Mercurial > repos > dfornika > data_manager_build_kraken2_database

annotate data_manager/kraken2_build_database.py @ 17:4c9f9d6098eb 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 db9eb9472b9f6caea6a0755697ee8d3a93e85b5b-dirty
author dfornika
date Mon, 06 May 2019 19:42:14 -0400
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children f005b6efd096
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17
4c9f9d6098eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit db9eb9472b9f6caea6a0755697ee8d3a93e85b5b-dirty
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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 subprocess
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12 import sys
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13 import tarfile
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14 from enum import Enum
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15
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16 try:
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17 # Python3
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18 from urllib.request import urlopen
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19 except ImportError:
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20 from urllib2 import urlopen
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23 DATA_TABLE_NAME = "kraken2_databases"
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26 class KrakenDatabaseTypes(Enum):
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27 standard = 'standard'
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28 minikraken = 'minikraken'
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29 special = 'special'
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30 custom = 'custom'
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32 def __str__(self):
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33 return self.value
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36 class SpecialDatabaseTypes(Enum):
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37 rdp = 'rdp'
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38 greengenes = 'greengenes'
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39 silva = 'silva'
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41 def __str__(self):
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42 return self.value
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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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52
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53 def kraken2_build_standard(data_manager_dict, 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"]),
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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"]),
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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
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86 args = [
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87 '--threads', str(kraken2_args["threads"]),
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88 '--clean',
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89 '--db', database_path
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90 ]
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91
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92 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
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93
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94 data_table_entry = {
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95 "value": database_value,
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96 "name": database_name,
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97 "path": database_path,
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98 }
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99
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100 _add_data_table_entry(data_manager_dict, data_table_entry)
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101
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102
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103 def kraken2_build_minikraken(data_manager_dict, minikraken2_version, target_directory, data_table_name=DATA_TABLE_NAME):
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104
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105 now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
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106
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107 database_value = "_".join([
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108 now,
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109 "minikraken2",
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110 minikraken2_version,
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111 "8GB",
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112 ])
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113
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114 database_name = " ".join([
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115 "Minikraken2",
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116 minikraken2_version,
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117 "(Created:",
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118 now + ")"
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119 ])
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120
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121 # download the minikraken2 data
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122 src = urlopen(
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123 'ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/minikraken2_%s_8GB_201904_UPDATE.tgz'
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124 % minikraken2_version
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125 )
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126 with open('tmp_data.tar.gz', 'wb') as dst:
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127 shutil.copyfileobj(src, dst)
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128 # unpack the downloaded archive to the target directory
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129 with tarfile.open('tmp_data.tar.gz', 'r:gz') as fh:
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130 fh.extractall(target_directory)
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131
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132 data_table_entry = {
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133 "value": database_value,
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134 "name": database_name,
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135 "path": database_value,
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136 }
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137
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138 _add_data_table_entry(data_manager_dict, data_table_entry)
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139
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140
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141 def kraken2_build_special(data_manager_dict, kraken2_args, target_directory, data_table_name=DATA_TABLE_NAME):
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142
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143 now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
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144
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145 special_database_names = {
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146 "rdp": "RDP",
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147 "greengenes": "Greengenes",
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148 "silva": "Silva",
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149 }
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150
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151 database_value = "_".join([
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152 now,
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153 kraken2_args["special_database_type"],
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154 "kmer-len", str(kraken2_args["kmer_len"]),
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155 "minimizer-len", str(kraken2_args["minimizer_len"]),
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156 "minimizer-spaces", str(kraken2_args["minimizer_spaces"]),
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157 ])
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158
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159 database_name = " ".join([
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160 special_database_names[kraken2_args["special_database_type"]],
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161 "(Created:",
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162 now + ",",
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163 "kmer-len=" + str(kraken2_args["kmer_len"]) + ",",
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164 "minimizer-len=" + str(kraken2_args["minimizer_len"]) + ",",
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165 "minimizer-spaces=" + str(kraken2_args["minimizer_spaces"]) + ")",
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166 ])
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167
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168 database_path = database_value
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169
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170 args = [
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171 '--threads', str(kraken2_args["threads"]),
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172 '--special', kraken2_args["special_database_type"],
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173 '--kmer-len', str(kraken2_args["kmer_len"]),
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174 '--minimizer-len', str(kraken2_args["minimizer_len"]),
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175 '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]),
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176 '--db', database_path
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177 ]
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178
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179 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
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180
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181 args = [
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182 '--threads', str(kraken2_args["threads"]),
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183 '--clean',
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184 '--db', database_path
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185 ]
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186
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187 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
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188
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189 data_table_entry = {
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190 "value": database_value,
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191 "name": database_name,
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192 "path": database_path,
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193 }
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194
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195 _add_data_table_entry(data_manager_dict, data_table_entry)
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196
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197
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198 def kraken2_build_custom(data_manager_dict, kraken2_args, custom_database_name, target_directory, data_table_name=DATA_TABLE_NAME):
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199
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200 args = [
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201 '--threads', str(kraken2_args["threads"]),
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202 '--download-taxonomy',
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203 '--db', custom_database_name
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204 ]
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205
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206 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
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207
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208 args = [
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209 '--threads', str(kraken2_args["threads"]),
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210 '--add-to-library', kraken2_args["custom_fasta"],
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211 '--db', custom_database_name
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212 ]
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213
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214 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
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215
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216 args = [
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217 '--threads', str(kraken2_args["threads"]),
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218 '--build',
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219 '--kmer-len', str(kraken2_args["kmer_len"]),
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220 '--minimizer-len', str(kraken2_args["minimizer_len"]),
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221 '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]),
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222 '--db', custom_database_name
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223 ]
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224
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225 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
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226
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227 args = [
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228 '--threads', str(kraken2_args["threads"]),
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229 '--clean',
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230 '--db', custom_database_name
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231 ]
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232
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233 subprocess.check_call(['kraken2-build'] + args, target_directory)
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234
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235 data_table_entry = {
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236 "value": custom_database_name,
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237 "name": custom_database_name,
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238 "path": custom_database_name
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239 }
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240
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241 _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry)
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242
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243
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244 def _add_data_table_entry(data_manager_dict, data_table_entry, data_table_name=DATA_TABLE_NAME):
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245 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
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246 data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get( data_table_name, [] )
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247 data_manager_dict['data_tables'][data_table_name].append( data_table_entry )
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248 return data_manager_dict
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249
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250
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251 def main():
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252 parser = argparse.ArgumentParser()
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253 parser.add_argument('data_manager_json')
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254 parser.add_argument('--kmer-len', dest='kmer_len', type=int, default=35, help='kmer length')
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255 parser.add_argument('--minimizer-len', dest='minimizer_len', type=int, default=31, help='minimizer length')
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256 parser.add_argument('--minimizer-spaces', dest='minimizer_spaces', default=6, help='minimizer spaces')
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257 parser.add_argument('--threads', dest='threads', default=1, help='threads')
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258 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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259 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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260 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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261 parser.add_argument('--custom-fasta', dest='custom_fasta', help='fasta file for custom database (only applies to --database-type custom)')
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262 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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263 args = parser.parse_args()
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264
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265 data_manager_input = json.loads(open(args.data_manager_json).read())
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266
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267 target_directory = data_manager_input['output_data'][0]['extra_files_path']
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268
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269 try:
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270 os.mkdir( target_directory )
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271 except OSError as exc:
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272 if exc.errno == errno.EEXIST and os.path.isdir( target_directory ):
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273 pass
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274 else:
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275 raise
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276
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277 data_manager_output = {}
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278
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279 print(args.database_type)
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280 if str(args.database_type) == 'standard':
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281 kraken2_args = {
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282 "kmer_len": args.kmer_len,
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283 "minimizer_len": args.minimizer_len,
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284 "minimizer_spaces": args.minimizer_spaces,
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285 "threads": args.threads,
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286 }
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287 kraken2_build_standard(
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288 data_manager_output,
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289 kraken2_args,
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290 target_directory,
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291 )
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292 elif str(args.database_type) == 'minikraken':
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293 kraken2_build_minikraken(
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294 data_manager_output,
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295 str(args.minikraken2_version),
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296 target_directory
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297 )
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298 elif str(args.database_type) == 'special':
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299 kraken2_args = {
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300 "special_database_type": str(args.special_database_type),
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301 "kmer_len": args.kmer_len,
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302 "minimizer_len": args.minimizer_len,
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303 "minimizer_spaces": args.minimizer_spaces,
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304 "threads": args.threads,
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305 }
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306 kraken2_build_special(
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307 data_manager_output,
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308 kraken2_args,
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309 target_directory,
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310 )
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311 elif str(args.database_type) == 'custom':
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312 kraken2_args = {
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313 "custom_fasta": args.custom_fasta,
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314 "kmer_len": args.kmer_len,
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315 "minimizer_len": args.minimizer_len,
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316 "minimizer_spaces": args.minimizer_spaces,
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317 "threads": args.threads,
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318 }
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319 kraken2_build_custom(
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320 data_manager_output,
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321 kraken2_args,
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322 args.custom_database_name,
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323 target_directory,
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324 )
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325 else:
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326 sys.exit("Invalid database type")
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327
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328 open(args.data_manager_json, 'w').write(json.dumps(data_manager_output))
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329
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330
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331 if __name__ == "__main__":
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332 main()