--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/clean_ltr.R	Tue Mar 08 13:24:33 2022 +0000
@@ -0,0 +1,175 @@
+#!/usr/bin/env Rscript
+initial_options <- commandArgs(trailingOnly = FALSE)
+file_arg_name <- "--file="
+script_name <- normalizePath(sub(file_arg_name, "", initial_options[grep
+                                                                    (file_arg_name,
+                                                                     initial_options)]))
+script_dir <- dirname(script_name)
+library(optparse)
+
+parser <- OptionParser()
+option_list <- list(
+  make_option(c("-g", "--gff3"), action = "store", type = "character",
+              help = "gff3  with LTR Transposable elements", default = NULL),
+  make_option(c("-s", "--reference_sequence"), action = "store", type = "character",
+              help = "reference sequence as fasta",
+              default = NULL),
+  make_option(c("-o", "--output"), action = "store", type = "character",
+              help = "output file prefix", default = NULL),
+  make_option(c("-c", "--cpu"), type =
+    "integer", default = 5, help = "Number of cpu to use [default %default]",
+              metavar = "number")
+
+)
+description <- paste(strwrap(""))
+
+epilogue <- ""
+parser <- OptionParser(option_list = option_list, epilogue = epilogue, description =
+  description, usage = "usage: %prog COMMAND [OPTIONS]")
+opt <- parse_args(parser, args = commandArgs(TRUE))
+
+
+# load packages
+suppressPackageStartupMessages({ library(rtracklayer)
+  library(Biostrings)
+  library(BSgenome)
+  library(parallel)
+   })
+
+# CONFIGURATION
+# load configuration files and functions:
+lineage_file <- paste0(script_dir, "/databases/lineage_domain_order.csv")
+ltr_utils_r <- paste0(script_dir, "/R/ltr_utils.R")
+if (file.exists(lineage_file)) {
+  lineage_info <- read.table(lineage_file, sep = "\t",
+                             header = TRUE,
+                             as.is = TRUE)
+  source(ltr_utils_r)
+}else {
+  lineage_file <- paste0(script_dir, "/.
+  ./share/dante_ltr/databases/lineage_domain_order.csv")
+  ltr_utils_r <- paste0(script_dir, "/.
+  ./share/dante_ltr/R/ltr_utils.R")
+  if (file.exists(lineage_file)) {
+    lineage_info <- read.table(lineage_file, sep = "\t",
+                               header = TRUE,
+                               as.is = TRUE)
+    source(ltr_utils_r)
+  }else {
+    (stop("configuration files not found"))
+  }
+}
+
+
+ncpus <- opt$cpu
+
+
+# load data
+cat("reading fasta...")
+s <- readDNAStringSet(opt$reference_sequence)  # genome assembly
+cat("done\n")
+outfile <- opt$output
+# clean sequence names:
+names(s) <- gsub(" .+", "", names(s))
+cat("reading gff...")
+g <- rtracklayer::import(opt$gff3, format = 'gff3')  # DANTE gff3
+cat("done\n")
+# testing
+if (FALSE) {
+  g <- rtracklayer::import("./test_data/sample_ltr_annotation.gff3")
+  s <- readDNAStringSet("./test_data/sample_genome.fasta")
+
+  g <- rtracklayer::import("./test_data/DANTE_LTR_Vfaba_chr5.gff3")
+  s <- readDNAStringSet("./test_data/211010_Vfaba_chr5.fasta")
+  names(s) <- gsub(" .+", "", names(s))
+  ncpus <- 10
+  lineage_info <- read.table("databases/lineage_domain_order.csv", sep = "\t", header =
+    TRUE, as.is = TRUE)
+  source("./R/ltr_utils.R")
+}
+
+
+# get te sequence based on rank
+
+# evaluate best TE -  DLTP grou
+s_te <- get_te_sequences(g, s)  # split by 'element quality'
+# best quality - split by lineage
+word_size <- 15
+# best TE
+TE_DLTP_info <- analyze_TE(s_te$DLTP, word_size = word_size, ncpus = ncpus)
+
+# TE rank 2:
+TE_DLT_plus_DLP_info <- analyze_TE(c(s_te$DLP, s_te$DLT), word_size = word_size, ncpus
+  = ncpus)
+TE_DLT_plus_DLP_info_DLTP_verified <- compare_TE_datasets(c(s_te$DLT, s_te$DLP), ncpus
+  = ncpus,
+                                                          TE_DLTP_info$seqs_representative,
+                                                          word_size = word_size
+)
+
+TE_DLT_plus_DLP_info_multiplicity <- verify_based_on_multiplicity(TE_DLT_plus_DLP_info)
+
+# create additional library from rank 2 verified by multiplicity
+id_for_additional_library <- setdiff(
+  TE_DLT_plus_DLP_info_multiplicity$id_ok_mp_verified,
+  TE_DLT_plus_DLP_info_DLTP_verified$id_ok_verified)
+
+if (length(id_for_additional_library) > 1) {
+  seqs_for_additional_library <- c(s_te$DLP, s_te$DLT)[names(c(s_te$DLP, s_te$DLT)) %in%
+                                                         id_for_additional_library]
+  seqs_additional_info <- analyze_TE(seqs_for_additional_library, word_size =
+    word_size, ncpus = ncpus)
+  seq_representative <- c(
+    TE_DLTP_info$seqs_representative,
+    seqs_additional_info$seqs_representative
+  )
+}else {
+  if (length(id_for_additional_library) == 1) {
+    seq_representative <- c(
+      TE_DLTP_info$seqs_representative,
+      c(s_te$DLP, s_te$DLT)[names(c(s_te$DLP, s_te$DLT)) %in% id_for_additional_library]
+    )
+  }else {
+    seq_representative <- TE_DLTP_info$seqs_representative
+  }
+}
+
+
+# TE  rank 3
+TE_DL_info_DLTP_verified <- compare_TE_datasets(
+  s_te$DL,
+  TE_DLTP_info$seqs_representative, min_coverage = 0.98,
+  ncpus = ncpus
+)
+
+
+R <- seq_diversity(seq_representative)$richness
+SI <- seq_diversity(seq_representative)$shannon_index
+
+# final RM library:
+seq_representative_no_ssr <- seq_representative[R > 20]
+
+ID <- g$ID[g$type == "transposable_element"]
+names(ID) <- paste0(seqnames(g), "_",
+                    start(g), "_",
+                    end(g), "#",
+                    g$Final_Classification
+)[g$type %in% "transposable_element"]
+
+# create clean gff3
+id_of_good_te <- unique(c(
+  TE_DLTP_info$te_conflict_info$ok,
+  TE_DLT_plus_DLP_info_DLTP_verified$id_ok_verified,
+  TE_DLT_plus_DLP_info_multiplicity$id_ok_mp_verified,
+  TE_DL_info_DLTP_verified$id_ok_verified)
+)
+
+c1 <- g$ID %in% ID[id_of_good_te]
+c2 <- sapply(g$Parent, function(x)ifelse(length(x) == 0, "", x)) %in% ID[id_of_good_te]
+
+gff_out <- g[c1 | c2]
+
+
+writeXStringSet(seq_representative, paste0(opt$output, "_RM_lib.fasta"))
+export(gff_out, paste0(opt$output, "_clean.gff3"), format = "gff3")
+