uShuffleR.RmduShuffle is a useful tool for shuffling biological sequences published by Minghui Jiang et.al. This package is R wrapper for the tool.
BiocManager::install("jianhong/uShuffleR")
library(uShuffleR)
f <- system.file("extdata", "test.fa", package="uShuffleR")
s <- shuffle(f)
s## DNAStringSet object of length 2:
## width seq names
## [1] 32 AGGTTTCATCGTAGACTGATTAGGTTCAAGGC read1_shuffle_1
## [2] 32 AGAAGGGTAGGCACTGAGTCATTTCGTTTATC read1_shuffle_2
library(Biostrings)
writeXStringSet(s, "shuffled.sequence.fa")## R Under development (unstable) (2021-04-08 r80148)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.2 LTS
##
## Matrix products: default
## BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=C
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats4 parallel stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] Biostrings_2.59.2 XVector_0.31.1 IRanges_2.25.7
## [4] S4Vectors_0.29.15 BiocGenerics_0.37.1 uShuffleR_0.0.2
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.6 knitr_1.31 magrittr_2.0.1 zlibbioc_1.37.0
## [5] R6_2.5.0 ragg_1.1.2 rlang_0.4.10 fastmap_1.1.0
## [9] stringr_1.4.0 tools_4.1.0 xfun_0.22 htmltools_0.5.1.1
## [13] systemfonts_1.0.1 yaml_2.2.1 digest_0.6.27 rprojroot_2.0.2
## [17] pkgdown_1.6.1 crayon_1.4.1 textshaping_0.3.3 fs_1.5.0
## [21] memoise_2.0.0 cachem_1.0.4 evaluate_0.14 rmarkdown_2.7
## [25] stringi_1.5.3 compiler_4.1.0 desc_1.3.0