data-raw/make_small_arabi_genome.md

In joelnitta/baitfindR: Find Baits for Sequence Capture

make_small_arabi_genome

Joel Nitta 5/11/2019

Make small version of Arabidopsis genome file for testing functions.

This only includes the first ca. 100,000 bases of chromosome 1.

library(tidyverse)

## ── Attaching packages ───────────────────────── tidyverse 1.2.1 ──

## ✔ ggplot2 3.1.0       ✔ purrr   0.3.2  
## ✔ tibble  2.1.1       ✔ dplyr   0.8.0.1
## ✔ tidyr   0.8.1       ✔ stringr 1.4.0  
## ✔ readr   1.3.1       ✔ forcats 0.3.0

## ── Conflicts ──────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag()    masks stats::lag()

# Download genome
download.file(
  url = "ftp://ftp.ensemblgenomes.org/pub/release-40/plants/fasta/arabidopsis_thaliana/dna/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa.gz",
  destfile = here::here("data-raw/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa.gz")
  )

# Unzip
R.utils::gunzip(
  filename = here::here("data-raw/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa.gz"),
  destname = here::here("data-raw/Arabidopsis_thaliana.TAIR10.dna.toplevel.fasta")
)

# Read in fasta
arabidopsis_genome <- ape::read.FASTA(here::here("data-raw/Arabidopsis_thaliana.TAIR10.dna.toplevel.fasta"))

# Fix names (only take first part of name separated by space)
names(arabidopsis_genome) <-
  names(arabidopsis_genome) %>% str_split(" ") %>% map_chr(1)

# Keep only first 100,000 nucleotides of chromosome 1
arabidopsis_genome_small <- arabidopsis_genome["1"]
arabidopsis_genome_small[["1"]] <- arabidopsis_genome_small[["1"]][1:100000]

# Write out FASTA file to inst/extdata
ape::write.FASTA(
  arabidopsis_genome_small,
  here::here("inst/extdata/Arabidopsis_thaliana_TAIR10_40_small.fasta"))

sessionInfo()

## R version 3.5.2 (2018-12-20)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS High Sierra 10.13.6
## 
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] forcats_0.3.0   stringr_1.4.0   dplyr_0.8.0.1   purrr_0.3.2    
## [5] readr_1.3.1     tidyr_0.8.1     tibble_2.1.1    ggplot2_3.1.0  
## [9] tidyverse_1.2.1
## 
## loaded via a namespace (and not attached):
##  [1] tidyselect_0.2.5  xfun_0.5          haven_1.1.2      
##  [4] lattice_0.20-38   colorspace_1.3-2  htmltools_0.3.6  
##  [7] yaml_2.2.0        rlang_0.3.1       R.oo_1.22.0      
## [10] pillar_1.3.1      glue_1.3.1        withr_2.1.2      
## [13] R.utils_2.7.0     modelr_0.1.2      readxl_1.1.0     
## [16] plyr_1.8.4        munsell_0.5.0     gtable_0.2.0     
## [19] cellranger_1.1.0  rvest_0.3.2       R.methodsS3_1.7.1
## [22] evaluate_0.13     knitr_1.21        parallel_3.5.2   
## [25] broom_0.5.0       Rcpp_1.0.1        scales_1.0.0     
## [28] backports_1.1.3   jsonlite_1.6      hms_0.4.2        
## [31] digest_0.6.18     stringi_1.4.3     grid_3.5.2       
## [34] rprojroot_1.3-2   here_0.1          cli_1.1.0        
## [37] tools_3.5.2       magrittr_1.5      lazyeval_0.2.1   
## [40] crayon_1.3.4      ape_5.3           pkgconfig_2.0.2  
## [43] xml2_1.2.0        lubridate_1.7.4   assertthat_0.2.1 
## [46] rmarkdown_1.11    httr_1.4.0        rstudioapi_0.9.0 
## [49] R6_2.4.0          nlme_3.1-137      compiler_3.5.2

joelnitta/baitfindR documentation built on May 7, 2020, 6:21 p.m.