Mercurial > repos > petr-novak > repeat_annotation_pipeline3
diff annotate_contigs.R @ 1:814cba36e435 draft
Uploaded
author | mvdbeek |
---|---|
date | Mon, 21 Feb 2022 10:21:39 +0000 |
parents | ea6a3059a6af |
children | 5366d5ea04bc |
line wrap: on
line diff
--- a/annotate_contigs.R Mon Oct 18 11:01:20 2021 +0000 +++ b/annotate_contigs.R Mon Feb 21 10:21:39 2022 +0000 @@ -4,15 +4,15 @@ ## output 3 - annotated fasta suppressPackageStartupMessages(library(Biostrings)) -clean_contigs = function(s){ +clean_contigs = function(s) { ## remove all N sc = as.character(s) - sc_trimmed = gsub("N+$", "", gsub("^N+","",s)) + sc_trimmed = gsub("N+$", "", gsub("^N+", "", s)) ## remove blank and short sequences: - sc_trimmed_not_empty = sc_trimmed[nchar(sc_trimmed) !=0] - sc_trimmed_short = sc_trimmed_not_empty[nchar(sc_trimmed_not_empty) <=20] - sc_trimmed_long = sc_trimmed_not_empty[nchar(sc_trimmed_not_empty) >20] - sc_trimmed_short_tarean = sc_trimmed_short[grep("sc_", names(sc_trimmed_short), fixed=TRUE)] + sc_trimmed_not_empty = sc_trimmed[nchar(sc_trimmed) != 0] + sc_trimmed_short = sc_trimmed_not_empty[nchar(sc_trimmed_not_empty) <= 20] + sc_trimmed_long = sc_trimmed_not_empty[nchar(sc_trimmed_not_empty) > 20] + sc_trimmed_short_tarean = sc_trimmed_short[grep("sc_", names(sc_trimmed_short), fixed = TRUE)] sc_out = DNAStringSet(c(sc_trimmed_long, sc_trimmed_short_tarean)) } @@ -29,27 +29,26 @@ hl = intersect(grep("cluster", tolower(x)), grep("automatic_annotation", tolower(x))) message("using line ", hl, " as header") -annotation_table=read.table(commandArgs(T)[2], sep="\t", header=TRUE, skip = hl - 1) +annotation_table = read.table(commandArgs(T)[2], sep = "\t", header = TRUE, skip = hl - 1) colnames(annotation_table) = tolower(colnames(annotation_table)) contigs = readDNAStringSet(commandArgs(T)[1]) -if("final_annotation" %in% colnames(annotation_table) & all(!is.na(annotation_table$final_annotation))){ +if ("final_annotation" %in% colnames(annotation_table) & all(!is.na(annotation_table$final_annotation))) { annot_dict = annotation_table$final_annotation message("using final annotation column") -}else{ +}else { message("using automatic annotation column") annot_dict = annotation_table$automatic_annotation } - -names(annot_dict) = paste0("CL",annotation_table$cluster) +names(annot_dict) = paste0("CL", annotation_table$cluster) #print(annot_dict) contigs_ok = clean_contigs(contigs) -contig_name = gsub("Contig.+","",names(contigs_ok)) +contig_name = gsub("Contig.+", "", names(contigs_ok)) ## keep only contigs which are in annot table include = contig_name %in% names(annot_dict) @@ -57,7 +56,7 @@ contig_name_inc = contig_name[include] contig_ok_include = contigs_ok[include] -new_name_with_annot = paste0(names(contig_ok_include),"#",annot_dict[contig_name_inc]) +new_name_with_annot = paste0(names(contig_ok_include), "#", annot_dict[contig_name_inc]) names(contig_ok_include) = new_name_with_annot writeXStringSet(contig_ok_include, filepath = commandArgs(T)[3])