text: #!/usr/bin/env python3
  # Copyright 2018 Lael D. Barlow
  # 
  # Licensed under the Apache License, Version 2.0 (the "License");
  # you may not use this file except in compliance with the License.
  # You may obtain a copy of the License at
  # 
  #     http://www.apache.org/licenses/LICENSE-2.0
  # 
  # Unless required by applicable law or agreed to in writing, software
  # distributed under the License is distributed on an "AS IS" BASIS,
  # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  # See the License for the specific language governing permissions and
  # limitations under the License.
  # 
  """This file contains definitions of variables used by scripts in the AMOEBAE
  toolkit. 
  """
  import os
  
  class DataPaths:
      """Provides an object with directory and file paths as attributes based on
      a given main AMOEBAE data directory path.
      """
      def __init__(self, root_amoebae_data_dir):
          # Check that the input path exists as a directory.
          assert os.path.isdir(root_amoebae_data_dir), """Input AMOEBAE data
          directory path does not exist."""
  
          # Set path to directory containing genome data (predicted peptide sequences,
          # nucleotide scaffolds, etc.).
          self.dbdirpath =\
          os.path.join(root_amoebae_data_dir, 'Genomes')
          assert os.path.isdir(self.dbdirpath), """Error: No directory at path:
          %s""" % self.dbdirpath
          
          # Set path to csv file with information about the relevant genome data.
          self.db_info_csv =\
          os.path.join(self.dbdirpath, '0_genome_info.csv')
          assert os.path.isfile(self.db_info_csv), """Error: No file at path:
          %s""" % self.db_info_csv
          
          # Set path to directory containing query files (.faa, .afaa, etc.).
          self.querydirpath =\
          os.path.join(root_amoebae_data_dir, 'Queries')
          assert os.path.isdir(self.querydirpath), """Error: No directory at path:
          %s""" % self.querydirpath
          
          # Set path to csv file with information about the relevant query files.
          self.query_info_csv =\
          os.path.join(self.querydirpath, '0_query_info.csv')
          assert os.path.isfile(self.query_info_csv), """Error: No file at path:
          %s""" % self.query_info_csv
          
  
  
  
  