Mercurial > repos > iuc > dram_set_database_locations

annotate dram_set_database_locations.py @ 0:6e52f03e612d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
author iuc
date Thu, 01 Sep 2022 17:16:35 +0000
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6e52f03e612d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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1 #!/usr/bin/env python
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3 import argparse
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4 import os
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5 import subprocess
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7 parser = argparse.ArgumentParser()
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9 parser.add_argument('--db_version', action='store', dest='db_version', help='Version of DRAM databases')
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10 parser.add_argument('--skip_uniref', action='store_true', dest='skip_uniref', default=False, help='Flag to Download and process uniref')
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11 parser.add_argument('--galaxy_data_manager_data_path', action='store', dest='galaxy_data_manager_data_path', help='Absolute Galaxy data manager data path')
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12 parser.add_argument('--output', action='store', dest='output', help='Output file')
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14 args = parser.parse_args()
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17 def get_new_dram_config_entry(db_version, old_entry, new_base_path):
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18 # Example old_entry:
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19 # KOfam db: /home/galaxies/gvk/jwd/003/3045/working/dataset_4268_files/kofam_profiles.hmm
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20 base_path, file_name = os.path.split(old_entry)
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21 # The new entry must be GALAXY_DATA_MANAGER_DATA_PATH/DRAM/${value}/file_name
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22 return os.path.join(new_base_path, 'DRAM', db_version, file_name)
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25 # At this point the DRAM config will look something like this.
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26 # Processed search databases
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27 # KEGG db: None
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28 # KOfam db: /home/galaxies/gvk/jwd/003/3045/working/dataset_4268_files/kofam_profiles.hmm
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29 # KOfam KO list: /home/galaxies/gvk/jwd/003/3045/working/dataset_4268_files/kofam_ko_list.tsv
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30 # UniRef db: None
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31 # Pfam db: /home/galaxies/gvk/jwd/003/3045/working/dataset_4268_files/pfam.mmspro
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32 # dbCAN db: /home/galaxies/gvk/jwd/003/3045/working/dataset_4268_files/dbCAN-HMMdb-V10.txt
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33 # RefSeq Viral db: /home/galaxies/gvk/jwd/003/3045/working/dataset_4268_files/refseq_viral.20220707.mmsdb
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34 # MEROPS peptidase db: /home/galaxies/gvk/jwd/003/3045/working/dataset_4268_files/peptidases.20220707.mmsdb
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35 # VOGDB db: /home/galaxies/gvk/jwd/003/3045/working/dataset_4268_files/vog_latest_hmms.txt
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36 #
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37 # Descriptions of search database entries
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38 # Pfam hmm dat: /home/galaxies/gvk/jwd/003/3045/working/dataset_4268_files/Pfam-A.hmm.dat.gz
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39 # dbCAN family activities: /home/galaxies/gvk/jwd/003/3045/working/dataset_4268_files/CAZyDB.07292021.fam-activities.txt
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40 # VOG annotations: /home/galaxies/gvk/jwd/003/3045/working/dataset_4268_files/vog_annotations_latest.tsv.gz
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41 #
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42 # Description db: /home/galaxies/gvk/jwd/003/3045/working/dataset_4268_files/description_db.sqlite
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43 #
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44 # DRAM distillation sheets
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45 # Genome summary form: /home/galaxies/gvk/jwd/003/3045/working/dataset_4268_files/genome_summary_form.20220707.tsv
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46 # Module step form: /home/galaxies/gvk/jwd/003/3045/working/dataset_4268_files/module_step_form.20220707.tsv
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47 # ETC module database: /home/galaxies/gvk/jwd/003/3045/working/dataset_4268_files/etc_mdoule_database.20220707.tsv
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48 # Function heatmap form: /home/galaxies/gvk/jwd/003/3045/working/dataset_4268_files/function_heatmap_form.20220707.tsv
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49 # AMG database: /home/galaxies/gvk/jwd/003/3045/working/dataset_4268_files/amg_database.20220707.tsv
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50
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51 # Write the current DRAM CONFIG to a file for processing.
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52 cmd = 'DRAM-setup.py print_config > dram_config.txt'
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53 subprocess.check_call(cmd, shell=True)
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54
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55 # Update the database locations that DRAM sets in it's CONFIG
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56 # to point to the configured GALAXY_DATA_MANAGER_DATA_PATH location
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57 # for the DRAM databases.
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58 cmd = 'DRAM-setup.py set_database_locations'
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59 with open('dram_config.txt', 'r') as fh:
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60 for line in fh:
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61 line = line.rstrip('\r\n')
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62 if line.startswith('KOfam db:'):
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63 cmd = '%s --kofam_hmm_loc %s' % (cmd, get_new_dram_config_entry(args.db_version, line, args.galaxy_data_manager_data_path))
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64 elif line.startswith('KOfam KO list:'):
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65 cmd = '%s --kofam_ko_list_loc %s' % (cmd, get_new_dram_config_entry(args.db_version, line, args.galaxy_data_manager_data_path))
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66 elif line.startswith('UniRef db:'):
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67 if not args.skip_uniref:
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68 cmd = '%s --uniref_db_loc %s' % (cmd, get_new_dram_config_entry(args.db_version, line, args.galaxy_data_manager_data_path))
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69 elif line.startswith('Pfam db:'):
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70 cmd = '%s --pfam_db_loc %s' % (cmd, get_new_dram_config_entry(args.db_version, line, args.galaxy_data_manager_data_path))
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71 elif line.startswith('dbCAN db:'):
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72 cmd = '%s --dbcan_db_loc %s' % (cmd, get_new_dram_config_entry(args.db_version, line, args.galaxy_data_manager_data_path))
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73 elif line.startswith('RefSeq Viral db:'):
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74 cmd = '%s --viral_db_loc %s' % (cmd, get_new_dram_config_entry(args.db_version, line, args.galaxy_data_manager_data_path))
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75 elif line.startswith('MEROPS peptidase db:'):
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76 cmd = '%s --peptidase_db_loc %s' % (cmd, get_new_dram_config_entry(args.db_version, line, args.galaxy_data_manager_data_path))
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77 elif line.startswith('VOGDB db:'):
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78 cmd = '%s --vogdb_db_loc %s' % (cmd, get_new_dram_config_entry(args.db_version, line, args.galaxy_data_manager_data_path))
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79 elif line.startswith('Pfam hmm dat:'):
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80 cmd = '%s --pfam_hmm_dat %s' % (cmd, get_new_dram_config_entry(args.db_version, line, args.galaxy_data_manager_data_path))
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81 elif line.startswith('dbCAN family activities:'):
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82 cmd = '%s --dbcan_fam_activities %s' % (cmd, get_new_dram_config_entry(args.db_version, line, args.galaxy_data_manager_data_path))
6e52f03e612d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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83 elif line.startswith('VOG annotations:'):
6e52f03e612d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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84 cmd = '%s --vog_annotations %s' % (cmd, get_new_dram_config_entry(args.db_version, line, args.galaxy_data_manager_data_path))
6e52f03e612d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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85 elif line.startswith('Description db:'):
6e52f03e612d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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86 cmd = '%s --description_db_loc %s' % (cmd, get_new_dram_config_entry(args.db_version, line, args.galaxy_data_manager_data_path))
6e52f03e612d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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87 elif line.startswith('Genome summary form:'):
6e52f03e612d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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88 cmd = '%s --genome_summary_form_loc %s' % (cmd, get_new_dram_config_entry(args.db_version, line, args.galaxy_data_manager_data_path))
6e52f03e612d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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89 elif line.startswith('Module step form:'):
6e52f03e612d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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90 cmd = '%s --module_step_form_loc %s' % (cmd, get_new_dram_config_entry(args.db_version, line, args.galaxy_data_manager_data_path))
6e52f03e612d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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91 elif line.startswith('ETC module database:'):
6e52f03e612d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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92 cmd = '%s --etc_module_database_loc %s' % (cmd, get_new_dram_config_entry(args.db_version, line, args.galaxy_data_manager_data_path))
6e52f03e612d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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93 elif line.startswith('Function heatmap form:'):
6e52f03e612d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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94 cmd = '%s --function_heatmap_form_loc %s' % (cmd, get_new_dram_config_entry(args.db_version, line, args.galaxy_data_manager_data_path))
6e52f03e612d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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95 elif line.startswith('AMG database:'):
6e52f03e612d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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96 cmd = '%s --amg_database_loc %s' % (cmd, get_new_dram_config_entry(args.db_version, line, args.galaxy_data_manager_data_path))
6e52f03e612d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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97 cmd = '%s --update_description_db' % cmd
6e52f03e612d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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98 subprocess.check_call(cmd, shell=True)
6e52f03e612d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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99
6e52f03e612d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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100 # Write the new DRAM CONFIG to a file to the output.
6e52f03e612d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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101 cmd = 'DRAM-setup.py print_config > %s' % args.output
6e52f03e612d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
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102 subprocess.check_call(cmd, shell=True)