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planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 97945a3ad655f1a0f99f577d0d423124460d900a
author nml
date Tue, 24 Oct 2023 21:28:06 +0000
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1 # Copyright Government of Canada 2018
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2 #
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3 # Written by: National Microbiology Laboratory, Public Health Agency of Canada
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4 #
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5 # Licensed under the Apache License, Version 2.0 (the "License"); you may not use
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6 # this work except in compliance with the License. You may obtain a copy of the
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7 # License at:
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8 #
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9 # http://www.apache.org/licenses/LICENSE-2.0
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10 #
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11 # Unless required by applicable law or agreed to in writing, software distributed
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12 # under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
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13 # CONDITIONS OF ANY KIND, either express or implied. See the License for the
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14 # specific language governing permissions and limitations under the License.
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17 # Parsing JSONs from Mykrobe Predict into CSV reports
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18 # Take the JSON output from Mykrobe, rearrange, output for LIMS
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19 # Adrian Zetner
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20 # August 2018
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21 # Updated August 2023
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23 # Libraries ####
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25 sink(stdout(), type = "message")
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27 suppressPackageStartupMessages({
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28 library(jsonlite)
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29 library(here)
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30 library(dplyr)
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31 library(purrr)
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32 library(tidyr)
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33 library(stringr)
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34 library(optparse)
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35 })
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37 # Define custom functions, variables, and paths. Collect and use CL arguments ####
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38
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39 # Here's a function to recreate that output table from the input JSON files for 2019
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41 getResults2019 <- function(listelement) {
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42 # Define list levels for various elements of the json
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43 phylo_group <-
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44 names(listelement[[1]][["phylogenetics"]][["phylo_group"]])
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45 if ("Non_tuberculosis_mycobacterium_complex" %in% phylo_group) {
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46 warning(
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47 paste(
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48 "Non-tuberculosis mycobacteria detected in file ",
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49 names(listelement),
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50 ". Skipping.",
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51 sep = ""
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52 )
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53 )
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54 return()
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55 }
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56
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57 species <-
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58 names(listelement[[1]][["phylogenetics"]][["species"]])
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59 lineage <-
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60 if (length(listelement[[1]][["phylogenetics"]][["lineage"]]) == 1) {
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61 names(listelement[[1]][["phylogenetics"]][["lineage"]])
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62 } else {
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63 listelement[[1]][["phylogenetics"]][["lineage"]][["lineage"]]
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64 }
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65
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66 # Start building a list of all your various elements
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67 temp <-
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68 list(
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69 mykrobe_version = listelement[[1]][["version"]][["mykrobe-predictor"]],
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70 file = names(listelement),
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71 # One element
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72 plate_name = "test",
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73 # This probably needs changing
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74 sample = "sequence_calls",
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75 # Likewise change this
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76 phylo_group = phylo_group,
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77 # As above
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78 species = species,
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79 # As above
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80 lineage = lineage,
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81 # As above
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82 # The following expressions drill down into the list elements and pull out what is needed.
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83 # It's inelegant and vulnerable to changes in the input formats but if they're consistent it'll work
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84 phylo_group_per_covg = listelement[[1]][["phylogenetics"]][["phylo_group"]][[phylo_group]][["percent_coverage"]],
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85 species_per_covg = listelement[[1]][["phylogenetics"]][["species"]][[species]][["percent_coverage"]],
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86 lineage_per_covg = listelement[[1]][["phylogenetics"]][["lineage"]][[lineage]][["percent_coverage"]],
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87 phylo_group_depth = listelement[[1]][["phylogenetics"]][["phylo_group"]][[phylo_group]][["median_depth"]],
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88 species_depth = listelement[[1]][["phylogenetics"]][["species"]][[species]][["median_depth"]],
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89 lineage_depth = listelement[[1]][["phylogenetics"]][["lineage"]][[lineage]][["median_depth"]],
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90 Mykrobe_Resistance_probe_set = basename(listelement[[1]][["probe_sets"]][2]) # Is it always the second?
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91 )
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92
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93 # Super cool nested and vectorized (for SPEED!) functions to grab the predictions for drug sensitivity and gene variants
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94 # Both produce character vectors of the same length as the number of drugs tested in the same order
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95 # All of these also check if there are missing values in drug/susceptibility/variant elements and adds the column anyhow
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96
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97 if (length(map_chr(listelement[[1]][["susceptibility"]], "predict")) != 0) {
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98 temp$susceptibility <-
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99 map_chr(listelement[[1]][["susceptibility"]], "predict")
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100 } else {
0
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101 temp$susceptibility <- NA
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102 }
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103
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104 if (length(names(listelement[[1]][["susceptibility"]])) != 0) {
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105 temp$drug <- names(listelement[[1]][["susceptibility"]])
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106 } else {
0
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107 temp$drug <- NA
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108 }
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109
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110 mapped.variants <-
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111 map(
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112 listelement[[1]][["susceptibility"]], # Dig into the lists, pull out variants and collapse into chr vector
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113 ~ imap(
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114 .x[["called_by"]], # imap is shorthand for map2(x, names(x), ...), calling .y gets you the name / index of the current element
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115 ~ paste(.y,
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116 .x[["info"]][["coverage"]][["alternate"]][["median_depth"]],
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117 .x[["info"]][["coverage"]][["reference"]][["median_depth"]],
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118 .x[["info"]][["conf"]],
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119 sep = ":"
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120 )
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121 )
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122 ) %>%
0
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123 map_chr(~ paste(.x, collapse = "__"))
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124
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125 if (length(mapped.variants) != 0) {
0
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126 temp$`variants (gene:alt_depth:wt_depth:conf)` <- mapped.variants
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127 } else {
0
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128 temp$`variants (gene:alt_depth:wt_depth:conf)` <- NA
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129 }
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130
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131 temp$`genes (prot_mut-ref_mut:percent_covg:depth)` <- NA
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132
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133 # Take that list and mash all the elements together as columns in a tibble, recycling as needed to fill in space
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134 # eg. phylo_group is repeated/recycled as many times as there are drugs tested
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135 as_tibble(temp)
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136 }
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137
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138 # Here's a function to recreate that output table from the input JSON files for panel 2020
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139
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140 getResults2020 <- function(listelement) {
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141 # Define list levels for various elements of the json
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142 phylo_group <-
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143 names(listelement[[1]][["phylogenetics"]][["phylo_group"]])
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144 if ("Non_tuberculosis_mycobacterium_complex" %in% phylo_group) {
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145 warning(
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146 paste(
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147 "Non-tuberculosis mycobacteria detected in file ",
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148 names(listelement),
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149 ". Skipping.",
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150 sep = ""
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151 )
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152 )
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153 return()
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154 }
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155
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156 species <-
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157 names(listelement[[1]][["phylogenetics"]][["species"]])
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158
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159 # Start building a list of all your various elements
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160 temp <-
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161 list(
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162 mykrobe_version = listelement[[1]][["version"]][["mykrobe-predictor"]],
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163 file = names(listelement),
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164 # One element
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165 plate_name = "test",
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166 # This probably needs changing
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167 sample = "sequence_calls",
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168 # Likewise change this
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169 phylo_group = phylo_group,
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170 # As above
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171 species = species,
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172 # As above
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173 # The following expressions drill down into the list elements and pull out what is needed.
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174 # It's inelegant and vulnerable to changes in the input formats but if they're consistent it'll work
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175 phylo_group_per_covg = listelement[[1]][["phylogenetics"]][["phylo_group"]][[phylo_group]][["percent_coverage"]],
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176 species_per_covg = listelement[[1]][["phylogenetics"]][["species"]][[species]][["percent_coverage"]],
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177 phylo_group_depth = listelement[[1]][["phylogenetics"]][["phylo_group"]][[phylo_group]][["median_depth"]],
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178 species_depth = listelement[[1]][["phylogenetics"]][["species"]][[species]][["median_depth"]],
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179 Mykrobe_Resistance_probe_set = basename(listelement[[1]][["probe_sets"]][2]) # Is it always the second?
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180 )
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181
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182 # Super cool nested and vectorized (for SPEED!) functions to grab the predictions for drug sensitivity and gene variants
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183 # Both produce character vectors of the same length as the number of drugs tested in the same order
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184 # All of these also check if there are missing values in drug/susceptibility/variant elements and adds the column anyhow
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185
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186 if (length(map_chr(listelement[[1]][["susceptibility"]], "predict")) != 0) {
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187 temp$susceptibility <-
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188 map_chr(listelement[[1]][["susceptibility"]], "predict")
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189 } else {
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190 temp$susceptibility <- NA
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191 }
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192
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193 if (length(names(listelement[[1]][["susceptibility"]])) != 0) {
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194 temp$drug <- names(listelement[[1]][["susceptibility"]])
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195 } else {
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196 temp$drug <- NA
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197 }
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198
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199 mapped.variants <-
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200 map(
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201 listelement[[1]][["susceptibility"]], # Dig into the lists, pull out variants and collapse into chr vector
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202 ~ imap(
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203 .x[["called_by"]], # imap is shorthand for map2(x, names(x), ...), calling .y gets you the name / index of the current element
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204 ~ paste(.y,
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205 .x[["info"]][["coverage"]][["alternate"]][["median_depth"]],
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206 .x[["info"]][["coverage"]][["reference"]][["median_depth"]],
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207 .x[["info"]][["conf"]],
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208 sep = ":"
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209 )
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210 )
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211 ) %>%
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212 map_chr(~ paste(.x, collapse = "__"))
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213
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214 if (length(mapped.variants) != 0) {
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215 temp$`variants (gene:alt_depth:wt_depth:conf)` <- mapped.variants
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216 } else {
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217 temp$`variants (gene:alt_depth:wt_depth:conf)` <- NA
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218 }
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219
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220 temp$`genes (prot_mut-ref_mut:percent_covg:depth)` <- NA
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221
0
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222 # Take that list and mash all the elements together as columns in a tibble, recycling as needed to fill in space
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223 # eg. phylo_group is repeated/recycled as many times as there are drugs tested
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224 as_tibble(temp)
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225 }
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226
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227 # Get command line arguments with optparse
6
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228 option_list <- list(
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229 make_option(
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230 c("-f", "--file"),
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231 type = "character",
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232 default = NULL,
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233 help = 'dataset file name or quoted comma separated names: eg. "file1,file2,file3"',
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234 metavar = "character"
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235 ),
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236 make_option(
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237 c("-d", "--dir"),
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238 type = "character",
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239 default = NULL,
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240 help = "directory location of json files",
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241 metavar = "character"
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242 ),
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diff changeset
243 make_option(
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244 c("-v", "--version"),
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245 type = "character",
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246 default = "",
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247 help = "Mykrobe Workflow Version",
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248 metavar = "character"
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249 ),
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diff changeset
250 make_option(
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251 c("-p", "--panel"),
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252 type = "character",
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253 default = "2019",
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254 help = "Mykrobe Panel Version: 2019 or 2020. [default= %default]",
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255 metavar = "character"
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256 ),
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diff changeset
257 make_option(
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diff changeset
258 c("-D", "--depth"),
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diff changeset
259 type = "integer",
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260 default = 5,
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diff changeset
261 help = "Minimum depth of coverage [default= %default]",
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diff changeset
262 metavar = "integer"
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diff changeset
263 ),
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parents: 5
diff changeset
264 make_option(
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diff changeset
265 c("-c", "--conf"),
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diff changeset
266 type = "integer",
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diff changeset
267 default = 10,
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268 help = "Minimum genotype confidence for variant genotyping [default= %default]",
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diff changeset
269 metavar = "integer"
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diff changeset
270 ),
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parents: 5
diff changeset
271 make_option(
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diff changeset
272 c("-n", "--name"),
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diff changeset
273 type = "character",
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diff changeset
274 default = "",
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diff changeset
275 help = "Name of the run",
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diff changeset
276 metavar = "character"
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diff changeset
277 ),
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diff changeset
278 make_option(
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diff changeset
279 c("-r", "--reportfile"),
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parents: 5
diff changeset
280 type = "character",
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diff changeset
281 default = "report",
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diff changeset
282 help = "File name for susceptibility report data",
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diff changeset
283 metavar = "character"
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diff changeset
284 ),
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parents: 5
diff changeset
285 make_option(
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diff changeset
286 c("-s", "--speciationfile"),
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parents: 5
diff changeset
287 type = "character",
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diff changeset
288 default = "jsondata",
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parents: 5
diff changeset
289 help = "File name for speciation data",
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parents: 5
diff changeset
290 metavar = "character"
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diff changeset
291 )
0
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292 )
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293
6
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294 opt_parser <- OptionParser(option_list = option_list)
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295 opt <- parse_args(opt_parser)
0
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296
6
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297 if (is.null(opt$file) && is.null(opt$dir)) {
0
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298 print_help(opt_parser)
6
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299 stop("At least one argument must be supplied to input file or directory",
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300 call. = FALSE
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301 )
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302 }
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303
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304 if (opt$panel != "2019" && opt$panel != "2020") {
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305 print_help(opt_parser)
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306 stop("Panel must be one of 2019 or 2020", call. = FALSE)
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307 }
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308
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309 # Parameters to take from Galaxy/CL as args or however works best
6
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310 params <- c(
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311 "", # Lims_Comment
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312 "", # Lims_INTComment
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313 opt$version, # Mykrobe_Workflow_Version
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314 opt$panel, # Mykrobe Panel Version
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315 opt$depth, # Mykrobe_min_depth_default_5
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316 opt$conf, # Mykrobe_min_conf_default_10
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317 "", # LIMS_file - empty as it's an upload field in LIMS
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diff changeset
318 opt$name
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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319 ) # Mutation_set_version
0
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320
6
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diff changeset
321 names(params) <- c(
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parents: 5
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322 "Lims_Comment",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
323 "Lims_INTComment",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
324 "Mykrobe_Workflow_Version",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
325 "Mykrobe_Panel_Version",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
326 "Mykrobe_min_depth_default_5",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
327 "Mykrobe_min_conf_default_10",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
328 "LIMS_file",
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diff changeset
329 "Mutation_set_version"
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diff changeset
330 )
0
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331
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diff changeset
332
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diff changeset
333 # A default report in the order our LIMS requires
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parents:
diff changeset
334
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
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parents:
diff changeset
335 # Make a default dataframe to combine the rest into and enforce column order / fill missing ones with NAs
6
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diff changeset
336 columns <- c(
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
337 "file",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
338 "Mykrobe_fabG1",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
339 "Mykrobe_katG",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
340 "Mykrobe_ahpC",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
341 "Mykrobe_inhA",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
342 "Mykrobe_ndh",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
343 "Isoniazid_R_mutations",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
344 "Isoniazid_Prediction",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
345 "Mykrobe_rpoB",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
346 "Rifampicin_R_mutations",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
347 "Rifampicin_Prediction",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
348 "Mykrobe_embB",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
349 "Mykrobe_embA",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
350 "Ethambutol_R_mutations",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
351 "Ethambutol_Prediction",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
352 "Mykrobe_pncA",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
353 "Mykrobe_rpsA",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
354 "Pyrazinamide_R_mutations",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
355 "Pyrazinamide_Prediction",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
356 "Mykrobe_Ofloxacin_gyrA",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
357 "Ofloxacin_R_mutations",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
358 "Ofloxacin_Prediction",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
359 "Mykrobe_Moxifloxacin_gyrA",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
360 "Moxifloxacin_R_mutations",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
361 "Moxifloxacin_Prediction",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
362 "Mykrobe_Ciprofloxacin_gyrA",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
363 "Ciprofloxacin_R_mutations",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
364 "Ciprofloxacin_Prediction",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
365 "Mykrobe_rpsL",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
366 "Mykrobe_Streptomycin_rrs",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
367 "Mykrobe_Streptomycin_gid",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
368 "Streptomycin_R_mutations",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
369 "Streptomycin_Prediction",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
370 "Mykrobe_Amikacin_rrs",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
371 "Amikacin_R_mutations",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
372 "Amikacin_Prediction",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
373 "Mykrobe_Capreomycin_rrs",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
374 "Mykrobe_Capreomycin_tlyA",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
375 "Capreomycin_R_mutations",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
376 "Capreomycin_Prediction",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
377 "Mykrobe_Kanamycin_rrs",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
378 "Mykrobe_Kanamycin_eis",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
379 "Kanamycin_R_mutations",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
380 "Kanamycin_Prediction",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
381 "Lims_Comment",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
382 "Lims_INTComment",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
383 "Mykrobe_Workflow_Version",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
384 "mykrobe_version",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
385 "Mykrobe_Resistance_probe_set",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
386 "Mykrobe_min_depth_default_5",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
387 "Mykrobe_min_conf_default_10",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
388 "LIMS_file",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
389 "Mutation_set_version"
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
390 )
0
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
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parents:
diff changeset
391
6
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
392 report <-
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
393 setNames(data.frame(matrix(
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
394 "",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
395 ncol = length(columns), nrow = 1
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
396 ), stringsAsFactors = FALSE), columns)
0
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
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parents:
diff changeset
397
6
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
398 report_cols <- c(
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
399 "file",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
400 "phylo_group",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
401 "species",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
402 "lineage",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
403 "phylo_group_per_covg",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
404 "species_per_covg",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
405 "lineage_per_covg",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
406 "phylo_group_depth",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
407 "species_depth",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
408 "lineage_depth"
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
409 )
0
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
410
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
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parents:
diff changeset
411 # List of drugs that are tested
6
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
412 all_drugs <- c(
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
413 "Isoniazid",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
414 "Rifampicin",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
415 "Ethambutol",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
416 "Pyrazinamide",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
417 "Moxifloxacin",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
418 "Ofloxacin",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
419 "Streptomycin",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
420 "Amikacin",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
421 "Capreomycin",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
422 "Kanamycin"
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
423 )
0
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
424
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
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parents:
diff changeset
425 # Do Stuff ####
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
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parents:
diff changeset
426
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
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parents:
diff changeset
427 # Import all the JSON files into a list of lists format ####
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
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diff changeset
428
6
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
429 if (is.null(opt$file)) {
0
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
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parents:
diff changeset
430 # opt$dir is used to get the list of files, a vector of non-duplicated files is then passed to map
6
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
431 files <- list.files(
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
432 path = opt$dir,
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
433 pattern = "*.json",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
434 full.names = TRUE
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
435 )
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
436 } else {
0
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
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parents:
diff changeset
437 files <- unlist(strsplit(opt$file, ","))
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
438 }
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
439
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
440 files <- files[!duplicated(basename(files))]
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
441
6
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
442 list.of.json.files <- map(
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
443 files,
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
444 ~ fromJSON(.x, simplifyDataFrame = FALSE)
0
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
445 )
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
446
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
447
6
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
448 # Apply the correct getResults function to each element in your list then bash it together into a final report
0
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
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parents:
diff changeset
449
6
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
450 if (opt$panel == "2019") {
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
451 temp <- map(list.of.json.files, getResults2019) %>%
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
452 bind_rows()
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
453 } else if (opt$panel == "2020") {
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
454 temp <- map(list.of.json.files, getResults2020) %>%
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
455 bind_rows()
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
456 columns <-
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
457 setdiff(
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
458 columns,
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
459 c(
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
460 "Mykrobe_Ciprofloxacin_gyrA",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
461 "Ciprofloxacin_R_mutations",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
462 "Ciprofloxacin_Prediction"
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
463 )
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
464 )
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
465 report_cols <- setdiff(
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
466 report_cols,
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
467 c(
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
468 "lineage",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
469 "lineage_per_covg",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
470 "lineage_depth"
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
471 )
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
472 )
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
473 } else {
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
474 stop("Panel must be one of 2019 or 2020", call. = FALSE)
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
475 }
0
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
476
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
477
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
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parents:
diff changeset
478 # Predictions of resistance or susceptibility
6
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
479
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
480 predictions.table <-
0
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
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parents:
diff changeset
481 temp %>%
6
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
482 select(file, drug, susceptibility) %>%
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
483 mutate(drug = paste(drug, "_Prediction", sep = "")) %>%
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
484 spread(drug, susceptibility, fill = "failed") %>%
0
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
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parents:
diff changeset
485 select(-starts_with("NA"))
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
486
6
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents: 5
diff changeset
487 if (length(predictions.table) == 1) {
0
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
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parents:
diff changeset
488 print(predictions.table)
6
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
489 stop("No susceptibility results in files specified. Did the testing fail?",
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490 call. = FALSE
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491 )
0
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492 }
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493
2
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diff changeset
494 # Variants, if present
6
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495 num.variants <-
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496 predictions.table %>%
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497 select(ends_with("_Prediction")) %>%
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498 unlist(use.names = FALSE) %>%
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499 str_count("[R,r]") %>%
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diff changeset
500 sum()
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501
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diff changeset
502 if (num.variants > 0) {
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diff changeset
503 # Multiple resistance mutations and confidence per drug in the X_R_mutations column
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diff changeset
504 # Actual protein changes in Mykrobe_X columns
0
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505
6
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diff changeset
506 variants.temp <-
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diff changeset
507 temp %>%
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508 select(file, drug, variants = `variants (gene:alt_depth:wt_depth:conf)`) %>%
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509 mutate(variants = replace(variants, variants == "", NA)) %>% # Make missing data consistent...
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diff changeset
510 filter(!is.na(variants)) %>% # ...Then get rid of it
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diff changeset
511 mutate(tempcols = paste(drug, "R_mutations", sep = "_")) %>%
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diff changeset
512 mutate(R_mutations = variants) %>%
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513 mutate(variants = strsplit(variants, "__")) %>% # Split the mutations across rows (list first then split across rows)
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514 unnest(variants) %>%
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diff changeset
515 separate(variants, c("gene", "mutation"), "_") %>%
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diff changeset
516 mutate(columnname = ifelse(
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517 gene %in% c("gyrA", "rrs", "eis", "gid"),
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diff changeset
518 # Check for columns that include the drug name or not and paste accordingly
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diff changeset
519 paste("Mykrobe", drug, gene, sep = "_"),
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diff changeset
520 paste("Mykrobe", gene, sep = "_")
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diff changeset
521 )) %>%
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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diff changeset
522 # Extract out the mutation information with a regex that covers all potential genes
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diff changeset
523 # This regex looks for whatever is ahead of the first colon and after the last hyphen
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diff changeset
524 mutate(mutation = str_match(mutation, "(.*)-.*:")[, 2]) %>%
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diff changeset
525 select(file, tempcols, R_mutations, columnname, mutation)
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diff changeset
526
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diff changeset
527 # Split each kind of variants into its own temp table then merge
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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diff changeset
528 variants.1 <-
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diff changeset
529 variants.temp %>%
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diff changeset
530 select(file, tempcols, R_mutations) %>%
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
531 distinct() %>%
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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diff changeset
532 spread(tempcols, R_mutations)
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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diff changeset
533
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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diff changeset
534 variants.2 <-
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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diff changeset
535 variants.temp %>%
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
536 select(file, columnname, mutation) %>%
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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diff changeset
537 group_by(file, columnname) %>%
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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diff changeset
538 summarise(mutation = paste(mutation, collapse = ";")) %>%
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
539 spread(columnname, mutation)
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
540
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
541 variants.table <-
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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diff changeset
542 full_join(variants.1, variants.2, by = "file")
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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diff changeset
543 } else {
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
544 variants.table <-
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
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diff changeset
545 data.frame(file = predictions.table$file, stringsAsFactors = FALSE)
2
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parents: 0
diff changeset
546 }
0
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parents:
diff changeset
547
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parents:
diff changeset
548
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diff changeset
549 # Make a report ####
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diff changeset
550
6
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diff changeset
551 report <-
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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diff changeset
552 temp %>%
0
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diff changeset
553 select(file, mykrobe_version, Mykrobe_Resistance_probe_set) %>% # Get important info from initial table
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diff changeset
554 distinct() %>% # Drop duped rows and combine all the tables together
6
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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diff changeset
555 full_join(variants.table) %>%
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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diff changeset
556 full_join(predictions.table) %>%
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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diff changeset
557 bind_rows(report) %>% # Use bind_rows to add columns (eg. unteseted drugs) to the final output
0
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parents:
diff changeset
558 filter(file != "")
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
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parents:
diff changeset
559
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
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parents:
diff changeset
560 # Only add the 'no mutation' replacement to the columns that actually have a result
6
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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diff changeset
561 report <-
0
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diff changeset
562 report %>%
6
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diff changeset
563 filter_at(vars(ends_with("_Prediction")), any_vars(. != "failed")) %>%
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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diff changeset
564 mutate_at(vars(starts_with("Mykrobe_")), funs(replace(., is.na(.), "No Mutation"))) %>%
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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diff changeset
565 full_join(anti_join(report, ., by = "file")) %>%
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
566 select(columns)
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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diff changeset
567
0
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
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parents:
diff changeset
568
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
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parents:
diff changeset
569 # Add in the parameters fed from Galaxy using named character vector
6
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
570 report <-
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents: 5
diff changeset
571 report %>%
0
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
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diff changeset
572 mutate(
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
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diff changeset
573 Lims_Comment = params["Lims_Comment"],
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
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parents:
diff changeset
574 Lims_INTComment = params["Lims_INTComment"],
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
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parents:
diff changeset
575 Mykrobe_Workflow_Version = params["Mykrobe_Workflow_Version"],
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
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parents:
diff changeset
576 Mykrobe_min_depth_default_5 = params["Mykrobe_min_depth_default_5"],
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
577 Mykrobe_min_conf_default_10 = params["Mykrobe_min_conf_default_10"],
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
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diff changeset
578 LIMS_file = params["LIMS_file"],
4
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parents: 2
diff changeset
579 Mutation_set_version = params["Mutation_set_version"]
0
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parents:
diff changeset
580 )
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parents:
diff changeset
581
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
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parents:
diff changeset
582 # Write some output
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
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parents:
diff changeset
583 # Report as is
6
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diff changeset
584 write.csv(report, "output-report.csv", row.names = FALSE)
0
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
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585 print("Writing Susceptibility report to CSV as output-report.csv")
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
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586
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
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587 # Select specific columns from temp and output them
6
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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588 # Addition of any_of accounts for both 2019 and 2020 panels
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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589
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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590 temp %>%
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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591 select_at( # This is a dplyr 0.8.3 function, superceded in newer versions but this tool is built around a number of specific deps
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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592 report_cols
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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593 ) %>%
0
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
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594 distinct() %>%
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8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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595 write.csv(file = "output-jsondata.csv", row.names = FALSE)
2
f2608dccd3e0 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 1d77b6cae26ef3456ff6d469d71c61cab6a19906-dirty
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596 print("Writing JSON data to CSV as output-jsondata.csv")
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8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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597 sink(NULL, type = "message") # close the sink
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6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
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598
4
8529045f0fdf planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 34d9c47b9451e5f7843028dba22b96d125fb09f5
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599 quit()