Removed outdated examples directory

examples/batch_processing.py

-import os
-import itertools
-
-analysis = 'denovo_map_par'
-
-species = ['perca_fluviatilis', 'ameirus_melas']
-
-m_values = [5, 10]
-n_values = [1, 2, 3, 4]
-M_values = [1, 2, 3, 4]
-
-root_dir = '/work/rferon/'
-species_dir = os.path.join(root_dir, 'species')
-batch_dir = os.path.join(root_dir, 'batch_processing')
-shell_dir = os.path.join(batch_dir, 'shell', analysis, 'analyses')
-python_dir = os.path.join(batch_dir, 'python', analysis)
-
-qsub_dir = os.path.join(batch_dir, 'qsub')
-qsub_all = os.path.join(qsub_dir, analysis + '_analyses.sh')
-qsub_file = open(qsub_all, 'w')
-
-for specie, m, n, M in itertools.product(species, m_values, n_values, M_values):
-
-    species_short = specie.split('_')[0][0] + '_' + specie.split('_')[1]
-
-    analysis_path = os.path.join(species_dir, specie, 'analyses', 'rad_seq', analysis)
-
-    results_path = os.path.join(analysis_path, 'results_' +
-                                'm_' + str(m) + '_' +
-                                'n_' + str(n) + '_' +
-                                'M_' + str(M))
-
-    shell_path = os.path.join(shell_dir,
-                              specie + '_' +
-                              'm_' + str(m) + '_' +
-                              'n_' + str(n) + '_' +
-                              'M_' + str(M) + '.sh')
-
-    python_path = os.path.join(python_dir,
-                               specie + '_' +
-                               'm_' + str(m) + '_' +
-                               'n_' + str(n) + '_' +
-                               'M_' + str(M) + '.py')
-
-    output_dir_base = os.path.join(batch_dir, 'results', analysis, specie)
-    if not os.path.isdir(output_dir_base):
-        os.mkdir(output_dir_base)
-    output_dir = os.path.join(output_dir_base, 'm_' + str(m) + '_' +
-                              'n_' + str(n) + '_' +
-                              'M_' + str(M))
-    if not os.path.isdir(output_dir):
-        os.mkdir(output_dir)
-
-    python_file = open(python_path, 'w')
-    python_file.write("import sys\n\n")
-    python_file.write("sys.path.append('/work/rferon/tools/radseq_analyses_pipeline')\n\n")
-    python_file.write("from radseq_analyses_pipeline import analyse_directory\n\n")
-    python_file.write("analyse_directory('" + results_path + "', '" + output_dir + "')\n")
-
-    shell_file = open(shell_path, 'w')
-    shell_file.write('python3 ' + python_path + '\n')
-
-    qsub_file.write('qsub ' + shell_path + '\n')

examples/extraction.py

-import os
-import sys
-from radseq_analyses_pipeline import analyse_directory
-from radseq_analyses_pipeline.parameters.positions import get_positions_list
-
-
-species = 'ameirus_melas'
-replicate = None
-m_value = 3
-
-positions_file_path = sys.argv[1]
-positions_list = get_positions_list(positions_file_path)
-
-root_dir = '/work/bimarazene/radseq_all/'
-extraction_dir = os.path.join(root_dir, 'analyses', 'extraction')
-
-if not os.path.isdir(os.path.join(extraction_dir, species)):
-    os.mkdir(os.path.join(extraction_dir, species))
-
-if replicate:
-    if not os.path.isdir(os.path.join(extraction_dir, species, replicate)):
-        os.mkdir(os.path.join(extraction_dir, species, replicate))
-    files_dir = os.path.join(root_dir, 'results', species, replicate, 'm_' + str(m_value))
-    analyses_dir = os.path.join(extraction_dir, species, replicate, 'm_' + str(m_value))
-else:
-    files_dir = os.path.join(root_dir, 'results', species, 'm_' + str(m_value))
-    analyses_dir = os.path.join(extraction_dir, species, 'm_' + str(m_value))
-
-# Path to population map
-popmap_path = os.path.join(root_dir, 'data', 'popmaps', species + '_popmap.csv')
-
-analyse_directory(root_dir, files_dir, analyses_dir,
-                  positions_list, popmap_path)