Mercurial > repos > thanhlv > data_manager_build_ariba_database

annotate data_manager/ariba_database_builder.py @ 9:218301fbbb99 draft default tip

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"planemo upload for repository https://github.com/thanhleviet/galaxy-tools commit 3a0b92d1a2dcd5c5b75e5b63727850139af21ace-dirty"
author thanhlv
date Fri, 02 Oct 2020 11:43:36 +0000
parents 78bf08fa1e75
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 import sys
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2 import subprocess
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3 import shlex
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4 import shutil
0
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5 import argparse
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6 import json
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7 import os
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8 import shutil
4
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9 import errno
9
218301fbbb99 "planemo upload for repository https://github.com/thanhleviet/galaxy-tools commit 3a0b92d1a2dcd5c5b75e5b63727850139af21ace-dirty"
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10 from pprint import pprint
0
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11
4
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12 data_table_name = "ariba_databases"
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13
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14 mlst_dict = {
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15 "achs" : "Achromobacter spp.",
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16 "acib1" : "Acinetobacter baumannii#1",
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17 "acib2" : "Acinetobacter baumannii#2",
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18 "aers" : "Aeromonas spp.",
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thanhlv
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19 "anap" : "Anaplasma phagocytophilum",
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20 "arcs" : "Arcobacter spp.",
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thanhlv
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21 "aspf" : "Aspergillus fumigatus",
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22 "bacc" : "Bacillus cereus",
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23 "bacl" : "Bacillus licheniformis",
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24 "bacs" : "Bacillus subtilis",
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25 "barb" : "Bartonella bacilliformis",
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26 "barh" : "Bartonella henselae",
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27 "bors" : "Bordetella spp.",
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28 "borr" : "Borrelia spp.",
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29 "brah" : "Brachyspira hampsonii",
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30 "brach" : "Brachyspira hyodysenteriae",
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31 "brai" : "Brachyspira intermedia",
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32 "brap" : "Brachyspira pilosicoli",
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33 "bras" : "Brachyspira spp.",
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thanhlv
parents: 3
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34 "brus" : "Brucella spp.",
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35 "bucc" : "Burkholderia cepacia complex",
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36 "burp" : "Burkholderia pseudomallei",
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37 "camc" : "Campylobacter concisus/curvus",
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38 "camf" : "Campylobacter fetus",
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39 "camh" : "Campylobacter helveticus",
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40 "rlis" : "Campylobacter hyointestinalis",
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41 "cami" : "Campylobacter insulaenigrae",
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42 "camj" : "Campylobacter jejuni",
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43 "caml" : "Campylobacter lanienae",
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44 "rari" : "Campylobacter lari",
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45 "cams" : "Campylobacter sputorum",
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46 "camu" : "Campylobacter upsaliensis",
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47 "cana" : "Candida albicans",
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48 "cang" : "Candida glabrata",
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49 "cank" : "Candida krusei",
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50 "cant" : "Candida tropicalis",
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51 "cals" : "Candidatus Liberibacter solanacearum",
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52 "carm" : "Carnobacterium maltaromaticum",
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53 "chls" : "Chlamydiales spp.",
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54 "citf" : "Citrobacter freundii",
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55 "clos" : "Clonorchis sinensis",
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56 "clob" : "Clostridium botulinum",
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57 "clod" : "Clostridium difficile",
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58 "mcum" : "Clostridium septicum",
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59 "cord" : "Corynebacterium diphtheriae",
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60 "cros" : "Cronobacter spp.",
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61 "dicn" : "Dichelobacter nodosus",
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62 "edws" : "Edwardsiella spp.",
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63 "entc" : "Enterobacter cloacae",
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64 "entf" : "Enterococcus faecalis",
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65 "sium" : "Enterococcus faecium",
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66 "escc1" : "Escherichia coli#1",
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67 "escc2" : "Escherichia coli#2",
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68 "flap" : "Flavobacterium psychrophilum",
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69 "gala" : "Gallibacterium anatis",
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70 "haei" : "Haemophilus influenzae",
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71 "haep" : "Haemophilus parasuis",
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72 "helc" : "Helicobacter cinaedi",
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73 "help" : "Helicobacter pylori",
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74 "hels" : "Helicobacter suis",
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75 "kink" : "Kingella kingae",
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76 "klea" : "Klebsiella aerogenes",
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77 "kleo" : "Klebsiella oxytoca",
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78 "klep" : "Klebsiella pneumoniae",
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79 "kuds" : "Kudoa septempunctata",
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80 "lacs" : "Lactobacillus salivarius",
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81 "leps" : "Leptospira spp.",
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82 "leps2" : "Leptospira spp.#2",
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83 "leps3" : "Leptospira spp.#3",
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84 "lism" : "Listeria monocytogenes",
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85 "macc" : "Macrococcus canis",
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86 "scus" : "Macrococcus caseolyticus",
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87 "manh" : "Mannheimia haemolytica",
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88 "melp" : "Melissococcus plutonius",
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89 "morc" : "Moraxella catarrhalis",
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90 "mycs" : "Mycobacteria spp.",
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91 "myca" : "Mycobacterium abscessus",
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92 "mycm" : "Mycobacterium massiliense",
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93 "mycoa" : "Mycoplasma agalactiae",
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94 "mycb" : "Mycoplasma bovis",
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95 "mych" : "Mycoplasma hyopneumoniae",
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96 "anis" : "Mycoplasma hyorhinis",
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97 "myci" : "Mycoplasma iowae",
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98 "mycp" : "Mycoplasma pneumoniae",
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99 "mycos" : "Mycoplasma synoviae",
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100 "neis" : "Neisseria spp.",
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101 "orit" : "Orientia tsutsugamushi",
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102 "ornr" : "Ornithobacterium rhinotracheale",
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103 "pael" : "Paenibacillus larvae",
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104 "pasm1" : "Pasteurella multocida#1",
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105 "pasm2" : "Pasteurella multocida#2",
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106 "pedp" : "Pediococcus pentosaceus",
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107 "phod" : "Photobacterium damselae",
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108 "piss" : "Piscirickettsia salmonis",
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109 "porg" : "Porphyromonas gingivalis",
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110 "proa" : "Propionibacterium acnes",
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111 "psea" : "Pseudomonas aeruginosa",
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112 "psef" : "Pseudomonas fluorescens",
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113 "psep" : "Pseudomonas putida",
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114 "rhos" : "Rhodococcus spp.",
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115 "riea" : "Riemerella anatipestifer",
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116 "sale" : "Salmonella enterica",
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117 "sapp" : "Saprolegnia parasitica",
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118 "sins" : "Sinorhizobium spp.",
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119 "staa" : "Staphylococcus aureus",
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120 "stae" : "Staphylococcus epidermidis",
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121 "stah" : "Staphylococcus haemolyticus",
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122 "snis" : "Staphylococcus hominis",
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123 "stal" : "Staphylococcus lugdunensis",
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124 "stap" : "Staphylococcus pseudintermedius",
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125 "stem" : "Stenotrophomonas maltophilia",
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126 "stra" : "Streptococcus agalactiae",
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127 "sbcx" : "Streptococcus bovis/equinus complex (SBSEC)",
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128 "strc" : "Streptococcus canis",
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129 "stde" : "Streptococcus dysgalactiae equisimilis",
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130 "strg" : "Streptococcus gallolyticus",
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131 "stro" : "Streptococcus oralis",
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132 "strp" : "Streptococcus pneumoniae",
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133 "snes" : "Streptococcus pyogenes",
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134 "strs" : "Streptococcus suis",
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135 "strt" : "Streptococcus thermophilus",
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136 "strt2" : "Streptococcus thermophilus#2",
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137 "stru" : "Streptococcus uberis",
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138 "strz" : "Streptococcus zooepidemicus",
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139 "sspp" : "Streptomyces spp",
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140 "tays" : "Taylorella spp.",
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141 "tens" : "Tenacibaculum spp.",
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142 "trep" : "Treponema pallidum",
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143 "triv" : "Trichomonas vaginalis",
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144 "ures" : "Ureaplasma spp.",
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145 "vibc" : "Vibrio cholerae",
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146 "vibc2" : "Vibrio cholerae#2",
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147 "vibp" : "Vibrio parahaemolyticus",
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148 "vibs" : "Vibrio spp.",
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149 "vibt" : "Vibrio tapetis",
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150 "vibv" : "Vibrio vulnificus",
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151 "wolb" : "Wolbachia",
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152 "xylf" : "Xylella fastidiosa",
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153 "yerp" : "Yersinia pseudotuberculosis",
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154 "yerr" : "Yersinia ruckeri",
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155 "yers" : "Yersinia spp."
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156 }
0
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157
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158
4
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159 genes_dict = {
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160 "card" : "CARD",
9
218301fbbb99 "planemo upload for repository https://github.com/thanhleviet/galaxy-tools commit 3a0b92d1a2dcd5c5b75e5b63727850139af21ace-dirty"
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161 "ncbi" : "ncbi",
4
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162 "resfinder" : "Resfinder",
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163 "plasmidfinder" : "Plasmidfinder",
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164 "megares" : "Megares",
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165 "argannot" : "Argannot",
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166 "vfdb_core" : "vfdb_core",
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167 "vfdb_full" : "vfdb_full",
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168 "virulencefinder" : "virulencefinder"
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169 }
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170
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171 def run_ariba(cmd):
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172 _cmd = shlex.split(cmd)
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173 subprocess.check_call(_cmd)
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174
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175 def build_mlst(mlst_db):
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176 mlst_species = mlst_dict[mlst_db]
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177 run_ariba("ariba pubmlstget '{}' out".format(mlst_species))
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178 output_path = os.getcwd()
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179 old = "{}/out/ref_db".format(output_path, mlst_db)
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180 new = "{}/{}".format(output_path, mlst_db)
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181 shutil.move(old, new)
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182
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183 def build_curated_db(gen_db):
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184 run_ariba("ariba getref {} out".format(gen_db))
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185 run_ariba("ariba prepareref -f out.fa -m out.tsv {}".format(gen_db))
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186
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187 def build_custom_db(fasta, coding, db_name):
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188 run_ariba("ariba prepareref --all_coding {} -f {} {}".format(coding, fasta, db_name))
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189
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190 def _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry):
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191 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
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192 data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] )
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193 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )
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194 return data_manager_dict
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195
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196 def main():
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197 parser = argparse.ArgumentParser()
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198 parser.add_argument('params')
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199 parser.add_argument( '-t', '--dbtype', dest='database_type', help='database type' )
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200 parser.add_argument( '-d', '--db', dest='db_name', help='database name' )
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201 parser.add_argument( '-c', '--coding', dest='coding', help='' )
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202 parser.add_argument( '-f', '--fasta', dest='fasta', help='' )
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203 args = parser.parse_args()
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204
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205 if args.database_type == "curated":
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206 build_curated_db(args.db_name)
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207 name = genes_dict[args.db_name]
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208 elif args.database_type == "mlst":
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209 build_mlst(args.db_name)
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210 name = mlst_dict[args.db_name]
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211 elif args.database_type == "fasta":
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212 build_custom_db(args.fasta, args.coding, args.db_name)
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213 name = args.db_name
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214
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215 params = json.loads(open(args.params).read())
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216 pprint(params)
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217 target_directory = params['output_data'][0]['extra_files_path']
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218
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219 if not os.path.isdir(target_directory):
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220 os.mkdir(target_directory)
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221
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222 output_path = os.getcwd()
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223 shutil.copytree(os.path.join(output_path, args.db_name), os.path.join(target_directory, args.db_name))
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224
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225 data_manager_dict = {}
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226
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227 data_table_entry = {
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228 "value": args.db_name,
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229 "name": name,
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230 "path": os.path.join(target_directory, args.db_name)
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231 }
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232 _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry)
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233 open(args.params, 'wb').write(json.dumps(data_manager_dict))
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234
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235 if __name__ == "__main__":
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236 main()