diff retrieve_bold.R @ 0:0608a259f2da draft default tip

planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/retrieve_bold.R	Fri Jun 21 08:55:50 2024 +0000
@@ -0,0 +1,64 @@
+#!/bin/Rscript
+
+library(bold)
+
+args = commandArgs(trailingOnly=TRUE)
+
+raw_marker_list <- paste(args[2],args[3],args[4],args[5],args[6], sep= ",")
+marker_list_W_none <- unique(strsplit(raw_marker_list, ",")[[1]])
+marker_list <- marker_list_W_none[marker_list_W_none != "None"]
+cat("researched marker(s):", marker_list, "\n\n")
+
+#Functions to retrieve the subtaxa of each family ((get)subtaxa) and search in Bold and download the available sequences of each subtaxa (get_fasta)
+get_fasta<-function(taxon,filename,arg_mark){
+  bold_res<-bold_seqspec(taxon=taxon)
+  cat(taxon, "marker list:", unique(bold_res$markercode), "\n")
+  x <- data.frame()
+  for (mark in arg_mark){x <- rbind(x, bold_res[bold_res$markercode == mark,])}
+  if (dim(x)[1] == 0){return(cat("no sequences were found with selected marker(s) for", taxon, "see existing marker list above",  "\n"))}
+  x[x==""]  <- NA 
+  b_acc <- x$processid
+  b_tax <- ifelse(!is.na(x$species_name),x$species_name,ifelse(!is.na(x$genus_name),x$genus_name,ifelse(
+    !is.na(x$family_name),x$family_name,ifelse(
+      !is.na(x$order_name),x$order_name,ifelse(
+        !is.na(x$class_name),x$class_name,x$phylum_name)))))
+  b_mark <- x$markercode
+  n_acc  <- ifelse(!is.na(x$genbank_accession),ifelse(!is.na(x$genbank_accession),paste0("|",x$genbank_accession),""),"")
+  
+  seq <- x$nucleotides
+  seqname <- paste(b_acc,b_tax,b_mark,sep="|")
+  seqname <- paste0(seqname,n_acc)
+  Y <- cbind(seqname,seq)
+  colnames(Y) <- c("name","seq")
+  fastaLines = c()
+  for (rowNum in 1:nrow(Y)){
+    fastaLines = c(fastaLines, as.character(paste(">", Y[rowNum,"name"], sep = "")))
+    fastaLines = c(fastaLines,as.character(Y[rowNum,"seq"]))
+  }
+  writeLines(fastaLines,filename)
+}
+
+
+
+taxlist  <- readLines(file(as.character(args[1])))
+
+for (i in 1:length(taxlist)) {
+    cat("Processing ", taxlist[i], "\n")
+    tryCatch({
+        get_fasta(taxlist[i],paste0(taxlist[i],"bold",".fasta"),marker_list)}, 
+        error=function(e){cat("ERROR :",conditionMessage(e), "\n")}
+   )
+}
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