I have this DNA stringset, but I want to create a new file.fa containing this information. What is an efficient way to save these? I've tried to use write.fasta but it crashed.
genes_seq <-
A DNAStringSet instance of length 254667
width seq names
[1] 2298 ATGGTGTCGTCTCCTTTCTATGTGAACAAGTTCA...AAAAAAATCAAAAACAAATCAAAAATCAAAAAA 22
[2] 2600 CTGACATAGATAAGTTTAGAGTTACCTCCCCTGT...GATACATACACATATATATCCATGTAAGATAGA 22
[3] 1351 ACACATTTATATATATTTATAAATATCAATAAAT...CGCATGTGTGTGTATGAGAGAGAGAGAGAGAGC 22
[4] 3668 TTGTTGATCAGCAGTAATGGTAAGGAAGTTAGTA...CACGAAATCATTGGGTTATTTTTTATACCAGTA 22
[5] 762 ATGACCATCTTTGGGGCAGAATCCACTTTTCATC...TCATTGGTCAGTTTTATTAAAGGCAGCATTTAA 22
... ... ...
[2544] 558 CTAGATCCTTCTCCTGCTGTTATCAAAAGTAGAC...ACTGATGTAATACTGCAATTAAACATGATAGCA 22
[2545] 1319 TTGAAAATGAATTATAGAAATGTCTTTTTCACGA...ACTTGCACTAAAACATTTAGCAATTTGGTTAGC 22
[2546] 1365 GTATTTTGTTTCAAATGTACAAGCTTGGACAACA...GACTGCATGCATTTACATTTATGTAAATACAAA 22
[2547] 1970 CAGAATACCAGAAACAGCGAAGAATTTTTCACAT...GAAATATATATGTGTGTGTATATATAAATAAAT 22
[2548] 260 TTTATTTTTATTCAAAAGACATGGACATTAAAGG...TCTACAGCTTTGCATTATGCTGTGACGGGGTAA OCBIM_22024624mg
>
The solution came from here https://bioinformatics.stackexchange.com/questions/3538/combine-fastq-by-writefastq-is-not-working-properly
# Non reproducible example
library(ShortRead)
library(Biostrings)
head(fasta)
# A DNAStringSet instance of length 6
# width seq names
# [1] 1786 GGGGAGCCCGCAGAATTCGGAAAAAATCGTACGCTAAGGTTTTCCGGGCATCCGTAAGGGCCGAAACTTCCCGTCTTCCAGTCTGCG...GGTGCATCGGCCGGCACCTTGCGCAGGTTGTCGGCGTTCATCTCACGCAGGGTCTGCACGGCTGCCAGCACGCCTTGCGCGGCCGGC NODE_108_length_1...
# [2] 590 GGTCAGCCAGGATTTCACTTTCCAGCCGGTCGAGCATCTGCACCAGCACCGGCGGGAACACCACACTGCCACCGTCTTCGCCGCCGG...TGACGGTCATACCGGTAAAGATAGTGCGCGTCACGGGCGATACGGTTATCCGGCCACATGCTGAGGGTGCTGTCCGGGTGCAGCTCC NODE_145_length_5...
# [3] 2618 CTCTCCCGCACCTACAGCAGTTACCGGACAAAAACGCCCGCGCCGGTGGGGAGCCTCGGCCCCGGCTGGAAAATGCCTGCGGATATC...GGACAGCACCCTCAGCATGTGGCCGGATAACCGTATCGCCCGTGACGCGCACTATCTTTACCGGTATGACCGTCACGGCAGGCTGAC NODE_96_length_26...
# [4] 446 CTGCTGTGCTGTTTTGGTCCATCGGTGCCGCATACATGCCCGATACAGCCGCGGCACCCAGCCAGCCCACAGGGTTCCACCATGCCA...AAATCCCCGTAAAGGCAGATGCGTGCCATGCCCGGTGACGCCAGAGGGAGTGTGTGCGTCGCTGCCATTTGTCGGTGTACCTCTCTC NODE_192_length_4...
# [5] 235 CCCCTGCAGCGGGTCATAATAGCGGTGGCGGTTGTAATACAGGCCGGACTCCTCATCATACTGCTGCCCCGGCAGGCGGATAAGCTG...CACGCTGTTGCCCCTTCCGTGCTGATAAGCGCCAGCGGCAGGCCGCGATGGTCGCAGTGGTACAGGTGGATTTTTCGCGCCGGCGTG NODE_556_length_2...
# [6] 650 CCCTGCCAGGTGTACTGCAGTTGTGGCTCCAGCATCAGGTTGTCAGTGATACTGAAGGGCAGACCGGTTTCCAGTGAGCCCAGCCAG...ACGATAAGCATTTTCACTGCGCAGGTACCAGTCTTCATCGCTGTCACGGTTCAGGGTGTAGTTAAAGGCGCCGGCCTGAAGCGGGCG NODE_137_length_6...
fasta_dir <- file.path(getwd(), "refs")
outfile <- file.path(dirname(fasta_dir), "seq_fasta.fasta")
writeFasta(fasta, outfile, mode = "a")