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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
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6 import utils
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7
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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', 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=0, help='Minimum single copy taxa required in orthogroup')
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22 parser.add_argument('--taxa_present', dest='taxa_present', type=int, default=0, 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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28 parser.add_argument('--output_ptortho_dir', dest='output_ptortho_dir', default=None, help='output_ptortho.files_path')
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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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30 parser.add_argument('--output_ptorthocs_dir', dest='output_ptorthocs_dir', default=None, help='output_ptorthocs.files_path')
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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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32 parser.add_argument('--output_ptsco_dir', dest='output_ptsco_dir', default=None, help='output_ptsco.files_path')
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33
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34 args = parser.parse_args()
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35
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36 # Build the command line.
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37 cmd = 'GeneFamilyClassifier'
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38 cmd += ' --proteins %s' % args.input
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39 cmd += ' --scaffold %s' % args.scaffold
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40 cmd += ' --method %s' % args.method
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41 cmd += ' --classifier %s' % args.classifier
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42 cmd += ' --config_dir %s' % args.config_dir
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43 cmd += ' --num_threads %d' % args.num_threads
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44 if args.super_orthogroups is not None:
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45 cmd += ' --super_orthogroups %s' % args.super_orthogroups
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46 if args.single_copy_custom is not None:
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47 cmd += ' --single_copy_custom %s' % args.single_copy_custom
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48 if args.single_copy_taxa > 0:
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49 cmd += ' --single_copy_taxa %d' % args.single_copy_taxa
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50 if args.taxa_present > 0:
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51 cmd += ' --taxa_present %d' % args.taxa_present
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52 if args.orthogroup_fasta is None:
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53 create_ortho_sequences = False
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54 else:
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55 create_ortho_sequences = True
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56 cmd += ' --orthogroup_fasta'
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57 if args.coding_sequences is None:
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58 create_corresponding_coding_sequences = False
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59 else:
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60 create_corresponding_coding_sequences = True
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61 cmd += ' --coding_sequences %s' % args.coding_sequences
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62
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63 # Run the command.
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64 utils.run_command(cmd)
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65
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66 # Handle hmmscan.log output.
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67 if args.classifier in ['hmmscan', 'both']:
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68 src_hmmscan_log = os.path.join(OUTPUT_DIR, 'hmmscan.log')
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69 if os.path.exists(src_hmmscan_log):
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70 if args.save_hmmscan_log is None:
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71 os.remove(src_hmmscan_log)
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72 else:
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73 shutil.move(src_hmmscan_log, args.hmmscan_log)
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74
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75 # Handle orthogroups outputs.
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76 if create_ortho_sequences:
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77 if create_corresponding_coding_sequences:
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78 out_file = args.output_ptorthocs
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79 orthogroups_fasta_dest_dir = args.output_ptorthocs_dir
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80 title = 'Orthogroups and corresponding coding sequences files'
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81 else:
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82 out_file = args.output_ptortho
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83 orthogroups_fasta_dest_dir = args.output_ptortho_dir
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84 title = 'Orthogroups files'
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85 orthogroups_fasta_src_dir = os.path.join(OUTPUT_DIR, 'orthogroups_fasta')
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86 utils.move_directory_files(orthogroups_fasta_src_dir, orthogroups_fasta_dest_dir)
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87 utils.write_html_output(out_file, title, orthogroups_fasta_dest_dir)
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88
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89 # Handle single copy orthogroup outputs.
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90 if args.output_ptsco is not None:
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91 single_copy_fasta_src_dir = os.path.join(OUTPUT_DIR, 'single_copy_fasta')
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92 single_copy_fasta_dest_dir = args.output_ptsco_dir
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93 title = 'Single copy orthogroups files'
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94 utils.move_directory_files(single_copy_fasta_src_dir, single_copy_fasta_dest_dir)
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95 utils.write_html_output(args.output_ptsco, title, single_copy_fasta_dest_dir)
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