How to use the biolib.common.check_dir_exists function in biolib

def bin_compare(self, options):
        """Bin compare command"""

        check_dir_exists(options.genome_nt_dir1)
        check_dir_exists(options.genome_nt_dir2)

        genomes_files1 = self._genome_files(options.genome_nt_dir1, options.genome_ext1)
        if not self._check_nuclotide_seqs(genomes_files1):
            self.logger.warning('All files must contain nucleotide sequences.')
            sys.exit()

        genomes_files2 = self._genome_files(options.genome_nt_dir2, options.genome_ext2)
        if not self._check_nuclotide_seqs(genomes_files2):
            self.logger.warning('All files must contain nucleotide sequences.')
            sys.exit()

        bin_comparer = BinComparer()
        bin_comparer.run(genomes_files1, genomes_files2, options.scaffold_file, options.output_file)

        self.logger.info('Detailed bin comparison written to: ' + options.output_file)

def ssu_erroneous(self, options):
        """Erroneous SSU command"""
        
        check_dependencies(('nhmmer', 'blastn'))

        check_dir_exists(options.genome_nt_dir)
        check_dir_exists(options.taxon_profile_dir)
        
        make_sure_path_exists(options.output_dir)
        
        genome_files = self._genome_files(options.genome_nt_dir, options.genome_ext)
        if not self._check_nuclotide_seqs(genome_files):
            self.logger.warning('All files must contain nucleotide sequences.')
            sys.exit()
             
        # identify scaffolds with 16S sequences
        ssu = SSU(options.cpus)
        ssu_hits = ssu.identify(genome_files, options.evalue, options.concatenate, options.output_dir)
        ssu_seq_files = ssu.extract(genome_files, ssu_hits, options.output_dir)
        ssu_classifications = ssu.classify(ssu_seq_files, options.ssu_db, options.ssu_taxonomy_file, options.evalue, options.output_dir)
        
        # report statistics for SSU scaffolds

def unbinned(self, options):
        """Unbinned Command"""

        check_dir_exists(options.genome_nt_dir)

        genomes_files = self._genome_files(options.genome_nt_dir, options.genome_ext)
        if not self._check_nuclotide_seqs(genomes_files):
            self.logger.warning('All files must contain nucleotide sequences.')
            sys.exit()

        unbinned = Unbinned()
        unbinned_seqs = unbinned.run(genomes_files, options.scaffold_file, options.min_seq_len)

        seq_io.write_fasta(unbinned_seqs, options.output_file)

        self.logger.info('Unbinned scaffolds written to: ' + options.output_file)

def ssu_erroneous(self, options):
        """Erroneous SSU command"""
        
        check_dependencies(('nhmmer', 'blastn'))

        check_dir_exists(options.genome_nt_dir)
        check_dir_exists(options.taxon_profile_dir)
        
        make_sure_path_exists(options.output_dir)
        
        genome_files = self._genome_files(options.genome_nt_dir, options.genome_ext)
        if not self._check_nuclotide_seqs(genome_files):
            self.logger.warning('All files must contain nucleotide sequences.')
            sys.exit()
             
        # identify scaffolds with 16S sequences
        ssu = SSU(options.cpus)
        ssu_hits = ssu.identify(genome_files, options.evalue, options.concatenate, options.output_dir)
        ssu_seq_files = ssu.extract(genome_files, ssu_hits, options.output_dir)
        ssu_classifications = ssu.classify(ssu_seq_files, options.ssu_db, options.ssu_taxonomy_file, options.evalue, options.output_dir)
        
        # report statistics for SSU scaffolds
        self.logger.info('Identifying scaffolds with 16S rRNA genes with divergent taxonomic classification.')

def call_genes(self, options):
        """Call genes command"""

        check_dir_exists(options.genome_nt_dir)
        make_sure_path_exists(options.output_dir)

        genome_files = self._genome_files(options.genome_nt_dir, options.genome_ext)
        if not self._check_nuclotide_seqs(genome_files):
            self.logger.warning('All files must contain nucleotide sequences.')
            sys.exit()

        # call genes in genomes
        prodigal = Prodigal(options.cpus)
        prodigal.run(genome_files, options.output_dir)
        self.logger.info('Genes in genomes written to: %s' % options.output_dir)

        # call genes in unbinned scaffolds
        if options.unbinned_file:
            unbinned_output_dir = os.path.join(options.output_dir, 'unbinned')
            prodigal.run([options.unbinned_file], unbinned_output_dir, meta=True)

"""Identify genomes files.

        Parameters
        ----------
        genome_dir : str
            Directory containing genomes of interest.
        genome_ext : str
            Extension of genome files.

        Returns
        -------
        list
            Path to genome files.
        """

        check_dir_exists(genome_dir)

        genome_files = []
        for f in os.listdir(genome_dir):
            if f.endswith(genome_ext):
                genome_files.append(os.path.join(genome_dir, f))

        if not genome_files:
            self.logger.warning('No genomes found. Check the --genome_ext or --protein_ext flag used to identify genomes.')
            sys.exit()

        return genome_files

def align(self, options):
        """Create MSA from marker genes."""
        
        if options.genome_dir:
            check_dir_exists(options.genome_dir)
            
        if options.batchfile:
            check_file_exists(options.batchfile)
            
        check_dir_exists(options.identify_dir)
        make_sure_path_exists(options.out_dir)
 
        marker_set_id = self._marker_set_id(options.bac120_ms,
                                            options.ar122_ms,
                                            options.rps23_ms)
          
        markers = Markers(options.threads)
        markers.align(options.genome_dir,
                        options.batchfile,
                        options.identify_dir,
                        marker_set_id,
                        options.taxa_filter,
                        options.min_perc_aa,
                        options.custom_msa_filters,
                        options.consensus,
                        options.min_perc_taxa,

def align(self, options):
        """Create MSA from marker genes."""
        
        if options.genome_dir:
            check_dir_exists(options.genome_dir)
            
        if options.batchfile:
            check_file_exists(options.batchfile)
            
        check_dir_exists(options.identify_dir)
        make_sure_path_exists(options.out_dir)
 
        marker_set_id = self._marker_set_id(options.bac120_ms,
                                            options.ar122_ms,
                                            options.rps23_ms)
          
        markers = Markers(options.threads)
        markers.align(options.genome_dir,
                        options.batchfile,
                        options.identify_dir,
                        marker_set_id,