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annotate MT2MQ.R @ 5:c3a418f7cf7f draft

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"planemo upload commit 499df83651e020e9106d70ec658edf86355f49d9"
author galaxyp
date Wed, 21 Oct 2020 16:39:25 +0000
parents 9c8e7137d331
children
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1 # MT2MQ: prepares metatranscriptomic outputs from ASaiM (HUMAnN2 and metaphlan) for metaquantome
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2
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3 # Load libraries
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4 suppressPackageStartupMessages(library(tidyverse))
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5 suppressPackageStartupMessages(library(taxize))
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6
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7 # Set parameters from arguments
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8 args <- commandArgs(trailingOnly = TRUE)
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9 data <- args[1]
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10 # data: full path to file or directory:
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11 # - if in functional or f-t mode, should be a tsv file of HUMAnN2 gene families, after regrouping and renaming to GO, joining samples, and renormalizing to CPM.
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12 # - if in taxonomic mode, should be a directory of tsv files of metaphlan genus-level results
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13 mode <- args[2]
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14 # mode:
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15 # -"f": function
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16 # -"t": taxonomy
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17 # -"ft": function-taxonomy
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18 ontology <- unlist(strsplit(args[3], split = ","))
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19 # ontology: only for function or f-t mode. A string of the GO namespace(s) to include, separated by commas.
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20 # ex: to include all: "molecular_function,biological_process,cellular_component"
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21
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22 int_file <- args[4]
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23 # int_file: full path and file name and extension to write intensity file
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24
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25 func_file <- args[5]
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26 # func_file: full path and file name and extension to write func file
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27
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28 tax_file <- args[6]
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29 # tax_file: full path and file name and extension to write tax file
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30
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31
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32 # Functional mode
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33 if (mode == "f") {
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34 int <- read.delim(file = data, header = TRUE, sep = "\t") %>%
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35 filter(!grepl(".+g__.+", X..Gene.Family)) %>%
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36 separate(col = X..Gene.Family, into = c("id", "Extra"), sep = ": ", fill = "left") %>%
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37 separate(col = Extra, into = c("namespace", "name"), sep = " ", fill = "left", extra = "merge") %>%
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38 mutate(namespace = if_else(namespace == "[MF]", true = "molecular_function", false = if_else(namespace == "[BP]", true = "biological_process", false = "cellular_component"))) %>%
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39 filter(namespace %in% ontology) %>%
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40 select(id, name, namespace, 4:ncol(.))
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41 func <- int %>%
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42 select(id) %>%
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43 mutate(gos = id)
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44 write.table(x = int, file = int_file, quote = FALSE, sep = "\t", row.names = FALSE)
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45 write.table(x = func, file = func_file, quote = FALSE, sep = "\t", row.names = FALSE)
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46 }
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47
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48 # Taxonomic mode
2
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49 if (mode == "t") {
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50 files <- dir(path = data)
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51 int <- tibble(filename = files) %>%
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52 mutate(file_contents = map(filename, ~read.delim(file = file.path(data, .), header = TRUE, sep = "\t"))) %>%
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53 unnest(cols = c(file_contents)) %>%
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54 rename(sample = filename) %>%
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55 separate(col = sample, into = c("sample", NA), sep = ".tsv") %>%
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56 pivot_wider(names_from = sample, values_from = abundance) %>%
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57 mutate(rank = "genus") %>%
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58 rename(name = genus) %>%
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59 mutate(name = as.character(name)) %>%
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60 mutate(id = get_uid(name, key = NULL, messages = FALSE)) %>%
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61 select(id, name, rank, 2:ncol(.))
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62 tax <- int %>%
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63 select(id) %>%
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64 mutate(tax = id)
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65 write.table(x = int, file = int_file, quote = FALSE, sep = "\t", row.names = FALSE)
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66 write.table(x = tax, file = tax_file, quote = FALSE, sep = "\t", row.names = FALSE)
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67 }
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68
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69 # Function-taxonomy mode
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70 if (mode == "ft") {
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71 ft <- read.delim(file = data, header = TRUE, sep = "\t") %>%
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72 filter(grepl(".+g__.+", X..Gene.Family)) %>%
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73 separate(col = X..Gene.Family, into = c("id", "Extra"), sep = ": ", fill = "left") %>%
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74 separate(col = Extra, into = c("namespace", "name"), sep = " ", fill = "left", extra = "merge") %>%
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75 separate(col = name, into = c("name", "taxa"), sep = "\\|", extra = "merge") %>%
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76 separate(col = taxa, into = c("Extra", "genus", "species"), sep = "__") %>%
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77 select(-"Extra") %>%
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78 mutate_if(is.character, str_replace_all, pattern = "\\.s", replacement = "") %>%
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79 mutate_at(c("species"), str_replace_all, pattern = "_", replacement = " ") %>%
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80 mutate(namespace = if_else(namespace == "[MF]", true = "molecular_function", false = if_else(namespace == "[BP]", true = "biological_process", false = "cellular_component"))) %>%
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81 filter(namespace %in% ontology) %>%
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82 select(id, name, namespace, 4:ncol(.))
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83 write.table(x = ft, file = int_file, quote = FALSE, sep = "\t", row.names = FALSE)
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84 }