Mercurial > repos > ecology > ecoregion_taxa_seeker
view recup_liste_taxon.R @ 0:e3cd588fd14a draft
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 2a2ae892fa2dbc1eff9c6a59c3ad8f3c27c1c78d
author | ecology |
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date | Wed, 18 Oct 2023 09:58:17 +0000 |
parents | |
children | 9dc992f80c25 |
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#This script allows us to create a file telling us for each taxon if we obtained a BRT model. As well as the list of taxa. #load packages library(dplyr, warn.conflicts = FALSE) library(taxonomyCleanr, warn.conflicts = FALSE) library(stringr, warn.conflicts = FALSE) #load arguments args = commandArgs(trailingOnly=TRUE) if (length(args)==0){ stop("This tool needs at least one argument") }else{ data <- args[1] preds <- args[2] enviro <- args[3] } env = read.table(enviro, header=T, na.strings = "na") occurrence_files = strsplit(data,",") preds_files = strsplit(preds,",") #########functions########## `%!in%` <- Negate(`%in%`) have_model = data.frame() pres = 0 have.model <- function(taxon_phylum,noms_sp,comptage_sp,brt_phylum){ for (tax in taxon_phylum) { if (tax %in% names(noms_sp)){ pres = sum(comptage_sp[tax]) } if (tax %in% brt_phylum$spe ) { brt = c(tax,"Yes", pres) have_model = rbind(have_model,brt, make.row.names = F)} else { brt = c(tax,"No", pres) have_model = rbind(have_model,brt, make.row.names = F)} } colnames(have_model) = c("Taxa","Model","Occurences") return(have_model)} ##########Execution######## brt = NULL for (j in 1:length(preds_files[[1]])){ brt <- rbind(brt,read.table(preds_files[[1]][j], header = TRUE, na.strings = "na")) } for (i in 1:length(occurrence_files[[1]])) { occurrence <- NULL cmpt <- NULL taxon <- list() occurrence <- read.table(occurrence_files[[1]][i], dec = ",", sep = ";", header = TRUE, na.strings = "na") taxon_names <- names(occurrence) new_taxon <- taxon_names[!(taxon_names %in% names(env)) & taxon_names != "station"] taxon <- c(taxon, new_taxon) cmpt <- occurrence[, new_taxon] cmpt <- as.data.frame(cmpt) have_model <- have.model(taxon, occurrence, cmpt, brt) } #Taxa for which a model was obtained have_model2 = subset(have_model, have_model$`Model` != "N") have_model3 = subset(have_model, have_model$`Model` != "N") #Obtain a list of taxa (cleaned) that have obtained a BRT model (file that can be submitted to the match taxa tool of the WoRMS database to obtain their classification and be able to sort duplicates between taxonomic ranks) have_model2$Taxa <- as.character(trim_taxa(have_model2$Taxa)) #Second clean-up (elimination of all taxa ending in sp1./sp2 etc which represents a duplicate) have_model2 <- have_model2 %>% filter(!str_ends(Taxa, "sp.1|sp[0-9]")) have_model3 <- have_model3 %>% filter(!str_ends(Taxa, "sp.1|sp[0-9]")) have_model <- have_model %>% filter(!str_ends(Taxa, "sp.1|sp[0-9]")) #extraction of the have_model object write.csv(have_model,file = "have_model.csv", quote = F, row.names = F) #getting list of taxa for next if not using worms list_taxon = have_model3$Taxa write.table(list_taxon, file= "list_taxa.txt", quote = F, row.names = F, col.names = F) #getting the final list to submit to worms liste_taxon = have_model2$Taxa write.table(liste_taxon,file = "list_taxa_clean.txt", quote = F, row.names = F, col.names = F)