How to write pairwiseAlignment in R in Fasta Format with Headers?

Question

[Yosi]

Hi there,

I try to write an R-script with which I can align a bench of sequences in one file with a single sequence in another file.

So far, I'm really happy with the results, but I have one big problem. How to write the pairwiseAlignment output in fasta format WITH header names?

I did this (among others):

seq1 <- readDNAStringSet("file1.fasta", use.names=T)
seq2 <- readDNAStringSet("file2.fasta", use.names=T)

mat <- nucleotideSubstitutionMatrix(match = 1, mismatch = -3, baseOnly= F)

# here I will introduce a for-loop to align every sequence against the sequence in file2
globalAlign <- pairwiseAlignment(seq1[1], seq2[1], type='global-local', substitutionMatrix=mat, gapOpening=10, gapExtension=-5)

r = BStringSet( c(toString(subject(globalAlign)), toString(pattern(globalAlign))) )
writeXStringSet(r,"out1.txt")

But my "out1.txt"-outfile looks like this:

>
ATGCGATGCTAGCTGCATAGCTCGATCG
>
ATGCGAT---AGCTGCATAGCT---TCG

Has anyone of you an idea how to include the sequence names so that it will look like this:

>seq_name_1
ATGCGATGCTAGCTGCATAGCTCGATCG
>seq_name_2
ATGCGAT---AGCTGCATAGCT---TCG

Many thanks in advance!

Answer 1

[Brice Sarver]

I tried this with two DNAString instances, a and b, with sequences "ACTG" and "GTCA". I then performed the global alignment the way you did, and I converted them to a BStringSet the same way you did. This is 'r'.

Objects of class XStringSet can have names assigned, but pairwiseAlignments cannot as far as I know. This makes sense; it's just a comparison, and you ought to know what you're comparing beforehand. This doesn't help when you want to write out the files. You can add the names this way:

> r
  A BStringSet instance of length 2
    width seq
[1]     4 GTCA
[2]     4 ACTG
> names(r)
NULL
> names(r) <- c("a", "b")
> r
  A BStringSet instance of length 2
    width seq                                               names
[1]     4 GTCA                                              a
[2]     4 ACTG                                              b​