You are right Sean, That's what is needed Thanks. The idea was to gene rate mate pair from single reads by combining reads with the same id. I extract the read id 8_1_3_659 from the full id HWI-EA332_8_1_3_659#GGGGNN/1b and substr(id(aln.data), 11, nchar(id(aln.data))-9) do that. Thanks again for your help ---------------------------------------------------------------- On Mon, Nov 30, 2009 at 4:29 PM, Sean Davis <seandavi@gmail.com> wrote: > On Mon, Nov 30, 2009 at 10:20 AM, Ramzi TEMANNI <ramzi.temanni@gmail.com> > wrote: > > Hi Sean, > > Thanks for your help as.character give 2 ids by row: > > [1] "HWI-EA332_8_1_3_659#GGGGNN/1" "HWI- EA332_8_1_3_1738#CCCCNN/1" > > [3] "HWI-EA332_8_1_3_1094#AGGANN/1" "HWI-EA332_8_1_3_558#TTTCNN/1" > > [5] "HWI-EA332_8_1_3_1920#AAAANN/1" "HWI-EA332_8_1_3_228#GGGGNN/1" > > it should be some accessors to extract one Id by row. > > i've take a look at suggested help but there's no useful info to extract > > what I want > > This is NOT two ids per row. It is one vector. R outputs two > elements per row only because your screen is wide enough for that. > > If you do: > > tmp <- as.character(id(aln)) > > class(tmp) > > tmp[1] > tmp[2] > tmp[1:5] > length(tmp) > > it might give you more of an idea what is going on. > > Sean > > > > > > > On Mon, Nov 30, 2009 at 3:40 PM, Sean Davis <seandavi@gmail.com> wrote: > >> > >> On Mon, Nov 30, 2009 at 9:27 AM, Ramzi TEMANNI <ramzi.temanni@gmail.com> > > >> wrote: > >> > Hi, > >> > I have a sequence loaded from bowtie alignment > >> > aln <- readAligned("./S1", pattern="S1_1.hg19.bowtie.align", > >> > type="Bowtie") > >> > I would like to to extract the id to select specific reads > >> > I run id(aln) and I get: > >> > id(aln) > >> > A BStringSet instance of length 4340867 > >> > width seq > >> > [1] 28 HWI-EA332_8_1_3_659#GGGGNN/1 > >> > [2] 29 HWI-EA332_8_1_3_1738#CCCCNN/1 > >> > [3] 29 HWI-EA332_8_1_3_1094#AGGANN/1 > >> > [4] 28 HWI-EA332_8_1_3_558#TTTCNN/1 > >> > [5] 29 HWI-EA332_8_1_3_1920#AAAANN/1 > >> > [6] 28 HWI-EA332_8_1_3_228#GGGGNN/1 > >> > [7] 29 HWI-EA332_8_1_3_1261#AGGGNN/1 > >> > [8] 28 HWI-EA332_8_1_3_908#ACTTNN/1 > >> > [9] 27 HWI-EA332_8_1_3_53#CTGCNN/1 > >> > ... ... ... > >> > [4340859] 33 HWI-EA332_8_120_1596_499#TTGANA/1 > >> > [4340860] 34 HWI-EA332_8_120_1599_1161#CCACNT/1 > >> > [4340861] 33 HWI-EA332_8_120_1601_255#CTCTNA/1 > >> > [4340862] 33 HWI-EA332_8_120_1601_504#CCATNC/1 > >> > [4340863] 33 HWI-EA332_8_120_1624_899#CTCTNT/1 > >> > [4340864] 33 HWI-EA332_8_120_1487_658#ACCCNA/1 > >> > [4340865] 32 HWI-EA332_8_120_1533_28#CACANG/1 > >> > [4340866] 33 HWI-EA332_8_120_1564_807#CCCGNG/1 > >> > [4340867] 34 HWI-EA332_8_120_1474_1350#CCTGNC/1 > >> > > >> > This BStringSet instance has 'width' and 'seq' > >> > runing str(id(aln)) i got this > >> > > >> > Formal class 'BStringSet' [package "Biostrings"] with 5 slots > >> > ..@ pool :Formal class 'SharedRaw_Pool' [package "IRanges"] > >> > with > >> > 2 slots > >> > .. .. ..@ xp_list :List of 1 > >> > .. .. .. ..$ :<externalptr> > >> > .. .. ..@ .link_to_cached_object_list:List of 1 > >> > .. .. .. ..$ :<environment: 0x2af6400=""> > >> > ..@ ranges :Formal class 'GroupedIRanges' [package "IRanges"] > >> > with > >> > 7 slots > >> > .. .. ..@ group : int [1:4340867] 1 1 1 1 1 1 1 1 1 1 ... > >> > .. .. ..@ start : int [1:4340867] 1 29 58 87 115 144 172 201 > >> > 229 > >> > 256 ... > >> > .. .. ..@ width : int [1:4340867] 28 29 29 28 29 28 29 28 27 > >> > 29 > >> > ... > >> > .. .. ..@ NAMES : NULL > >> > .. .. ..@ elementMetadata: NULL > >> > .. .. ..@ elementType : chr "integer" > >> > .. .. ..@ metadata : list() > >> > ..@ elementMetadata: NULL > >> > ..@ elementType : chr "BString" > >> > ..@ metadata : list() > >> > > >> > But i'm wondering how to extract only the 'seq' from all that and > store > >> > result in a table ? > >> > >> as.character(id(aln)) > >> > >> will return a character vector of the names. You might want to look > >> at the help for AlignedRead-class and BStringSet-class for some help > >> in understanding these classes and what can be done with them. It may > >> be that you will not need to go to character vector to do what you > >> want with the reads. > >> > >> Sean > > > > > [[alternative HTML version deleted]]

On Mon, Nov 30, 2009 at 10:20 AM, Ramzi TEMANNI <ramzi.temanni at="" gmail.com=""> wrote: > Hi Sean, > Thanks for your help as.character give 2 ids by row: > [1] "HWI-EA332_8_1_3_659#GGGGNN/1"? "HWI-EA332_8_1_3_1738#CCCCNN/1" > [3] "HWI-EA332_8_1_3_1094#AGGANN/1" "HWI-EA332_8_1_3_558#TTTCNN/1" > [5] "HWI-EA332_8_1_3_1920#AAAANN/1" "HWI-EA332_8_1_3_228#GGGGNN/1" > it should be some accessors to extract one Id by row. > i've take a look at suggested help but there's no useful info to extract > what I want This is NOT two ids per row. It is one vector. R outputs two elements per row only because your screen is wide enough for that. If you do: tmp <- as.character(id(aln)) class(tmp) tmp[1] tmp[2] tmp[1:5] length(tmp) it might give you more of an idea what is going on. Sean > > On Mon, Nov 30, 2009 at 3:40 PM, Sean Davis <seandavi at="" gmail.com=""> wrote: >> >> On Mon, Nov 30, 2009 at 9:27 AM, Ramzi TEMANNI <ramzi.temanni at="" gmail.com=""> >> wrote: >> > Hi, >> > I have a sequence loaded from bowtie alignment >> > aln <- readAligned("./S1", pattern="S1_1.hg19.bowtie.align", >> > type="Bowtie") >> > I would like to to extract the id to select specific reads >> > I run id(aln) and I get: >> > id(aln) >> > ?A BStringSet instance of length 4340867 >> > ? ? ? ? ?width seq >> > ? ? ?[1] ? ?28 HWI-EA332_8_1_3_659#GGGGNN/1 >> > ? ? ?[2] ? ?29 HWI-EA332_8_1_3_1738#CCCCNN/1 >> > ? ? ?[3] ? ?29 HWI-EA332_8_1_3_1094#AGGANN/1 >> > ? ? ?[4] ? ?28 HWI-EA332_8_1_3_558#TTTCNN/1 >> > ? ? ?[5] ? ?29 HWI-EA332_8_1_3_1920#AAAANN/1 >> > ? ? ?[6] ? ?28 HWI-EA332_8_1_3_228#GGGGNN/1 >> > ? ? ?[7] ? ?29 HWI-EA332_8_1_3_1261#AGGGNN/1 >> > ? ? ?[8] ? ?28 HWI-EA332_8_1_3_908#ACTTNN/1 >> > ? ? ?[9] ? ?27 HWI-EA332_8_1_3_53#CTGCNN/1 >> > ? ? ?... ? ... ... >> > [4340859] ? ?33 HWI-EA332_8_120_1596_499#TTGANA/1 >> > [4340860] ? ?34 HWI-EA332_8_120_1599_1161#CCACNT/1 >> > [4340861] ? ?33 HWI-EA332_8_120_1601_255#CTCTNA/1 >> > [4340862] ? ?33 HWI-EA332_8_120_1601_504#CCATNC/1 >> > [4340863] ? ?33 HWI-EA332_8_120_1624_899#CTCTNT/1 >> > [4340864] ? ?33 HWI-EA332_8_120_1487_658#ACCCNA/1 >> > [4340865] ? ?32 HWI-EA332_8_120_1533_28#CACANG/1 >> > [4340866] ? ?33 HWI-EA332_8_120_1564_807#CCCGNG/1 >> > [4340867] ? ?34 HWI-EA332_8_120_1474_1350#CCTGNC/1 >> > >> > This BStringSet instance has 'width' and 'seq' >> > runing str(id(aln)) i got this >> > >> > Formal class 'BStringSet' [package "Biostrings"] with 5 slots >> > ?..@ pool ? ? ? ? ? :Formal class 'SharedRaw_Pool' [package "IRanges"] >> > with >> > 2 slots >> > ?.. .. ..@ xp_list ? ? ? ? ? ? ? ? ? ?:List of 1 >> > ?.. .. .. ..$ :<externalptr> >> > ?.. .. ..@ .link_to_cached_object_list:List of 1 >> > ?.. .. .. ..$ :<environment: 0x2af6400=""> >> > ?..@ ranges ? ? ? ? :Formal class 'GroupedIRanges' [package "IRanges"] >> > with >> > 7 slots >> > ?.. .. ..@ group ? ? ? ? ?: int [1:4340867] 1 1 1 1 1 1 1 1 1 1 ... >> > ?.. .. ..@ start ? ? ? ? ?: int [1:4340867] 1 29 58 87 115 144 172 201 >> > 229 >> > 256 ... >> > ?.. .. ..@ width ? ? ? ? ?: int [1:4340867] 28 29 29 28 29 28 29 28 27 >> > 29 >> > ... >> > ?.. .. ..@ NAMES ? ? ? ? ?: NULL >> > ?.. .. ..@ elementMetadata: NULL >> > ?.. .. ..@ elementType ? ?: chr "integer" >> > ?.. .. ..@ metadata ? ? ? : list() >> > ?..@ elementMetadata: NULL >> > ?..@ elementType ? ?: chr "BString" >> > ?..@ metadata ? ? ? : list() >> > >> > But i'm wondering how to extract only the 'seq' from all that and store >> > result in a table ? >> >> as.character(id(aln)) >> >> will return a character vector of the names. ?You might want to look >> at the help for AlignedRead-class and BStringSet-class for some help >> in understanding these classes and what can be done with them. ?It may >> be that you will not need to go to character vector to do what you >> want with the reads. >> >> Sean > >