Mercurial > repos > dfornika > data_manager_build_mob_suite_database

annotate data_manager/mob_suite_build_database.py @ 32:45c033d596f0 draft

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planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_mob_suite_database/ commit e01e33974da213b2df2bb12d3180a875567a60e4-dirty
author dfornika
date Wed, 26 Jun 2019 15:44:07 -0400
parents b37cf95d8b3b
children ef3f3fd059fa
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1 #!/usr/bin/env python
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3 from __future__ import print_function
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5 import argparse
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6 import datetime
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7 import errno
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8 import json
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9 import os
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10 import shutil
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11 import string
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12 import subprocess
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13 import sys
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14 import time
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15 import uuid
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18 DATA_TABLE_NAME = "mob_suite_databases"
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21 def mob_suite_build_database_mob_cluster(target_directory, mob_cluster_args, database_name, data_table_name=DATA_TABLE_NAME):
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23 now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
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25 database_value = str(uuid.uuid4())
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27 database_name = database_name
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29 database_path = database_value
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31 mob_cluster_args_list = [
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32 '--num_threads', mob_cluster_args['num_threads'],
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33 '--infile', mob_cluster_args['infile'],
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34 '--outdir', database_path,
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35 '--mode', mob_cluster_args['mode'],
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36 ]
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38 print(json.dumps(mob_cluster_args_list))
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40 print("Sleeping for 20s")
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41 time.sleep(20)
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42 print("Sleep ending")
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44 subprocess.check_call(['mob_cluster'] + mob_cluster_args_list, cwd=target_directory)
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46 print("Sleeping for 20s")
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47 time.sleep(20)
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48 print("Sleep ending")
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50 makeblastdb_args_list = [
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51 '-in', os.path.join(database_path, 'references_updated.fasta'),
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52 '-dbtype', 'nucl',
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53 ]
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55 subprocess.check_call(['makeblastdb'] + makeblastdb_args_list, cwd=target_directory)
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57 mash_sketch_args_list = [
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58 '-i', os.path.join(database_path, 'references_updated.fasta'),
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59 ]
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61 subprocess.check_call(['mash', 'sketch'] + mash_sketch_args_list, cwd=target_directory)
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63 bagit_args_list = [
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64 database_path,
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67 subprocess.call(['bagit.py'] + bagit_args_list, cwd=target_directory)
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69 data_table_entry = {
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70 "data_tables": {
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71 data_table_name: [
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72 {
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73 "value": database_value,
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74 "name": database_name,
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75 "path": os.path.join(database_path, 'data')
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76 }
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78 }
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79 }
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80
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81 return data_table_entry
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82
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83
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84 def main():
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85 parser = argparse.ArgumentParser()
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86 parser.add_argument('data_manager_json')
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87 parser.add_argument('--threads', dest='threads', default=1, help='threads')
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88 parser.add_argument('--input', dest='input', help='Plasmid Assemblies (.fasta)')
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89 parser.add_argument('--database-name', dest='database_name', help='Database Name')
0
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90 args = parser.parse_args()
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91
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92 data_manager_input = json.loads(open(args.data_manager_json).read())
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93
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94 target_directory = data_manager_input['output_data'][0]['extra_files_path']
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95
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96 try:
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97 os.mkdir( target_directory )
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98 except OSError as exc:
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99 if exc.errno == errno.EEXIST and os.path.isdir( target_directory ):
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100 pass
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101 else:
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102 raise
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103
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104 data_manager_output = {}
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105
6
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106 mob_cluster_args = {
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107 'num_threads': args.threads,
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108 'infile': args.input,
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109 'mode': 'build',
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110 }
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111
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112 data_manager_output = mob_suite_build_database_mob_cluster(
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113 target_directory,
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114 mob_cluster_args,
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115 args.database_name,
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116 )
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117
0
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119 open(args.data_manager_json, 'wb').write(json.dumps(data_manager_output))
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120
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121
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122 if __name__ == "__main__":
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123 main()