Writing fasta files using R package seqinr?

user_1467250 0
Viewed 14117

When I use write.fasta in seqinr, the file that it outputs looks like this:

>Sequence name 1

>Sequence name 2

>Sequence name 3
...etc

Sequence 1 Sequence 2 Sequence 3 ...etc

In other words, the sequence names are all at the beginning of the file, and then the sequences are output together at the end of the file.

What I'd like to do is this:

>Sequence name 1
Sequence 1
>Sequence name 2
Sequence 2
>Sequence name 3
Sequence 3
...etc

Is that possible with write.fasta?

fasta r
4 Answers

A minimal example:

write.fasta(as.list(c('AAA', 'CCC')), names=c("a", "b"), 
                               as.string=FALSE, file.out="foo.fa")
user_15600580

I got stuck with this and got some help from a friend. You need to define the sequences in a list here is an example of code where the input from maxquant output is a csv with a column called sequence and a name column called 'leading razor protein':

library(tidyverse)
library(seqinr)
MU = read_csv('data.csv')
seqs = as.list(dplyr::pull(MU, Sequence))
names = dplyr::pull(MU, `Leading razor protein`)
write.fasta(seqs, names, "MU.fasta",
            open = "w", as.string = FALSE)
user_121309570
Related