How to iterate entries in a function to create two new character vectors

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I am struggling to separate a single string input into a series of inputs. The user gives a list of FASTA formatted sequences (see example below). I'm able to separate the inputs into their own

ex:

">Rosalind_6404
CCTGCGGAAGATCGGCACTAGAATAGCCAGAACCGTTTCTCTGAGGCTTCCGGCCTTCCC
TCCCACTAATAATTCTGAGG
.>Rosalind_5959
CCATCGGTAGCGCATCCTTAGTCCAATTAAGTCCCTATCCAGGCGCTCCGCCGAAGGTCT
ATATCCATTTGTCAGCAGACACGC
"
[1] "Rosalind_6404CCTGCGGAAGATCGGCACTAGAATAGCCAGAACCGTTTCTCTGAGGCTTCCGGCCTTCCCTCCCACTAATAATTCTGAGG"    
[2] "Rosalind_5959CCATCGGTAGCGCATCCTTAGTCCAATTAAGTCCCTATCCAGGCGCTCCGCCGAAGGTCTATATCCATTTGTCAGCAGACACGC"

But I am struggling to find a way to create a function that splits the "Rosalind_6404" from the gene sequence to the unknown amount of FASTA sequences while creating new vectors for the split elements. Ultimately, the result would look something such as:

.> "Rosalind_6404" "Rosalind5959"
.> "CCTGCGGAAGATCGGCACTAGAATAGCCAGAACCGTTTCTCTGAGGCTTCCGGCCTTCCCTCCCACTAATAATTCTGAGG","CCATCGGTAGCGCATCCTTAGTCCAATTAAGTCCCTATCCAGGCGCTCCGCCGAAGGTCTATATCCATTTGTCAGCAGACACGC"

I was hoping the convert_entries function would allow me to iterate over all the elements of the prepped_s character vector and split the elements into two new vectors with the same index number.

s <- ">Rosalind_6404
CCTGCGGAAGATCGGCACTAGAATAGCCAGAACCGTTTCTCTGAGGCTTCCGGCCTTCCC
TCCCACTAATAATTCTGAGG
>Rosalind_5959
CCATCGGTAGCGCATCCTTAGTCCAATTAAGTCCCTATCCAGGCGCTCCGCCGAAGGTCT
ATATCCATTTGTCAGCAGACACGC"

split_s <- strsplit(s, ">")
ul_split_s<- unlist(split_s)
fixed_s <- gsub("\n","", ul_split_s)
prepped_s <- fixed_s[-1]
prepped_s
nchar(prepped_s[2])
print(prepped_s[2])

entry_tags <- list()
entry_seqs <- list()

entries <- length(prepped_s)
unlist(entries)
first <- prepped_s[1]

convert_entries <- function() {
  for (i in entries) {
    tag <- substr(prepped_s[i], start = 1, stop = 13)
    entry_tags <- append(entry_tags, tag)
    return(entry_tags)
  } 
}
entry_tags <- convert_entries()
print(entry_tags)

Please help in any way you can, thanks!

fasta bioinformatics r
3 Answers

One option with tidyverse

library(dplyr)
library(tidyr)
library(stringr)
tibble(col1 = s) %>% 
   separate_rows(col1, sep="\n") %>%
   group_by(grp = cumsum(str_detect(col1, '^>'))) %>%
   summarise(prefix = first(col1), 
             col1 = str_c(col1[-1], collapse=""), .groups = 'drop') %>% 
   select(-grp)

-output

# A tibble: 2 x 2
  prefix           col1                                                                                
  <chr>          <chr>                                                                               
1 >Rosalind_6404 CCTGCGGAAGATCGGCACTAGAATAGCCAGAACCGTTTCTCTGAGGCTTCCGGCCTTCCCTCCCACTAATAATTCTGAGG    
2 >Rosalind_5959 CCATCGGTAGCGCATCCTTAGTCCAATTAAGTCCCTATCCAGGCGCTCCGCCGAAGGTCTATATCCATTTGTCAGCAGACACGC
user_37322710

Using seqinr package:

library(seqinr)

# example fasta file
write(">Rosalind_6404
CCTGCGGAAGATCGGCACTAGAATAGCCAGAACCGTTTCTCTGAGGCTTCCGGCCTTCCC
TCCCACTAATAATTCTGAGG
>Rosalind_5959
CCATCGGTAGCGCATCCTTAGTCCAATTAAGTCCCTATCCAGGCGCTCCGCCGAAGGTCT
ATATCCATTTGTCAGCAGACACGC", "myFile.fasta")

# read the fasta file
x <- read.fasta("myFile.fasta", as.string = TRUE, forceDNAtolower = FALSE)

# get the names
names(x)
# [1] "Rosalind_6404" "Rosalind_5959"

# get the seq
x$Rosalind_6404
# [1] "CCTGCGGAAGATCGGCACTAGAATAGCCAGAACCGTTTCTCTGAGGCTTCCGGCCTTCCCTCCCACTAATAATTCTGAGG"
# attr(,"name")
# [1] "Rosalind_6404"
# attr(,"Annot")
# [1] ">Rosalind_6404"
# attr(,"class")
# [1] "SeqFastadna"
user_6800680

In base R you could do:

t(gsub('\n', '', regmatches(s, gregexec("([A-Z][a-z_0-9]+)\n([A-Z\n]+)", s))[[1]][-1,]))
     [,1]            [,2]                                                                                  
[1,] "Rosalind_6404" "CCTGCGGAAGATCGGCACTAGAATAGCCAGAACCGTTTCTCTGAGGCTTCCGGCCTTCCCTCCCACTAATAATTCTGAGG"    
[2,] "Rosalind_5959" "CCATCGGTAGCGCATCCTTAGTCCAATTAAGTCCCTATCCAGGCGCTCCGCCGAAGGTCTATATCCATTTGTCAGCAGACACGC"

NOTE: I transposed the matrix so that you may vie the results. Ignore the use of t function

Another base R solution:

  read.table(text=sub('\n', ' ', gsub('(\\D)\n', '\\1', unlist(strsplit(s, '>')))))
             V1                                                                                   V2
1 Rosalind_6404     CCTGCGGAAGATCGGCACTAGAATAGCCAGAACCGTTTCTCTGAGGCTTCCGGCCTTCCCTCCCACTAATAATTCTGAGG
2 Rosalind_5959 CCATCGGTAGCGCATCCTTAGTCCAATTAAGTCCCTATCCAGGCGCTCCGCCGAAGGTCTATATCCATTTGTCAGCAGACACGC

or even

proto <- data.frame(name = character(), value = character())
new_s <- gsub('\n', '', unlist(strsplit(s, '>')))
strcapture("([A-Z][a-z_0-9]+)([A-Z]+)", grep('\\w', new_s, value = T), proto)

           name                                                                                value
1 Rosalind_6404     CCTGCGGAAGATCGGCACTAGAATAGCCAGAACCGTTTCTCTGAGGCTTCCGGCCTTCCCTCCCACTAATAATTCTGAGG
2 Rosalind_5959 CCATCGGTAGCGCATCCTTAGTCCAATTAAGTCCCTATCCAGGCGCTCCGCCGAAGGTCTATATCCATTTGTCAGCAGACACGC
user_83802720
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