/posting- guide/<http: bioconductor.org="" help="" mailing-list="" posting-guide=""/> > > Thanks! > H. > > > Thanks, >> Viritha >> 2011/8/16 Hervé Pagès <hpages@fhcrc.org <mailto:hpages@fhcrc.org="">> >> >> >> Hi Viritha, >> >> >> On 11-08-16 08:01 AM, viritha kaza wrote: >> >> Hi group, >> I am interested in retrieving about 2000 sequences with the >> specific >> chromosome number,start and end site. >> I was thinking of using BSgenome package for this. >> >> >> source("http://bioconductor.__**org/biocLite.R >> <http: bioconductor.org="" **bioclite.r<http:="" bioconducto="" r.org="" bioclite.r=""> >> >") >> >> >> biocLite("BSgenome","BSgenome.**__Hsapiens.UCSC.hg19") >> >> >> library(BSgenome) >> >> >> library("BSgenome.Hsapiens.__**UCSC.hg19") >> >> >> myseq<- getSeq(Hsapiens,"chr2",start=_**_10000,end=10020) >> >> >> # this would work for specific values. >> >> #So I tried to use a dataframe where it would retrieve >> chromosome number >> from by using >> >> full<-as.matrix(read.table(“__**test_seq.txt”,sep=’\t’,quote=” >> **__”,header=True, >> >> as.is <http: as.is=""/>=TRUE)) >> >> >> >> Why are you doing as.matrix here? Do you *really* want all the columns >> to be coerced to the same type? (which in your case is probably >> character because you have already one column of that type). >> >> >> >> full.df<-data.frame(full) >> >> >> So you're back to a data.frame, except that now all the columns are >> character vectors :-/ >> >> >> >> # test_seq contains this information >> >> #chromosome Start End >> #chr2 10000 10020 >> #chr3 10000 10020 >> >> >> Why not copy and paste what you get when you just type full.df? That >> way would know exactly what you ended up with (if full.df is too big, >> just show us the output of head(full.df)). >> Anyway, it looks like you'll have to get rid of those #. Otherwise >> passing Hsapiens,full.df$chromosome to getSeq() with those # in it >> will surely cause problems. >> >> >> >> myseq<- >> getSeq(Hsapiens,full.df$__**chromosome,start=10000,end=__** >> 10020) >> >> >> #but then when I use start=full.df$Start. It naturally throws an >> error >> saying 'start' must be a vector of integers >> >> Questions: >> >> How Do I handle this? >> >> >> By having full.df$Start be a vector of integers and also by reading >> the man page for getSeq(). >> >> >> >> Does start here mean that each chromosome numbering starts from 1? >> >> >> Yes, the first base at the 5' end of the + strand (or 3' end of the - >> strand) is considered to be position 1. >> >> >> >> How do I split each sequence retrieved and create as fasta >> format (>)with >> sequence name attached to them retrieved from my input file? >> >> >> How do you want to "split" each sequence retrieved? As a good starting >> point you could have a look at write.XStringSet(). Note that >> the names you put on your DNAStringSet object will be used as the >> record description lines in the resulting FASTA file. >> >> Cheers, >> H. >> >> >> >> >> sessionInfo() >> >> >> R version 2.13.0 (2011-04-13) >> Platform: i386-pc-mingw32/i386 (32-bit) >> >> locale: >> [1] LC_COLLATE=English_United States.1252 >> [2] LC_CTYPE=English_United States.1252 >> [3] LC_MONETARY=English_United States.1252 >> [4] 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] BSgenome.Hsapiens.UCSC.hg19_1.**__3.17 BSgenome_1.20.0 >> [3] Biostrings_2.20.1 GenomicRanges_1.4.6 >> [5] IRanges_1.10.4 >> >> loaded via a namespace (and not attached): >> [1] tools_2.13.0 >> >> >> >> Waiting for your suggestions, >> >> Thank you, >> >> Viritha >> >> [[alternative HTML version deleted]] >> >> >> >> >> ______________________________**___________________ >> Bioconductor mailing list >> Bioconductor@r-project.org <mailto:bioconductor@r-**project.org<bioconductor@r-project.org>> >> >> >> https://stat.ethz.ch/mailman/_**_listinfo/bioconductor<https :="" stat.ethz.ch="" mailman="" __listinfo="" bioconductor=""> >> <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="" gmane.__science.biology.informatics="" .__conductor=""> >> <http: news.gmane.org="" gmane.**science.biology.informatics.**="">> conductor<http: news.gmane.org="" gmane.science.biology.informatics.c="" onductor=""> >> > >> >> >> >> -- >> 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@fhcrc.org <mailto:hpages@fhcrc.org> >> Phone: (206) 667-5791 <tel:%28206%29%20667-5791> >> Fax: (206) 667-1319 <tel:%28206%29%20667-1319> >> >> >> > > -- > 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@fhcrc.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > [[alternative HTML version deleted]]