code: def scaffolds_to_contigs(infile, outfile, number_contigs=False):
      '''Makes a file of contigs from scaffolds by splitting at every N.
         Use number_contigs=True to add .1, .2, etc onto end of each
         contig, instead of default to append coordinates.'''
      seq_reader = sequences.file_reader(infile)
      fout = utils.open_file_write(outfile)
  
      for seq in seq_reader:
          contigs = seq.contig_coords()
          counter = 1
          for contig in contigs:
              if number_contigs:
                  name = seq.id + '.' + str(counter)
                  counter += 1
              else:
                  name = '.'.join([seq.id, str(contig.start + 1), str(contig.end + 1)])
              print(sequences.Fasta(name, seq[contig.start:contig.end+1]), file=fout)
  
      utils.close(foutf scaffolds_to_contigs(infile, outfile, number_contigs=False):
      '''Makes a file of contigs from scaffolds by splitting at every N.
         Use number_contigs=True to add .1, .2, etc onto end of each
         contig, instead of default to append coordinates.'''
      seq_reader = sequences.file_reader(infile)
      fout = utils.open_file_write(outfile)
  
      for seq in seq_reader:
          contigs = seq.contig_coords()
          counter = 1
          for contig in contigs:
              if number_contigs:
                  name = seq.id + '.' + str(counter)
                  counter += 1
              else:
                  name = '.'.join([seq.id, str(contig.start + 1), str(contig.end + 1)])
              print(sequences.Fasta(name, seq[contig.start:contig.end+1]), file=fout)
  
      utils.close(fout)
docs: Makes a file of contigs from scaffolds by splitting at every N.
         Use number_contigs=True to add .1, .2, etc onto end of each
         contig, instead of default to append coordinates.