Mercurial > repos > ecology > retrieve_bold
diff retrieve_bold.R @ 0:0608a259f2da draft default tip
planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
author | ecology |
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date | Fri, 21 Jun 2024 08:55:50 +0000 |
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--- /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")} + ) +} + + + + + + + + + + + + +