Using R for bioinformatics here: 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 and use it as an argument?
$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
A very minimal reproducible example. Interestingly, this will not work if each element of the list has a name (i.e. just returns the same list). Make sure that names(dna_list) <- NULL. I am unsure of the specific reason for this, perhaps someone else may know and would care to comment.
require(Biostrings)
x0 <- DNAStringSet(c("CTCCCAGTAT", "TTCCCGA", "TACCTAGAG"))
x1 <- DNAStringSet(c("AGGTCGT", "GTCAGTGGTCCCC", "CATTTTAGG"))
x2 <- DNAStringSet(c("TGCTAGCTA", "AGTCTTGC", "AGCTTTCGAG"))
dna_list <- list(x0, x1, x2)
> dna_list
[[1]]
A DNAStringSet instance of length 3
width seq
[1] 10 CTCCCAGTAT
[2] 7 TTCCCGA
[3] 9 TACCTAGAG
[[2]]
A DNAStringSet instance of length 3
width seq
[1] 7 AGGTCGT
[2] 13 GTCAGTGGTCCCC
[3] 9 CATTTTAGG
[[3]]
A DNAStringSet instance of length 3
width seq
[1] 9 TGCTAGCTA
[2] 8 AGTCTTGC
[3] 10 AGCTTTCGAG
do.call(c, dna_list)
> do.call(c, dna_list)
A DNAStringSet instance of length 9
width seq
[1] 10 CTCCCAGTAT
[2] 7 TTCCCGA
[3] 9 TACCTAGAG
[4] 7 AGGTCGT
[5] 13 GTCAGTGGTCCCC
[6] 9 CATTTTAGG
[7] 9 TGCTAGCTA
[8] 8 AGTCTTGC
[9] 10 AGCTTTCGAG