How to bin a long continuous string into section of nth characters?

Question

suppose I have a long continous string like this.

x='aattggcccagtgtgtacaatcagtgcaggagctaatcccggactccttcgtcccctgtgtcgctgcgctgtgcagcgacgaagccgagcggctcactcgtctcaatcacctcagcttcgcggagctgcttaagcccttctcccgcctcacttccgaggttcacatgagagatcctaataatcaacttcacgtaattaaaaatttgaagatagcagtaagcaacattgtcacccagccacctcagcctggagccatccggaagcttttgaatgatgttgtttctggcagtcagcctgcagaaggattagtagctaatgtgattacagcaggagattatgaccttaacatcagtgAAAAAGCAAAGGACAAAAGATCTTTCTCGGGTGTTTCATTCTTACAGTCCATATGATCACAAGATTGGTGAAAGACAACAAGTGTTAGTAACAGAAGAATCTTTTGATTCCAAGTTTTATGTTGCACACAATCAATTCTATGAGCAGGTTTTAGTGCCAAAGAACCCTGCGTTCATGGGGAAGATGGTTGAAGTGGACATCTATGAATCAGGCAAACATTTTATGAAAGGGCAGCCAGTATCTGATGCCAAAGTGTACACGCCCTCCATCAGCAAACCGCTAGCAAAGGGAGAAGTCTCGGGTTTGACAAAGGACTTCAGAAATGGGCTTGGGAACCAGCTGAGTTCAGGATCCCACACCTCTGCTGCATCTCAGTGTGACTCAGCGAGTTCCAGAATGGTGCTGCCCATGCCAAGGCTACATCAAGACTGTGCGCTGAGGATGTCCGTGGGCTTGGCTCTGCTGGGTCTTCTTTTTGCTTTTTTTGTCAAGGTCTATAATTAGGGA'

I would like to split this string into 10 characters with space in between. So far I tried this but its a bit clumsy and does'nt always bin the characters into 10

gregexpr(".{10}|.{9}|.{8}|.{7}|.{6}|.{5}|.{4}|.{3}|.{2}|.{1}", x ))[[1]]

the issue with the above code is when the string ends with anything other than 10 characters, nth-1 characters have to hard coded.

i think you are looking for 10-mers ( k-mers) its very important in genetics, especially the 3-mers (triplets) — user12256545, Nov 09 '21 at 23:31

score 3 · Accepted Answer · answered Nov 09 '21 at 19:58

This is a little bit cheesy, but:

c(                             ## drop "omit" attribute
  na.omit(                     ## drop NA values (from end)
    unlist(                    ## collapse from data frame to vector
       read.fwf(               ## read fixed-width "file"
            textConnection(x), ## treat string as a file
                 widths = rep(10,    ## string width
                               1000  ## a 'big enough' value
           )))))

Or if you like (in recent-ish versions of R that have |>)

(x
   |> textConnection()
   |> read.fwf(widths = rep(10, 1000))
   |> unlist()
   |> na.omit()
   |> c()
)

```|>``` something new. Now R looks like F? Is it a new trend? — manro, Nov 09 '21 at 20:23

How to bin a long continuous string into section of nth characters?

1 Answers1