old_contents: #!/usr/bin/python
  
  """
  Copyright 2016 EMBL-European Bioinformatics Institute
  
  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.
  """
  
  import argparse, urllib2, gzip, shutil, shlex, subprocess, os.path, json
  
  from pycompss.api.task import task
  from pycompss.api.parameter import *
  
  from common import common
  
  if __name__ == "__main__":
      import sys
      import os
      
      # Set up the command line parameters
      parser = argparse.ArgumentParser(description="Genome assembly and indexing")
      parser.add_argument("--species", help="Species (homo_sapiens)")
      parser.add_argument("--assembly", help="Assembly (GRCh38)")
      parser.add_argument("--project_id", help="Project ID of the dataset")
      parser.add_argument("--run_ids", help="JSON file with list of the experiment run IDs and background data (if available) of the dataset")
      parser.add_argument("--data_dir", help="Data directory; location to download ERR FASTQ files and save results")
  
      # Get the matching parameters from the command line
      args = parser.parse_args()
      
      project     = args.project_id
      run_id_file = args.run_ids
      species     = args.species
      assembly    = args.assembly
      data_dir    = args.data_dir
      
      cf = common()
      
      if data_dir[-1] != "/":
          data_dir += "/"
      
      try:
          os.makedirs(data_dir)
      except:
          pass
  
      try:
          os.makedirs(data_dir + project)
      except:
          pass
      
      try:
          os.makedirs(data_dir + species + "_" + assembly)
      except:
          pass
      
      # Get the assembly
      genome_fa = cf.getGenomeFile(data_dir, species, assembly)
  
new_contents: #!/usr/bin/python
  
  """
  Copyright 2016 EMBL-European Bioinformatics Institute
  
  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.
  """
  
  import argparse, urllib2, gzip, shutil, shlex, subprocess, os.path, json
  
  from pycompss.api.task import task
  from pycompss.api.parameter import *
  
  from common import common
  
  if __name__ == "__main__":
      import sys
      import os
      
      # Set up the command line parameters
      parser = argparse.ArgumentParser(description="Genome assembly and indexing")
      parser.add_argument("--species", help="Species (homo_sapiens)")
      parser.add_argument("--assembly", help="Assembly (GRCh38)")
      parser.add_argument("--project_id", help="Project ID of the dataset")
      parser.add_argument("--run_ids", help="JSON file with list of the experiment run IDs and background data (if available) of the dataset")
      parser.add_argument("--data_dir", help="Data directory; location to download ERR FASTQ files and save results")
  
      # Get the matching parameters from the command line
      args = parser.parse_args()
      
      project     = args.project_id
      run_id_file = args.run_ids
      species     = args.species
      assembly    = args.assembly
      data_dir    = args.data_dir
      
      cf = common()
      
      if data_dir[-1] != "/":
          data_dir += "/"
      
      try:
          os.makedirs(data_dir)
      except:
          pass
  
      try:
          os.makedirs(data_dir + project)
      except:
          pass
      
      try:
          os.makedirs(data_dir + species + "_" + assembly)
      except:
          pass
      
      # Get the assembly
      #genome_fa = cf.getGenomeFile(data_dir, species, assembly, False)
      genome_fa = cf.getGenomeFile(data_dir, species, assembly, False)
  
subject: Test commands for downloading the genome assemblies