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planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
author ecology
date Fri, 21 Jun 2024 08:55:36 +0000
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485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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1 #!/bin/Rscript
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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3 library(bold)
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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5 args = commandArgs(trailingOnly=TRUE)
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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7 raw_marker_list <- paste(args[2],args[3],args[4],args[5],args[6], sep= ",")
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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8 marker_list_W_none <- unique(strsplit(raw_marker_list, ",")[[1]])
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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9 marker_list <- marker_list_W_none[marker_list_W_none != "None"]
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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10 cat("researched marker(s):", marker_list, "\n\n")
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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12 #Functions to retrieve the subtaxa of each family ((get)subtaxa) and search in Bold and download the available sequences of each subtaxa (get_fasta)
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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13 get_fasta<-function(taxon,filename,arg_mark){
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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14 bold_res<-bold_seqspec(taxon=taxon)
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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15 cat(taxon, "marker list:", unique(bold_res$markercode), "\n")
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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16 x <- data.frame()
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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17 for (mark in arg_mark){x <- rbind(x, bold_res[bold_res$markercode == mark,])}
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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18 if (dim(x)[1] == 0){return(cat("no sequences were found with selected marker(s) for", taxon, "see existing marker list above", "\n"))}
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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19 x[x==""] <- NA
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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20 b_acc <- x$processid
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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21 b_tax <- ifelse(!is.na(x$species_name),x$species_name,ifelse(!is.na(x$genus_name),x$genus_name,ifelse(
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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22 !is.na(x$family_name),x$family_name,ifelse(
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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23 !is.na(x$order_name),x$order_name,ifelse(
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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24 !is.na(x$class_name),x$class_name,x$phylum_name)))))
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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25 b_mark <- x$markercode
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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26 n_acc <- ifelse(!is.na(x$genbank_accession),ifelse(!is.na(x$genbank_accession),paste0("|",x$genbank_accession),""),"")
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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28 seq <- x$nucleotides
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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29 seqname <- paste(b_acc,b_tax,b_mark,sep="|")
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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30 seqname <- paste0(seqname,n_acc)
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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31 Y <- cbind(seqname,seq)
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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32 colnames(Y) <- c("name","seq")
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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33 fastaLines = c()
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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34 for (rowNum in 1:nrow(Y)){
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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35 fastaLines = c(fastaLines, as.character(paste(">", Y[rowNum,"name"], sep = "")))
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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36 fastaLines = c(fastaLines,as.character(Y[rowNum,"seq"]))
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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37 }
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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38 writeLines(fastaLines,filename)
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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39 }
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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43 taxlist <- readLines(file(as.character(args[1])))
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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45 for (i in 1:length(taxlist)) {
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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46 cat("Processing ", taxlist[i], "\n")
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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47 tryCatch({
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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48 get_fasta(taxlist[i],paste0(taxlist[i],"bold",".fasta"),marker_list)},
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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49 error=function(e){cat("ERROR :",conditionMessage(e), "\n")}
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50 )
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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51 }
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