Mercurial > repos > petr-novak > repeat_annotation_pipeline3

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planemo upload commit a61591d548f42ff417781e7fe7418dc2901ccc23
author petr-novak
date Tue, 26 Sep 2023 07:28:04 +0000
parents 5366d5ea04bc
children
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1 #!/usr/bin/env Rscript
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2 # function from questionr R package:
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3 wtable <- function(x, y = NULL, weights = NULL, digits = 3, normwt = FALSE, useNA = c("no", "ifany", "always"), na.rm = TRUE, na.show = FALSE, exclude = NULL)
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4 {
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5 if (is.null(weights)) {
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6 warning("no weights argument given, using uniform weights of 1")
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7 weights <- rep(1, length(x))
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8 }
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9 if (length(x) != length(weights)) stop("x and weights lengths must be the same")
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10 if (!is.null(y) & (length(x) != length(y))) stop("x and y lengths must be the same")
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11 miss.usena <- missing(useNA)
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12 useNA <- match.arg(useNA)
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13 weights[is.na(weights)] <- 0
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14 if (normwt) {
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15 weights <- weights * length(x)/sum(weights)
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16 }
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17
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18 if (!missing(na.show) || !missing(na.rm)) {
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19 warning("'na.rm' and 'na.show' are ignored when 'useNA' is provided.")
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20 }
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21 if (useNA != "no" || (na.show && miss.usena)) {
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22 if (match(NA, exclude, nomatch = 0L)) {
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23 warning("'exclude' containing NA and 'useNA' != \"no\"' are a bit contradicting")
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24 }
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25 x <- addNA(x)
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26 if (!is.null(y)) y <- addNA(y)
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27 }
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28 if (useNA == "no" || (na.rm && miss.usena)) {
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29 s <- !is.na(x) & !is.na(weights)
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30 if (!is.null(y)) s <- s & !is.na(y)
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31 x <- x[s, drop = FALSE]
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32 if (!is.null(y)) y <- y[s, drop = FALSE]
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33 weights <- weights[s]
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34 }
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35 if (!is.null(exclude)) {
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36 s <- !(x %in% exclude)
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37 if (!is.null(y)) s <- s & !(y %in% exclude)
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38 x <- factor(x[s, drop = FALSE])
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39 if (!is.null(y)) y <- factor(y[s, drop = FALSE])
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40 weights <- weights[s]
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41 }
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42 if (is.null(y)) {
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43 result <- tapply(weights, x, sum, simplify = TRUE)
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44 }
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45 else {
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46 result <- tapply(weights, list(x,y), sum, simplify = TRUE)
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47 }
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48 result[is.na(result)] <- 0
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49 tab <- as.table(result)
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50 if (useNA == "ifany") {
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51 if (!is.null(y)) {
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52 if (sum(tab[,is.na(colnames(tab))]) == 0) tab <- tab[,!is.na(colnames(tab))]
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53 if (sum(tab[is.na(rownames(tab)),]) == 0) tab <- tab[!is.na(rownames(tab)),]
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54 } else {
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55 if (tab[is.na(names(tab))] == 0) tab <- tab[!is.na(names(tab))]
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56 }
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57 }
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58 tab
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59 }
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60
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61 suppressPackageStartupMessages(library(rtracklayer))
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62 library(parallel)
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63 g1 <- import(commandArgs(T)[1], format = "GFF")
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64 g2 <- import(commandArgs(T)[2], format = "GFF")
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65 # assume non inrarange overlaps!
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66 attribute_name <- commandArgs(T)[3]
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67 if (FALSE){
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68 g1 <- import("test_data/RM_LTR_TE.gff3")
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69 g2 <- import("test_data/RM_RE.gff3")
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70 g2 <- import("test_data/RM_RE_CL.gff3")
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71 g2 <- import("test_data/RM_RE_v3.gff3")
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72 g2 <- import("test_data/RM_RE_v4.gff3")
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73 g1 <- import("test_data/RM_RE_v4.gff3")
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74
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75 attribute_name <- "Name"
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76 }
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77
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78 g1$SOURCE <- 1
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79 g2$SOURCE <- 2
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80
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81 g12 <- append(g1,g2)
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82 g12_disjoin <- disjoin(g12, ignore.strand=TRUE, with.revmap=TRUE)
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83
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84 g12$sel_attr <- mcols(g12)[,attribute_name]
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85
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86 annot_name <- mclapply(as.list(g12_disjoin$revmap), FUN = function(x)g12$sel_attr[x], mc.cores = 8)
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87 annot_source <- mclapply(as.list(g12_disjoin$revmap), FUN = function(x)g12$SOURCE[x], mc.cores = 8)
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88
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89 c1 <- sapply(annot_source, function (x) 1 %in% x & !(2 %in% x))
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90 c2 <- sapply(annot_source, function (x) 2 %in% x & !(1 %in% x))
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91 c12 <- !(c1 | c2)
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92
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93
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94 n1 <- cbind(sapply(annot_name[c1], "[", 1 ), "No Annotation")
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95 n2 <- cbind("No Annotation", sapply(annot_name[c2], "[", 1))
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96
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97 n12 <- do.call(rbind, annot_name[c12])
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98
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99 n12all <- matrix(character(), ncol = 2, nrow = length(g12_disjoin))
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100
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101 if (any(c1)){
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102 n12all[c1,] <- n1
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103 }
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104 if (any(c2)){
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105 n12all[c2,] <- n2
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106 }
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107 if (any(c12)){
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108 n12all[c12,] <- n12
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109 }
6
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110
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111 traw <- wtable(n12all[,1], n12all[,2], weights = width(g12_disjoin))
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112 tbl_df <- as.data.frame((traw))
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parents:
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113 tbl_df <- tbl_df[order(tbl_df$Freq, decreasing = TRUE),]
b53f5a456d01 "planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
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114 colnames(tbl_df) <- c("Annotation1", "Annotation2", "Overlap[bp]")
b53f5a456d01 "planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
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115
b53f5a456d01 "planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
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116 ## NOTE - if name change - modify it in xml too
b53f5a456d01 "planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
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117 write.table(tbl_df, file = 'annotation_overlap_long.csv', sep="\t", quote=FALSE, row.names = FALSE)
b53f5a456d01 "planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
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118
b53f5a456d01 "planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
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119 tbl <- as.matrix(traw)
b53f5a456d01 "planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
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120 tbl <- tbl[order(rowSums(tbl), decreasing = TRUE),]
b53f5a456d01 "planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
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121 tbl <- tbl[, order(colSums(tbl), decreasing = TRUE)]
b53f5a456d01 "planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
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122 write.table(tbl, file= 'annotation_overlap.csv', sep="\t", quote = FALSE)
b53f5a456d01 "planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
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123