old_contents: from Bio import SeqIO
  from mutation_orchestrator import Mutation_Orchestrator
  import copy
  
  input_fasta_file = '../data/subsampled_hg38.fa'
  iterations = 100
  output_fasta_file = 'tests/output.fasta'
  
  def main():
      # read genome fasta
      original_genome = {}
      mutated_genome = {}
      for seq_record in SeqIO.parse(input_fasta_file, "fasta"):
          original_genome[seq_record.id] = seq_record
          mutated_genome[seq_record.id] = seq_record.seq.tomutable()
  
      orchestrator = Mutation_Orchestrator()
  
      # add SNVs
      for i in range(iterations):
          mutated_genome = orchestrator.snv(mutated_genome)
  
      # write fasta
      output_seqs = []
      for chrom in mutated_genome:
          output_seq = SeqIO.SeqRecord(seq=mutated_genome[chrom].toseq(),
                id=chrom, description='', name='')
          output_seqs.append(output_seq)
  
      with open(output_fasta_file, "w") as output_handle:
          SeqIO.write(output_seqs, output_handle, "fasta")
  
  if __name__ == "__main__":
      main()
  
new_contents: from Bio import SeqIO
  from mutation_orchestrator import Mutation_Orchestrator
  import copy
  
  input_fasta_file = '../data/subsampled_hg38.fa'
  iterations = 100
  output_fasta_file = 'tests/output.fasta'
  
  def write_bam(mutated_genome):
      raise NotImplementedError
  
  def write_fasta(mutated_genome):
      # write fasta
      output_seqs = []
      for chrom in mutated_genome:
          output_seq = SeqIO.SeqRecord(seq=mutated_genome[chrom].toseq(),
                id=chrom, description='', name='')
          output_seqs.append(output_seq)
  
      with open(output_fasta_file, "w") as output_handle:
          SeqIO.write(output_seqs, output_handle, "fasta")
  
  def main():
      # read genome fasta
      original_genome = {}
      mutated_genome = {}
      for seq_record in SeqIO.parse(input_fasta_file, "fasta"):
          original_genome[seq_record.id] = seq_record
          mutated_genome[seq_record.id] = seq_record.seq.tomutable()
  
      orchestrator = Mutation_Orchestrator()
  
      # add SNVs
      for i in range(iterations):
          mutated_genome = orchestrator.snv(mutated_genome)
  
      write_fasta(mutated_genome)
      write_bam(mutated_genome)
  
  if __name__ == "__main__":
      main()
  
subject: write bam unimplemented error