Mercurial > repos > petr-novak > dante_ltr

annotate clean_ltr.R @ 0:7b0bbe7477c4 draft

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"planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
author petr-novak
date Tue, 08 Mar 2022 13:24:33 +0000
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children 6ae4a341d1f3
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1 #!/usr/bin/env Rscript
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2 initial_options <- commandArgs(trailingOnly = FALSE)
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3 file_arg_name <- "--file="
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4 script_name <- normalizePath(sub(file_arg_name, "", initial_options[grep
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5 (file_arg_name,
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6 initial_options)]))
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7 script_dir <- dirname(script_name)
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8 library(optparse)
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9
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10 parser <- OptionParser()
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11 option_list <- list(
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12 make_option(c("-g", "--gff3"), action = "store", type = "character",
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13 help = "gff3 with LTR Transposable elements", default = NULL),
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14 make_option(c("-s", "--reference_sequence"), action = "store", type = "character",
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15 help = "reference sequence as fasta",
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16 default = NULL),
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17 make_option(c("-o", "--output"), action = "store", type = "character",
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18 help = "output file prefix", default = NULL),
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19 make_option(c("-c", "--cpu"), type =
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20 "integer", default = 5, help = "Number of cpu to use [default %default]",
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21 metavar = "number")
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22
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23 )
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24 description <- paste(strwrap(""))
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25
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26 epilogue <- ""
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27 parser <- OptionParser(option_list = option_list, epilogue = epilogue, description =
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28 description, usage = "usage: %prog COMMAND [OPTIONS]")
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29 opt <- parse_args(parser, args = commandArgs(TRUE))
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30
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31
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32 # load packages
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33 suppressPackageStartupMessages({ library(rtracklayer)
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34 library(Biostrings)
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35 library(BSgenome)
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36 library(parallel)
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37 })
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38
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39 # CONFIGURATION
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40 # load configuration files and functions:
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41 lineage_file <- paste0(script_dir, "/databases/lineage_domain_order.csv")
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42 ltr_utils_r <- paste0(script_dir, "/R/ltr_utils.R")
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43 if (file.exists(lineage_file)) {
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44 lineage_info <- read.table(lineage_file, sep = "\t",
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45 header = TRUE,
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46 as.is = TRUE)
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47 source(ltr_utils_r)
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48 }else {
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49 lineage_file <- paste0(script_dir, "/.
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50 ./share/dante_ltr/databases/lineage_domain_order.csv")
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51 ltr_utils_r <- paste0(script_dir, "/.
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52 ./share/dante_ltr/R/ltr_utils.R")
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53 if (file.exists(lineage_file)) {
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54 lineage_info <- read.table(lineage_file, sep = "\t",
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55 header = TRUE,
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56 as.is = TRUE)
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57 source(ltr_utils_r)
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58 }else {
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59 (stop("configuration files not found"))
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60 }
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61 }
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62
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63
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64 ncpus <- opt$cpu
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65
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66
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67 # load data
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68 cat("reading fasta...")
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69 s <- readDNAStringSet(opt$reference_sequence) # genome assembly
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70 cat("done\n")
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71 outfile <- opt$output
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72 # clean sequence names:
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73 names(s) <- gsub(" .+", "", names(s))
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74 cat("reading gff...")
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75 g <- rtracklayer::import(opt$gff3, format = 'gff3') # DANTE gff3
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76 cat("done\n")
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77 # testing
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78 if (FALSE) {
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79 g <- rtracklayer::import("./test_data/sample_ltr_annotation.gff3")
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80 s <- readDNAStringSet("./test_data/sample_genome.fasta")
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81
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82 g <- rtracklayer::import("./test_data/DANTE_LTR_Vfaba_chr5.gff3")
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83 s <- readDNAStringSet("./test_data/211010_Vfaba_chr5.fasta")
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84 names(s) <- gsub(" .+", "", names(s))
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85 ncpus <- 10
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86 lineage_info <- read.table("databases/lineage_domain_order.csv", sep = "\t", header =
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87 TRUE, as.is = TRUE)
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88 source("./R/ltr_utils.R")
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89 }
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90
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91
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92 # get te sequence based on rank
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93
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94 # evaluate best TE - DLTP grou
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95 s_te <- get_te_sequences(g, s) # split by 'element quality'
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96 # best quality - split by lineage
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97 word_size <- 15
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98 # best TE
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99 TE_DLTP_info <- analyze_TE(s_te$DLTP, word_size = word_size, ncpus = ncpus)
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100
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101 # TE rank 2:
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102 TE_DLT_plus_DLP_info <- analyze_TE(c(s_te$DLP, s_te$DLT), word_size = word_size, ncpus
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103 = ncpus)
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104 TE_DLT_plus_DLP_info_DLTP_verified <- compare_TE_datasets(c(s_te$DLT, s_te$DLP), ncpus
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105 = ncpus,
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106 TE_DLTP_info$seqs_representative,
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107 word_size = word_size
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108 )
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109
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110 TE_DLT_plus_DLP_info_multiplicity <- verify_based_on_multiplicity(TE_DLT_plus_DLP_info)
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111
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112 # create additional library from rank 2 verified by multiplicity
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113 id_for_additional_library <- setdiff(
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114 TE_DLT_plus_DLP_info_multiplicity$id_ok_mp_verified,
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115 TE_DLT_plus_DLP_info_DLTP_verified$id_ok_verified)
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116
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117 if (length(id_for_additional_library) > 1) {
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118 seqs_for_additional_library <- c(s_te$DLP, s_te$DLT)[names(c(s_te$DLP, s_te$DLT)) %in%
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119 id_for_additional_library]
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120 seqs_additional_info <- analyze_TE(seqs_for_additional_library, word_size =
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121 word_size, ncpus = ncpus)
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122 seq_representative <- c(
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123 TE_DLTP_info$seqs_representative,
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124 seqs_additional_info$seqs_representative
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125 )
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126 }else {
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127 if (length(id_for_additional_library) == 1) {
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128 seq_representative <- c(
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129 TE_DLTP_info$seqs_representative,
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130 c(s_te$DLP, s_te$DLT)[names(c(s_te$DLP, s_te$DLT)) %in% id_for_additional_library]
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131 )
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132 }else {
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133 seq_representative <- TE_DLTP_info$seqs_representative
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134 }
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135 }
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136
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137
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138 # TE rank 3
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139 TE_DL_info_DLTP_verified <- compare_TE_datasets(
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140 s_te$DL,
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141 TE_DLTP_info$seqs_representative, min_coverage = 0.98,
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142 ncpus = ncpus
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143 )
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144
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145
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146 R <- seq_diversity(seq_representative)$richness
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147 SI <- seq_diversity(seq_representative)$shannon_index
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148
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149 # final RM library:
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150 seq_representative_no_ssr <- seq_representative[R > 20]
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151
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152 ID <- g$ID[g$type == "transposable_element"]
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153 names(ID) <- paste0(seqnames(g), "_",
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154 start(g), "_",
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155 end(g), "#",
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156 g$Final_Classification
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157 )[g$type %in% "transposable_element"]
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158
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159 # create clean gff3
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160 id_of_good_te <- unique(c(
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161 TE_DLTP_info$te_conflict_info$ok,
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162 TE_DLT_plus_DLP_info_DLTP_verified$id_ok_verified,
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163 TE_DLT_plus_DLP_info_multiplicity$id_ok_mp_verified,
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164 TE_DL_info_DLTP_verified$id_ok_verified)
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165 )
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166
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167 c1 <- g$ID %in% ID[id_of_good_te]
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168 c2 <- sapply(g$Parent, function(x)ifelse(length(x) == 0, "", x)) %in% ID[id_of_good_te]
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169
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170 gff_out <- g[c1 | c2]
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171
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172
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173 writeXStringSet(seq_representative, paste0(opt$output, "_RM_lib.fasta"))
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174 export(gff_out, paste0(opt$output, "_clean.gff3"), format = "gff3")
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175