Mercurial > repos > dfornika > data_manager_build_kraken2_database

annotate data_manager/kraken2_build_special.py @ 12:039a65ff445d draft

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planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 70494d589aa1990618ebc7a895e91477d41c3203-dirty
author dfornika
date Tue, 05 Mar 2019 15:11:05 -0500
parents 1dc93ae264e6
children
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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 string
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11 import subprocess
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12 import sys
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15 DATA_TABLE_NAME = "kraken2_databases"
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17 def run(args, cwd):
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18 proc = subprocess.Popen(args=args, shell=False, cwd=cwd)
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19 return_code = proc.wait()
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20 if return_code:
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21 print("Error building database.", file=sys.stderr)
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22 sys.exit( return_code )
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24 def kraken2_build_standard(data_manager_dict, kraken2_args, target_directory, data_table_name=DATA_TABLE_NAME):
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26 now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
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28 special_database_names = {
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29 "rdp": "RDP",
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30 "greengenes": "Greengenes",
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31 "silva": "Silva",
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32 }
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34 database_value = "_".join([
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35 now,
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36 kraken2_args["special"],
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37 "kmer-len", str(kraken2_args["kmer_len"]),
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38 "minimizer-len", str(kraken2_args["minimizer_len"]),
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39 "minimizer-spaces", str(kraken2_args["minimizer_spaces"]),
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40 ])
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42 database_name = " ".join([
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43 special_database_names[kraken2_args["special"]],
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44 "(Created:",
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45 now + ",",
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46 "kmer-len=" + str(kraken2_args["kmer_len"]) + ",",
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47 "minimizer-len=" + str(kraken2_args["minimizer_len"]) + ",",
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48 "minimizer-spaces=" + str(kraken2_args["minimizer_spaces"]) + ")",
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49 ])
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51 database_path = database_value
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53 args = [
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54 '--threads', str(kraken2_args["threads"]),
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55 '--special', kraken2_args["special"],
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56 '--kmer-len', str(kraken2_args["kmer_len"]),
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57 '--minimizer-len', str(kraken2_args["minimizer_len"]),
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58 '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]),
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59 '--db', database_path
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60 ]
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62 run(['kraken2-build'] + args, target_directory)
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64 args = [
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65 '--threads', str(kraken2_args["threads"]),
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66 '--clean',
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67 '--db', database_path
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68 ]
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70 run(['kraken2-build'] + args, target_directory)
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72 data_table_entry = {
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73 "value": database_value,
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74 "name": database_name,
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75 "path": database_path,
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76 }
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77
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78 _add_data_table_entry(data_manager_dict, data_table_entry)
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80
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81 def _add_data_table_entry(data_manager_dict, data_table_entry, data_table_name=DATA_TABLE_NAME):
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82 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
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83 data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get( data_table_name, [] )
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84 data_manager_dict['data_tables'][data_table_name].append( data_table_entry )
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85 return data_manager_dict
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86
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87
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88 def main():
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89 parser = argparse.ArgumentParser()
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90 parser.add_argument('data_manager_json')
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91 parser.add_argument( '-b', '--db-type', dest='db_type', help='database type (one of: silva, rdp, greengenes)' )
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92 parser.add_argument( '-k', '--kmer-len', dest='kmer_len', type=int, default=35, help='kmer length' )
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93 parser.add_argument( '-m', '--minimizer-len', dest='minimizer_len', type=int, default=31, help='minimizer length' )
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94 parser.add_argument( '-s', '--minimizer-spaces', dest='minimizer_spaces', default=6, help='minimizer spaces' )
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95 parser.add_argument( '-t', '--threads', dest='threads', default=1, help='threads' )
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96 args = parser.parse_args()
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97
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98 kraken2_args = {
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99 "special": args.db_type,
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100 "kmer_len": args.kmer_len,
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101 "minimizer_len": args.minimizer_len,
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102 "minimizer_spaces": args.minimizer_spaces,
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103 "threads": args.threads,
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104 }
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105
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106 data_manager_input = json.loads(open(args.data_manager_json).read())
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107
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108 target_directory = data_manager_input['output_data'][0]['extra_files_path']
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109
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110 try:
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111 os.mkdir( target_directory )
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112 except OSError as exc:
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113 if exc.errno == errno.EEXIST and os.path.isdir( target_directory ):
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114 pass
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115 else:
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116 raise
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117
9
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118 data_manager_output = {}
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119
7
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120 kraken2_build_standard(
9
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121 data_manager_output,
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122 kraken2_args,
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123 target_directory,
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124 )
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125
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126 open(args.data_manager_json, 'wb').write(json.dumps(data_manager_output))
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127
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128
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129 if __name__ == "__main__":
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130 main()