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96
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1 #!/usr/bin/env python
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2 import argparse
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3 import os
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4 import shutil
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5 import subprocess
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6 import sys
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7 import tempfile
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8
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9 BUFF_SIZE = 1048576
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10 OUTPUT_DIR = 'geneFamilyClassification_dir'
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11
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12 parser = argparse.ArgumentParser()
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13 parser.add_argument('--input', dest='input', help="Input dataset")
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14 parser.add_argument('--scaffold', dest='scaffold', default='mode', help='Orthogroups or gene families proteins scaffold')
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15 parser.add_argument('--method', dest='method', help='Protein clustering method')
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16 parser.add_argument('--classifier', dest='classifier', help='Protein classification method')
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17 parser.add_argument('--config_dir', dest='config_dir', help='Directory containing default configuration files')
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18 parser.add_argument('--num_threads', dest='num_threads', type=int, help='Number of threads to use for execution')
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19 parser.add_argument('--super_orthogroups', dest='super_orthogroups', default=None, help='Super orthogroups clustering specification')
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20 parser.add_argument('--single_copy_custom', dest='single_copy_custom', default=None, help='Custom single copy orthogroup configuration')
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21 parser.add_argument('--single_copy_taxa', dest='single_copy_taxa', type=int, default=None, help='"Minimum single copy taxa required in orthogroup')
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22 parser.add_argument('--taxa_present', dest='taxa_present', type=int, default=None, help='Minimum taxa required in single copy orthogroup')
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23 parser.add_argument('--orthogroup_fasta', dest='orthogroup_fasta', default=None, help='Flag to create orthogroup sequences')
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24 parser.add_argument('--coding_sequences', dest='coding_sequences', default=None, help='Flag to create orthogroup coding sequences')
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25 parser.add_argument('--save_hmmscan_log', dest='save_hmmscan_log', default=None, help='Flag to save the hmmscan log')
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26 parser.add_argument('--hmmscan_log', dest='hmmscan_log', default=None, help='hmmscan log file')
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27 parser.add_argument('--output_ptortho', dest='output_ptortho', default=None, help='Output for orthogroups')
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101
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28 parser.add_argument('--output_ptortho_dir', dest='output_ptortho_dir', default=None, help='output_ptortho.files_path')
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96
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29 parser.add_argument('--output_ptorthocs', dest='output_ptorthocs', default=None, help='Output for orthogroups with corresponding coding sequences')
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101
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30 parser.add_argument('--output_ptorthocs_dir', dest='output_ptorthocs_dir', default=None, help='output_ptorthocs.files_path')
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96
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31 parser.add_argument('--output_ptsco', dest='output_ptsco', default=None, help='Output for single copy orthogroups')
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101
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32 parser.add_argument('--output_ptsco_dir', dest='output_ptsco_dir', default=None, help='output_ptsco.files_path')
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96
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33
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34 args = parser.parse_args()
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35
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36
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37 def get_stderr_exception(tmp_err, tmp_stderr, tmp_out, tmp_stdout, include_stdout=False):
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38 tmp_stderr.close()
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39 """
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40 Return a stderr string of reasonable size.
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41 """
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42 # Get stderr, allowing for case where it's very large.
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43 tmp_stderr = open(tmp_err, 'rb')
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44 stderr_str = ''
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45 buffsize = BUFF_SIZE
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46 try:
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47 while True:
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48 stderr_str += tmp_stderr.read(buffsize)
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49 if not stderr_str or len(stderr_str) % buffsize != 0:
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50 break
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51 except OverflowError:
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52 pass
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53 tmp_stderr.close()
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54 if include_stdout:
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55 tmp_stdout = open(tmp_out, 'rb')
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56 stdout_str = ''
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57 buffsize = BUFF_SIZE
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58 try:
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59 while True:
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60 stdout_str += tmp_stdout.read(buffsize)
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61 if not stdout_str or len(stdout_str) % buffsize != 0:
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62 break
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63 except OverflowError:
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64 pass
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65 tmp_stdout.close()
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66 if include_stdout:
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67 return 'STDOUT\n%s\n\nSTDERR\n%s\n' % (stdout_str, stderr_str)
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68 return stderr_str
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69
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70
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71 def move_directory_files(source_dir, destination_dir):
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72 source_directory = os.path.abspath(source_dir)
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73 destination_directory = os.path.abspath(destination_dir)
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74 if not os.path.isdir(destination_directory):
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75 os.makedirs(destination_directory)
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76 for dir_entry in os.listdir(source_directory):
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77 source_entry = os.path.join(source_directory, dir_entry)
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78 shutil.move(source_entry, destination_directory)
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79
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80
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81 def stop_err(msg):
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82 sys.stderr.write(msg)
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83 sys.exit(1)
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84
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85
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86 def write_html_output(output, title, dir):
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107
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87 with open(output, 'w') as fh:
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109
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88 fh.write('<html><head><title>%s</title></head>\n' % title)
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89 fh.write('<body><p/><table>\n')
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90 fh.write('<tr><th>Size</th><th>Name</th></tr>\n')
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106
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91 for fname in os.listdir(dir):
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109
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92 size = str(os.path.getsixe(fname))
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93 link = '<a href="%s" type="text/plain">%s</a>\n' % (fname, fname)
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94 fh.write('<tr><td>%s</td><td>%s</td></tr>\n' % (size, link))
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95 fh.write('</table></body></html>\n')
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96
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96
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97
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98 # Define command response buffers.
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99 tmp_out = tempfile.NamedTemporaryFile().name
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100 tmp_stdout = open(tmp_out, 'wb')
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101 tmp_err = tempfile.NamedTemporaryFile().name
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102 tmp_stderr = open(tmp_err, 'wb')
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103 # Build the command line.
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104 cmd = 'GeneFamilyClassifier'
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105 cmd += ' --proteins %s' % args.input
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106 cmd += ' --scaffold %s' % args.scaffold
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107 cmd += ' --method %s' % args.method
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108 cmd += ' --classifier %s' % args.classifier
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109 cmd += ' --config_dir %s' % args.config_dir
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110 cmd += ' --num_threads %d' % args.num_threads
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111 if args.super_orthogroups is not None:
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112 cmd += ' --super_orthogroups %s' % args.super_orthogroups
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113 if args.single_copy_custom is not None:
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114 cmd += ' --single_copy_custom %s' % args.single_copy_custom
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115 if args.single_copy_taxa is not None:
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116 cmd += ' --single_copy_taxa %d' % args.single_copy_taxa
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117 if args.taxa_present is not None:
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118 cmd += ' --taxa_present %d' % args.taxa_present
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119 if args.orthogroup_fasta is None:
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120 create_ortho_sequences = False
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121 else:
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122 create_ortho_sequences = True
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123 cmd += ' --orthogroup_fasta'
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124 if args.coding_sequences is None:
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125 create_corresponding_coding_sequences = False
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126 else:
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127 create_corresponding_coding_sequences = True
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128 cmd += ' --coding_sequences %s' % args.coding_sequences
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129 # Run the command.
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130 proc = subprocess.Popen(args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True)
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131 rc = proc.wait()
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132 # Handle execution errors.
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133 if rc != 0:
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134 error_message = get_stderr_exception(tmp_err, tmp_stderr, tmp_out, tmp_stdout)
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135 stop_err( error_message )
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136 # Handle hmmscan.log output.
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137 if args.classifier in ['hmmscan', 'both']:
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138 src_hmmscan_log = os.path.join(OUTPUT_DIR, 'hmmscan.log')
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139 if os.path.exists(src_hmmscan_log):
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140 if args.save_hmmscan_log is None:
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141 os.remove(args.hmmscan_log)
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142 else:
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143 shutil.move(src_hmmscan_log, args.hmmscan_log)
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144 # Handle orthogroups outputs.
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145 if create_ortho_sequences:
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146 if create_corresponding_coding_sequences:
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147 out_file = args.output_ptorthocs
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101
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148 orthogroups_fasta_dest_dir = args.output_ptorthocs_dir
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109
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149 title = 'Orthogroups and corresponding coding sequences files'
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96
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150 else:
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151 out_file = args.output_ptortho
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101
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152 orthogroups_fasta_dest_dir = args.output_ptortho_dir
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109
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153 title = 'Orthogroups files'
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96
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154 orthogroups_fasta_src_dir = os.path.join(OUTPUT_DIR, 'orthogroups_fasta')
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103
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155 move_directory_files(orthogroups_fasta_src_dir, orthogroups_fasta_dest_dir)
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96
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156 write_html_output(out_file, title, orthogroups_fasta_dest_dir)
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157 # Handle single copy orthogroup outputs.
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158 if args.output_ptsco is not None:
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159 single_copy_fasta_src_dir = os.path.join(OUTPUT_DIR, 'single_copy_fasta')
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101
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160 single_copy_fasta_dest_dir = args.output_ptsco_dir
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109
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161 title = 'Single copy orthogroups files'
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96
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162 move_directory_files(single_copy_fasta_src_dir, single_copy_fasta_dest_dir)
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163 write_html_output(args.output_ptsco, title, single_copy_fasta_dest_dir)
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