Biopython not installed correctly error when trying to call python script from R on a MacOS

Question

[devarts]

I'm trying to run a script in r that relies on calling a python script. I'm using a Mac with Python 3.8.2 installed and Biopython installed through Python 3, but I keep getting the following error. I've uninstalled and reinstalled Python 3 and Biopython, but continue to get the following error. "BioPython not installed correctly (see http://biopython.org)"

Does anyone have any ideas about what is going on and how to resolve it? The key part of the script and where the problem is seems to be this.

  cmnd<-paste0('./anaconda3/envs/python3.8.2/bin/python3.8 ','"', pfile, '"'," -f ", '"', source_file, '"', "  ", '-m simple -M reduced_alphabet_2 -k 10 -o ', '"', dest_file, '"')
  cat(cmnd)
  system(cmnd)

The whole script chunk is as follows.

kGenFasta <- function(i) {
#for(i in 1:192){
  pfile<-"./SIEVE-Ub-master/KmerFeatures.py"
  #source_file<-paste0("/Applications/kayes/tailocin\ work/S\ tailocin/tailorcinData/",i,".fa")

  source_file<-paste0("./PHASTERzero_cleaned_proteins/X_cleaned_files/",i,".fasta")


  if (file.exists(source_file)){
    print(i)

  #dest_file<-paste0("/Applications/kayes/tailocin\ work/J\ work/tailocin/red_0/kmer_",i,".csv")
  dest_file<-paste0("./PHASTER_zero_proteins/PHASTERzero_cleaned_proteins/X_cleaned_files/red_2/kmer_",i,".csv")




  cmnd<-paste0('/Users/evar698/anaconda3/envs/python3.8.2/bin/python3.8 ','"', pfile, '"'," -f ", '"', source_file, '"', "  ", '-m simple -M reduced_alphabet_2 -k 10 -o ', '"', dest_file, '"')
  cat(cmnd)
  system(cmnd)


}
}

#library(lme4)
core<-detectCores()-2
core
#set.seed( 123, kind = "L'Ecuyer-CMRG" )
tmxList <- mclapply(1:77, kGenFasta, mc.cores = core)

[Joe]

What happens if you try to invoke a dummy python command (so, not Biopython)? e.g. have R call a script which just prints out some version numbers or writes a dummy file.

[devarts]

Dummy Python commands work. What I found is that parts of the Biopython that was being called within the python script, that was being called, were deprecated. Changing those, made it work.

Answer 1

[devarts]

What I found is that parts of the Biopython that was being called within the python script, that was being called, were deprecated. Changing those, made it work.