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 ?
Thanks in advance for your help.
Best Regards,
Mohamed-Ramzi Temanni,
Leiden, The Netherlands
----------------------------------------------------------------
[[alternative HTML version deleted]]
_______________________________________________
Bioc-sig-sequencing mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
