Mercurial > repos > iuc > data_manager_build_kraken2_database

annotate data_manager/kraken2_build_database.py @ 1:6ba1ec5f86fc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5f6f447482ad7e127af78204ffd583c51509a0be
author iuc
date Sat, 03 Aug 2019 05:31:12 -0400
parents e4cdf82de430
children edacc4bcd3cb
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e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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1 #!/usr/bin/env python
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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3 from __future__ import print_function
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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4
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5 import argparse
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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6 import datetime
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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7 import errno
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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8 import json
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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9 import os
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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10 import shutil
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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11 import subprocess
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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12 import sys
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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13 import tarfile
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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14 from enum import Enum
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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15
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16 try:
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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17 # Python3
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18 from urllib.request import urlopen
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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19 except ImportError:
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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20 from urllib2 import urlopen
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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23 DATA_TABLE_NAME = "kraken2_databases"
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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26 class KrakenDatabaseTypes(Enum):
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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27 standard = 'standard'
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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28 minikraken = 'minikraken'
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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29 special = 'special'
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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30 custom = 'custom'
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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31
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32 def __str__(self):
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33 return self.value
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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35
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36 class SpecialDatabaseTypes(Enum):
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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37 rdp = 'rdp'
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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38 greengenes = 'greengenes'
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39 silva = 'silva'
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40
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41 def __str__(self):
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42 return self.value
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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43
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44
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45 class Minikraken2Versions(Enum):
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46 v1 = 'v1'
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47 v2 = 'v2'
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48
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49 def __str__(self):
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50 return self.value
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51
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52
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53 def kraken2_build_standard(kraken2_args, target_directory, data_table_name=DATA_TABLE_NAME):
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54 now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
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55
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56 database_value = "_".join([
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57 now,
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58 "standard",
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59 "kmer-len", str(kraken2_args["kmer_len"]),
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60 "minimizer-len", str(kraken2_args["minimizer_len"]),
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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61 "minimizer-spaces", str(kraken2_args["minimizer_spaces"]),
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62 ])
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63
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64 database_name = " ".join([
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65 "Standard",
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66 "(Created:",
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67 now + ",",
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68 "kmer-len=" + str(kraken2_args["kmer_len"]) + ",",
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69 "minimizer-len=" + str(kraken2_args["minimizer_len"]) + ",",
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70 "minimizer-spaces=" + str(kraken2_args["minimizer_spaces"]) + ")",
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71 ])
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72
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73 database_path = database_value
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74
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75 args = [
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76 '--threads', str(kraken2_args["threads"]),
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77 '--standard',
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78 '--kmer-len', str(kraken2_args["kmer_len"]),
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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79 '--minimizer-len', str(kraken2_args["minimizer_len"]),
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80 '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]),
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81 '--db', database_path
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82 ]
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83
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84 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
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85
1
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86 if kraken2_args["clean"]:
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87 args = [
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88 '--threads', str(kraken2_args["threads"]),
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89 '--clean',
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90 '--db', database_path
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91 ]
0
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92
1
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93 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
0
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94
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95 data_table_entry = {
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96 'data_tables': {
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97 data_table_name: [
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98 {
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99 "value": database_value,
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100 "name": database_name,
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101 "path": database_path,
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102 }
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103 ]
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104 }
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105 }
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106
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107 return data_table_entry
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108
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109
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110 def kraken2_build_minikraken(minikraken2_version, target_directory, data_table_name=DATA_TABLE_NAME):
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111
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112 now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
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113
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114 database_value = "_".join([
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115 now,
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116 "minikraken2",
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117 minikraken2_version,
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118 "8GB",
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119 ])
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120
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121 database_name = " ".join([
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122 "Minikraken2",
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123 minikraken2_version,
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124 "(Created:",
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125 now + ")"
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126 ])
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127
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128 database_path = database_value
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129
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130 # download the minikraken2 data
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131 src = urlopen(
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132 'ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/minikraken2_%s_8GB_201904_UPDATE.tgz'
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133 % minikraken2_version
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134 )
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135 with open('tmp_data.tar.gz', 'wb') as dst:
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136 shutil.copyfileobj(src, dst)
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137 # unpack the downloaded archive to the target directory
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138 with tarfile.open('tmp_data.tar.gz', 'r:gz') as fh:
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139 for member in fh.getmembers():
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140 if member.isreg():
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141 member.name = os.path.basename(member.name)
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142 fh.extract(member, os.path.join(target_directory, database_path))
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143
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144 data_table_entry = {
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145 'data_tables': {
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146 data_table_name: [
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147 {
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148 "value": database_value,
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149 "name": database_name,
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150 "path": database_path,
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151 }
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152 ]
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153 }
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154 }
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155
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156 return data_table_entry
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157
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158
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159 def kraken2_build_special(kraken2_args, target_directory, data_table_name=DATA_TABLE_NAME):
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160
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161 now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
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162
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163 special_database_names = {
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164 "rdp": "RDP",
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165 "greengenes": "Greengenes",
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166 "silva": "Silva",
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167 }
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168
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169 database_value = "_".join([
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170 now,
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171 kraken2_args["special_database_type"],
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172 "kmer-len", str(kraken2_args["kmer_len"]),
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173 "minimizer-len", str(kraken2_args["minimizer_len"]),
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174 "minimizer-spaces", str(kraken2_args["minimizer_spaces"]),
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175 ])
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176
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177 database_name = " ".join([
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178 special_database_names[kraken2_args["special_database_type"]],
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179 "(Created:",
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180 now + ",",
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181 "kmer-len=" + str(kraken2_args["kmer_len"]) + ",",
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182 "minimizer-len=" + str(kraken2_args["minimizer_len"]) + ",",
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183 "minimizer-spaces=" + str(kraken2_args["minimizer_spaces"]) + ")",
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184 ])
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185
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186 database_path = database_value
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187
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188 args = [
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189 '--threads', str(kraken2_args["threads"]),
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190 '--special', kraken2_args["special_database_type"],
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191 '--kmer-len', str(kraken2_args["kmer_len"]),
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192 '--minimizer-len', str(kraken2_args["minimizer_len"]),
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193 '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]),
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194 '--db', database_path
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195 ]
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196
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197 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
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198
1
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199 if kraken2_args["clean"]:
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200 args = [
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201 '--threads', str(kraken2_args["threads"]),
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202 '--clean',
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203 '--db', database_path
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204 ]
0
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205
1
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206 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
0
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207
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208 data_table_entry = {
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209 'data_tables': {
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210 data_table_name: [
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211 {
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212 "value": database_value,
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213 "name": database_name,
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214 "path": database_path,
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215 }
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216 ]
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217 }
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218 }
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219
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220 return data_table_entry
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221
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222
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223 def kraken2_build_custom(kraken2_args, custom_database_name, target_directory, data_table_name=DATA_TABLE_NAME):
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224
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225 args = [
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226 '--threads', str(kraken2_args["threads"]),
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227 '--download-taxonomy',
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228 '--db', custom_database_name,
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229 ]
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230
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231 if kraken2_args['skip_maps']:
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232 args.append('--skip-maps')
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233
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234 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
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235
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236 args = [
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237 '--threads', str(kraken2_args["threads"]),
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238 '--add-to-library', kraken2_args["custom_fasta"],
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239 '--db', custom_database_name
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240 ]
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241
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242 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
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243
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244 args = [
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245 '--threads', str(kraken2_args["threads"]),
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246 '--build',
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247 '--kmer-len', str(kraken2_args["kmer_len"]),
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248 '--minimizer-len', str(kraken2_args["minimizer_len"]),
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249 '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]),
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250 '--db', custom_database_name
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251 ]
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252
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253 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
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254
1
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255 if kraken2_args["clean"]:
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256 args = [
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257 '--threads', str(kraken2_args["threads"]),
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258 '--clean',
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259 '--db', custom_database_name
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260 ]
0
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261
1
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262 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
0
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263
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264 data_table_entry = {
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265 'data_tables': {
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266 data_table_name: [
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267 {
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268 "value": custom_database_name,
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269 "name": custom_database_name,
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270 "path": custom_database_name
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271 }
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272 ]
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273 }
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274 }
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275
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276 return data_table_entry
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277
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278
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279 def main():
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280 parser = argparse.ArgumentParser()
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281 parser.add_argument('data_manager_json')
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282 parser.add_argument('--kmer-len', dest='kmer_len', type=int, default=35, help='kmer length')
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283 parser.add_argument('--minimizer-len', dest='minimizer_len', type=int, default=31, help='minimizer length')
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284 parser.add_argument('--minimizer-spaces', dest='minimizer_spaces', default=6, help='minimizer spaces')
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285 parser.add_argument('--threads', dest='threads', default=1, help='threads')
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286 parser.add_argument('--database-type', dest='database_type', type=KrakenDatabaseTypes, choices=list(KrakenDatabaseTypes), required=True, help='type of kraken database to build')
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287 parser.add_argument('--minikraken2-version', dest='minikraken2_version', type=Minikraken2Versions, choices=list(Minikraken2Versions), help='MiniKraken2 version (only applies to --database-type minikraken)')
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288 parser.add_argument('--special-database-type', dest='special_database_type', type=SpecialDatabaseTypes, choices=list(SpecialDatabaseTypes), help='type of special database to build (only applies to --database-type special)')
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289 parser.add_argument('--custom-fasta', dest='custom_fasta', help='fasta file for custom database (only applies to --database-type custom)')
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290 parser.add_argument('--custom-database-name', dest='custom_database_name', help='Name for custom database (only applies to --database-type custom)')
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291 parser.add_argument('--skip-maps', dest='skip_maps', action='store_true', help='')
1
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292 parser.add_argument('--clean', dest='clean', action='store_true', help='Clean up extra files')
0
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293 args = parser.parse_args()
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294
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295 data_manager_input = json.loads(open(args.data_manager_json).read())
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296
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297 target_directory = data_manager_input['output_data'][0]['extra_files_path']
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298
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299 try:
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300 os.mkdir( target_directory )
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301 except OSError as exc:
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302 if exc.errno == errno.EEXIST and os.path.isdir( target_directory ):
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303 pass
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304 else:
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305 raise
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306
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307 data_manager_output = {}
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308
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309 if str(args.database_type) == 'standard':
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310 kraken2_args = {
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311 "kmer_len": args.kmer_len,
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312 "minimizer_len": args.minimizer_len,
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313 "minimizer_spaces": args.minimizer_spaces,
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314 "threads": args.threads,
1
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315 "clean": args.clean,
0
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316 }
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317 data_manager_output = kraken2_build_standard(
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318 kraken2_args,
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319 target_directory,
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320 )
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321 elif str(args.database_type) == 'minikraken':
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322 data_manager_output = kraken2_build_minikraken(
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323 str(args.minikraken2_version),
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324 target_directory
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325 )
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326 elif str(args.database_type) == 'special':
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327 kraken2_args = {
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328 "special_database_type": str(args.special_database_type),
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329 "kmer_len": args.kmer_len,
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330 "minimizer_len": args.minimizer_len,
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331 "minimizer_spaces": args.minimizer_spaces,
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332 "threads": args.threads,
1
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333 "clean": args.clean,
0
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334 }
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335 data_manager_output = kraken2_build_special(
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336 kraken2_args,
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337 target_directory,
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338 )
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339 elif str(args.database_type) == 'custom':
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340 kraken2_args = {
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341 "custom_fasta": args.custom_fasta,
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342 "skip_maps": args.skip_maps,
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343 "kmer_len": args.kmer_len,
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344 "minimizer_len": args.minimizer_len,
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345 "minimizer_spaces": args.minimizer_spaces,
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346 "threads": args.threads,
1
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347 "clean": args.clean,
0
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348 }
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349 data_manager_output = kraken2_build_custom(
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350 kraken2_args,
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351 args.custom_database_name,
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352 target_directory,
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353 )
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354 else:
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355 sys.exit("Invalid database type")
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356
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357 open(args.data_manager_json, 'w').write(json.dumps(data_manager_output))
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358
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359
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360 if __name__ == "__main__":
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361 main()