How to write a list of DNAStringsets as a FASTA file in R

Question

[newscient]

Starter in using R and Bioconductor for bioinformatics projects, my question is:

I have a list of DNAstringsSets (seen below) and want to use the writeXstringset() function which takes a DNAstringset object as an argument in order to save as a FASTA file.Anyone knows how is it possible to collapse the list of DNAstringsets into a single DNAStringset object?

$NM_008866
  A DNAStringSet instance of length 13
     width seq                                                        names               
 [1]   693 ATGTGCGGCAACAACATGTCCGCTCCGA...GATAAGCTCCTACCTCCAATTGATTGA NM_008866
 [2]    72 ATGGATGGGCAGAAGCCTTTGCAGGTAT...AATACATCTGTCCACATGCCCCTGTGA NM_008866
 [3]   114 ATGGGCAGAAGCCTTTGCAGGTATCAAA...GAATATGGCTATGCCTTCTTGGTTTGA NM_008866
 [4]   213 ATGGCATTCCTTCTAACAGGATTATTTT...AGTGCCATGGAGATTGTGACCCTTTAG NM_008866
 [5]    63 ATGTCAAGCACTTCATTGATAAGCTCCT...TTGATTGACATCACTAAGAGGCCTTGA NM_008866
 ...   ... ...
 [9]   219 ATGGCCCTTCTATTGGGAGACCAGGCTT...CAGAGGCAGGCGGATCTCTGTCAATAG NM_008866
[10]   144 ATGTTATGCTTAAAACCAAATACTGTTC...CAGTCTCCTGTACAAATATTAAAATAA NM_008866
[11]    78 ATGTTGCAAAAATTATGGTTATTTCTGA...CCAACCAACCAAGAAGCACCTTTATAA NM_008866
[12]    75 ATGGTTATTTCTGAACGGTTGCTTTTCT...AGAAGCACCTTTATAAACAGGTGCTAA NM_008866
[13]    90 ATGTCTGGATTTAAAACAATTTCAAACA...AATTTACTTCAGTTATTCTATCTGTAA

$NM_001159750
  A DNAStringSet instance of length 9
    width seq                                                         names               
[1]   903 ATGGAGGACGAGGTGGTTCGCATTGCCA...ATGTGGAAATCGGTGGAAGTTCTGTTGA NM_001159750
[2]   105 ATGGACCATCAACTGATAAAGACCCTGA...AGAGAAGAAAGTTCCAGCAGCAATGTAA NM_001159750
[3]    75 ATGAGACAAATGCTCGAGATACATATGT...CCAAGCACTTCTGATTCTGTGCGATTAA NM_001159750
[4]    75 ATGATTATGTTGCAATTGGAGCTGATGA...ATTGAGGAAGCTATATATCAAGAAATAA NM_001159750
[5]   129 ATGAATGTGGAAATCGGTGGAAGTTCTG...GCCAGGCAACTCGTTTCCTTGCAAGTGA NM_001159750
[6]    63 ATGTGGAAATCGGTGGAAGTTCTGTTGA...AGAATTGGCAAAGTATCTGGACCATTAA NM_001159750
[7]   102 ATGTGTCCCACTTGTTTTGCTAGTAATA...TATAGTAAAGGCCACTTTTATAAATTAA NM_001159750
[8]   102 ATGGAAAACAATATGTCCATGTTAAAAG...CGGGAGGCAGAGGCAGGCGGATTTCTGA NM_001159750
[9]    75 ATGGATAATTTCTGTCACTTTAAAAATA...TAGTTTAAAAGTAATAAGGTTAAAATAG NM_001159750

$NM_011541
  A DNAStringSet instance of length 9
    width seq                                                         names               
[1]   906 ATGGAGGACGAGGTGGTTCGCATTGCCA...ATGTGGAAATCGGTGGAAGTTCTGTTGA NM_011541
[2]   108 ATGGACCATCAACTGATAAAGACCCTGA...GAAGAAAGTAGTTCCAGCAGCAATGTAA NM_011541
[3]    75 ATGAGACAAATGCTCGAGATACATATGT...CCAAGCACTTCTGATTCTGTGCGATTAA NM_011541
[4]    75 ATGATTATGTTGCAATTGGAGCTGATGA...ATTGAGGAAGCTATATATCAAGAAATAA NM_011541
[5]   129 ATGAATGTGGAAATCGGTGGAAGTTCTG...GCCAGGCAACTCGTTTCCTTGCAAGTGA NM_011541
[6]    63 ATGTGGAAATCGGTGGAAGTTCTGTTGA...AGAATTGGCAAAGTATCTGGACCATTAA NM_011541
[7]   102 ATGTGTCCCACTTGTTTTGCTAGTAATA...TATAGTAAAGGCCACTTTTATAAATTAA NM_011541
[8]   102 ATGGAAAACAATATGTCCATGTTAAAAG...CGGGAGGCAGAGGCAGGCGGATTTCTGA NM_011541
[9]    75 ATGGATAATTTCTGTCACTTTAAAAATA...TAGTTTAAAAGTAATAAGGTTAAAATAG NM_011541

$NM_001159751
  A DNAStringSet instance of length 9
    width seq                                                         names               
[1]   939 ATGTGTCCCTCGGTGTGTACCACTTTCC...ATGTGGAAATCGGTGGAAGTTCTGTTGA NM_001159751
[2]   108 ATGGACCATCAACTGATAAAGACCCTGA...GAAGAAAGTAGTTCCAGCAGCAATGTAA NM_001159751
[3]    75 ATGAGACAAATGCTCGAGATACATATGT...CCAAGCACTTCTGATTCTGTGCGATTAA NM_001159751
[4]    75 ATGATTATGTTGCAATTGGAGCTGATGA...ATTGAGGAAGCTATATATCAAGAAATAA NM_001159751
[5]   129 ATGAATGTGGAAATCGGTGGAAGTTCTG...GCCAGGCAACTCGTTTCCTTGCAAGTGA NM_001159751
[6]    63 ATGTGGAAATCGGTGGAAGTTCTGTTGA...AGAATTGGCAAAGTATCTGGACCATTAA NM_001159751
[7]   102 ATGTGTCCCACTTGTTTTGCTAGTAATA...TATAGTAAAGGCCACTTTTATAAATTAA NM_001159751
[8]   102 ATGGAAAACAATATGTCCATGTTAAAAG...CGGGAGGCAGAGGCAGGCGGATTTCTGA NM_001159751
[9]    75 ATGGATAATTTCTGTCACTTTAAAAATA...TAGTTTAAAAGTAATAAGGTTAAAATAG NM_001159751

[seidel]

Answered at stackexchange using:do.call(c, dna_list)

[newscient]

Thanks, i used the do.call, but first i had to get rid of the names in my DNAStringSet by using

names(dna_list)<- NULL

Answer 1

[dillonchan97]

Hi, I am aware that this post is very old! I ran into a similar problem, putting many DNAStrings into a list. This is how I solved it:

list_of_DNAStrings # your list of DNAStrings
LargeDNAStringSet <- DNAStringSet(sapply(list_of_DNAStrings, `[[`, 1)) 
# the sapply gets a DNAString from each member of the list. 
# This works if typeof(list_of_DNAStrings[[1]]) is S4, or DNAStrings.
writeXStringSet(LargeDNAStringSet, 'fname.fa')

Answer 2

[Ram]

Maybe try union() method to join all the DNAStringSets? The manual says it works on XStringSets and DNAStringSet is derived from XStringSet.

[newscient]

Yes but how can I use union() on a list of DNAStringSet? I see that it needs single DNAStringsets as arguments

[Ram]

I'd either write a loop, like so:

i<-1
growing<-set[i-1]
while (i<=len(set))
to_add<-set[i]
growing<-union(growing,to_add)
i<-i+1
END_LOOP

(Sorry, not too familiar with R)

Or use a Reduce function, from here

Answer 3

[alslonik]

Just in case someone needed to save it as a list of fastas, like me, you can it with a for loop:

for (i in names(myAAStringSetList)) {
  writeXStringSet(myAAStringSetList[[i]], filepath = paste0("path/to/your/directory/",i, ".fasta"), format = "fasta")
}