Handling DNA sequence loaded from a file
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@agaz-hussain-wani-7620
Last seen 4.4 years ago
India

I have a file with DNA sequence of length 900 characters. I use Biostrings package to read the sequence from the file into R.

library(Biostrings)

ref <- readDNAStringSet(filepath)

 

I get something like

 

A DNAStringSet instance of length 1
width seq                               names               
[1]   900 AACTGGTTACCTGCCGTGAGTAAATTAAAATT...GACGCAACGGTTCCGACTACTCTGCTGCGGTG AGCTTTTCATTCTGACT...

I would like to know, how to get the full DNA sequence into other variable. How to access the full sequence.

 

r biostrings DNAsequence • 1.5k views
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It is there, only some of the letters are showing. What do you want to do with your sequence now that you have read it in?

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I want to have the full sequence as a character string and do some operation on that. Suppose I want to display the first 500 characters or do some string operation on that.

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On the one hand you could display them with as.character(ref) but if you wanted to do something you'd typically use a function, e.g., reverseComplement(ref) or narrow(ref, 500). This would return another DNAStringSet, which you could then coerce to character if you wanted, but really there's not much to be gained by looking at 500 letters (or 3 billion, or 10 million 100-mers) with the naked eye. Check out the help page ?DNAStringSet including the examples to get some ideas; the infrastructure is very flexible.

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Looking at your DNAStringSet, I wonder what the file that you are reading from looks like? readDNAStringSet is expecting a FASTA file

> An.identifer
AAACAACCA

and the identifier is used as the 'name'; it seems like you have a 'name' that is a sequence. If you have a plain text file with 1 DNA sequence per line, you could do something like

DNAStringSet(readLines(filepath))
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Thanks for your comments. When I try as.character(ref), I get something like 

ATGGCCCCCTTTGCCCAGGGAAAGGGCCCCTGGGGGGGGTTTTTTTGCCCACGTGCAGTCAGTCAGTAAGTCAAGTCAATGACGTCAATGCAACGTGCAAAAAAAAAAAAAGGAAATTAAAGGGCCCTGACGTGCAGCCAGTCAGTCAAAGGG 
                                                                                                                                                       "" 

When I try to find the number of characters 

nchar(ref)

It returns 0. What is going wrong??. 

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Do you mean nchar(ref) ? Please cut-and-paste from your R session into the support site, because it is very important to be precise. I have

> ref = DNAStringSet(c("AAATT", "AAA"))
> nchar(ref)
[1] 5 3

using the current version of software. What is the output of your sessionInfo()?

> sessionInfo()
R version 3.2.4 Patched (2016-03-16 r70348)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

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=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] Biostrings_2.38.4    XVector_0.10.0       IRanges_2.4.8       
[4] S4Vectors_0.8.11     BiocGenerics_0.16.1  BiocInstaller_1.20.1

loaded via a namespace (and not attached):
[1] zlibbioc_1.16.0

 

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Thanks a lot for writing . Its my bad that I could not notice the error early in my FASTA file. Everything looks fine now. 

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will this only work with a FATSA file or can I do this with a txt file?

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Please don't add comments to a 6 year old post. If you have a question, please submit a new question.

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