diff summarize_cluster_table.R @ 18:d7f3eff34c27 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/summarize_cluster_table.R	Fri May 14 11:08:46 2021 +0000
@@ -0,0 +1,57 @@
+#!/usr/bin/env Rscript
+library(optparse)
+option_list <- list( 
+  make_option(c("-c", "--cluster_table"), default=NA, type = "character",
+              help="file from RepeatExplorer2 clustering - CLUSTER_TABLE.csv"),
+
+  make_option(c("-m", "--comparative_counts"),default = NA,type = "character",
+              help="file from RepeatExplorer2 output - COMPARATIVE_ANALYSIS_COUNTS.csv"),
+  make_option(c("-o", "--output"), type="character",
+              help="output file name")
+)
+
+
+opt = parse_args(OptionParser(option_list = option_list))
+
+## for testing
+cluster_annotation = opt$cluster_table
+header_line = grep(".*Cluster.*Supercluster.*Size", readLines(cluster_annotation))
+annot = read.table(cluster_annotation, sep="\t",header=TRUE,as.is=TRUE, skip = header_line - 1)
+
+
+input_read_counts = as.numeric(strsplit(
+  grep("Number_of_analyzed_reads",
+       readLines(con=cluster_annotation, n=header_line),
+       value=TRUE)
+ ,split="\t")[[1]][2]
+)
+
+## complete classification table:
+unique_groups = sort(unique(annot$Final_annotatio))
+
+groups_to_remove = grep("contamination|organelle", unique_groups, value=TRUE)
+groups_to_keep =  unique_groups[!(unique_groups %in% groups_to_remove)]
+
+if (length(groups_to_remove)>0){
+  input_count_reads_corrected = input_read_counts - sum(annot$Size_adjusted[annot$Final_annotation %in% groups_to_remove])
+
+}else{
+  input_count_reads_corrected = input_read_counts 
+}
+
+proportion = numeric()
+sum_of_reads = numeric()
+for (g in groups_to_keep){
+  sum_of_reads[g] = sum(annot$Size_adjusted[annot$Final_annotation %in% g])
+  proportion[g] = sum_of_reads[g] / input_count_reads_corrected
+}
+
+
+
+summary_table = data.frame(Annotation = groups_to_keep,
+                           Number_of_reads = sum_of_reads,
+                           "Proportion[%]" = proportion * 100 , check.names = FALSE)
+
+print(opt$output)
+write.table(summary_table,file = opt$output,
+            row.names = FALSE, col.names = TRUE, sep="\t")