Zenodo to R Download

Author: Madison Raposa

Zenodo_to_R_Updated.R

@@ -0,0 +1,36 @@
+get_amplicon <- function(amplicon) {
+  #put R code inside here
+  
+  library(dplyr)
+  library(tidyverse)
+  
+  ## Read in the table from zenodo using the url
+  sample_att = read.csv(
+    'https://zenodo.org/record/3774043/files/SRA%20Sample%20Worksheet.csv'
+  )
+  
+  amp = filter(sample_att, samp_mat_process == amplicon)
+  amp
+  
+  ## Pull the column containing the sample names.fastq
+  amp %>% pull(sample_title.fastq)
+  
+  ## Change rbcl into a vector
+  amp_name <- as.vector(amp$sample_title.fastq)
+  
+  ## Create the urls for the files using the paste function and download the files
+  urls = vector()
+  for (x in 1:length(amp_name)) {
+    urls[x] = paste('https://zenodo.org/record/3736457/files/',
+                    amp_name[x],
+                    sep = '')
+    download.file(urls[x], amp_name[x])
+  }
+  
+  return()
+}
+
+get_amplicon('rbcLa_amplicon')
+
+
+get_amplicon("ITS2_amplicon")