old_contents: import sys
  import os
  from subprocess import call
  #This step constructs the reference index to which the reads are eventually aligned. The input for this script are the core genomes while the output is a Bowtie index called core_genome_index.
  cmd ="bowtie2-build core_genomes.fasta core_genome_index"
  call(cmd,shell=True)
  
new_contents: import sys
  import os
  from subprocess import call
  #This step constructs the reference index to which the reads are eventually aligned. 
  #The input for this script are the core genomes while the output is a Bowtie2 reference index.
  #The reference index produced is of the same name as the input core genomes.
  argu = sys.argv[1]
  fname = argu.split(".")
  core_genomes = fname[0]
  cmd ="bowtie2-build "+core_genomes+".fasta "+core_genomes
  call(cmd,shell=True)
  
subject: Update BIB_prepare_index.py