Using getFrag to extract sequence fragments

Question

[margo]

I have a DNA sequence in SeqFastadna format as a result of seqnir package in R. I am using the getFrag() function to extract sequence fragments. For example my SeqFastadna object (f) looks like this:

$genome
   [1] "t" "t" "a" "a" "a" "a" "a" "a" "g" "a" "g" "a" "t" "c"
[1] "genome"
attr(,"Annot")
[1] ">genome, complete genome"
attr(,"class")
[1] "SeqFastadna"

When using the getFrag function getFrag(f, 1, 5), it prints out unnecessary information. I am only wanting the 5 bases, however this function is printing out other attributes too:

[1] "t" "t" "a" "a" "a"
attr(,"seqMother")
[1] "genome"
attr(,"begin")
[1] 1
attr(,"end")
[1] 5
attr(,"class")
[1] "SeqFrag"

Is there any way where I can just return the bases and have the following output?:

[1] "t" "t" "a" "a" "a"

Answer 1

[Basti]

You can unlist it to remove attributes : unlist(getFrag(f,1,5))

[rpolicastro]

This won't remove attributes. You can use the as.character generic or remove them directly attributes(frag) <- NULL.

[Basti]

My code produces the desired output, which is of class character and without attributes. as.character will not produce the desired output and attributes(getFrag(f,1,5)) is already NULL.

[rpolicastro]

From what information they provided the output is a vector, which would be equivalent to the below code that uses a vector of characters as input.

library("seqinr")

s <- read.fasta(file = system.file("sequences/malM.fasta", package = "seqinr"))

> getFrag(s[[1]], 1, 10)
 [1] "a" "t" "g" "a" "a" "a" "a" "t" "g" "a"
attr(,"seqMother")
[1] "XYLEECOM.MALM"
attr(,"begin")
[1] 1
attr(,"end")
[1] 10
attr(,"class")
[1] "SeqFrag"

In this case unlist won't work since it's not a list.

> getFrag(s[[1]], 1, 10) |> unlist()
 [1] "a" "t" "g" "a" "a" "a" "a" "t" "g" "a"
attr(,"seqMother")
[1] "XYLEECOM.MALM"
attr(,"begin")
[1] 1
attr(,"end")
[1] 10
attr(,"class")
[1] "SeqFrag"

But as.character would work (same with setting attributes to NULL).

> getFrag(s[[1]], 1, 10) |> as.character()
 [1] "a" "t" "g" "a" "a" "a" "a" "t" "g" "a"

Your code would work if the input was an unaltered SeqFastadna object, but that wouldn't match with the OP's output.

> getFrag(s, 1, 10)
[[1]]
 [1] "a" "t" "g" "a" "a" "a" "a" "t" "g" "a"
attr(,"seqMother")
[1] "XYLEECOM.MALM"
attr(,"begin")
[1] 1
attr(,"end")
[1] 10
attr(,"class")
[1] "SeqFrag"

> getFrag(s, 1, 10) |> unlist()
 [1] "a" "t" "g" "a" "a" "a" "a" "t" "g" "a"

It is possible that OP didn't provide the full output though, in which case your code would work incidentally.

[Basti]

Indeed, thank you for the clarifications.

[margo]

The unlist option gave me the desired output. Thank you!