Mercurial > repos > petr-novak > dante_ltr

annotate R/ltr_utils.R @ 5:0c3111ab729b draft

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"planemo upload commit 5a81f1734493a3acf5ff24a573fa2887d92b58a8"
author petr-novak
date Mon, 16 May 2022 07:50:41 +0000
parents 6ae4a341d1f3
children c33d6583e548
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1 add_coordinates_of_closest_neighbor <- function(gff) {
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2 gff <- gff[order(seqnames(gff), start(gff))]
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3 # split to chromosomes:
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4 gff_parts <- split(gff, seqnames(gff))
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5 upstreams <- c(sapply(gff_parts, function(x) c(1, head(end(x), -1))))
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6 downstreams <- c(sapply(gff_parts, function(x) c(start(x)[-1], seqlengths(x)[runValue(seqnames(x[1]))])))
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7 gff_updated <- unlist(gff_parts)
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8 gff_updated$upstream_domain <- unlist(upstreams)
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9 gff_updated$downstream_domain <- unlist(downstreams)
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10 names(gff_updated) <- NULL
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11 return(gff_updated)
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12 }
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13
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14 get_domain_clusters <- function(gff) {
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15 # get consecutive domains from same linage
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16 # must be sorted!
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17 gag_plus <- as.numeric(cumsum(gff$Name == "GAG" & strand(gff) == '+'))
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18 gag_minus <- rev(as.numeric(cumsum(rev(gff$Name == "GAG" & strand(gff) == '-'))))
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19 # split based on classification - must be same and consecutive
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20 x <- rle(gff$Final_Classification)
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21 # split on strand change
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22 s <- rep(seq_along(runLength(strand(gff))), runLength(strand(gff)))
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23 domain_cluster <- paste0(rep(seq_along(x$lengths), x$lengths), "_", seqnames(gff),
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24 "_", gag_plus, "_", gag_minus, "_", s)
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25 gff_clusters <- split(as.data.frame(gff), factor(domain_cluster, levels = unique(domain_cluster)))
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26 gff_clusters
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27 }
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28
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29 clean_domain_clusters <- function(gcl) {
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30 ## remove clusters wich does not have enough domains or domains
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31 ## are on different strand
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32 N_domains <- sapply(gcl, nrow)
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33 N_unique_domains <- sapply(gcl, function(x)length(unique(x$Name)))
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34 S <- sapply(gcl, function(x)paste(sort(unique(x$strand)), collapse = " "))
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35 S_OK <- S %in% c("+", "-")
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36 min_domains <- 5
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37 maxlength <- 15000 # max span between domains
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38 span <- sapply(gcl, function(x)max(x$end) - min(x$start))
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39 cond1 <- S_OK &
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40 N_unique_domains == N_domains &
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41 N_domains >= min_domains &
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42 span <= maxlength
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43 return(gcl[cond1])
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44 }
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45
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46 check_ranges <- function(gx, s, offset = OFFSET) {
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47 # check is range is not out of sequence length
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48 START <- sapply(gx, function(x)min(x$start)) - offset
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49 END <- sapply(gx, function(x)max(x$end)) + offset
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50 MAX <- seqlengths(s)[sapply(gx, function(x)as.character(x$seqnames[1]))]
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51 good_ranges <- (START > 0) & (END <= MAX)
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52 return(good_ranges)
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53 }
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54
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55 get_ranges <- function(gx, offset = OFFSET) {
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56 S <- sapply(gx, function(x)min(x$start))
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57 E <- sapply(gx, function(x)max(x$end))
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58 gr <- GRanges(seqnames = sapply(gx, function(x)x$seqnames[1]), IRanges(start = S - offset, end = E + offset))
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59 }
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60
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61 get_ranges_left <- function(gx, offset = OFFSET, offset2 = 300) {
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62 S <- sapply(gx, function(x)min(x$start))
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63 max_offset <- S - sapply(gx, function(x)min(x$upstream_domain))
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64 offset_adjusted <- ifelse(max_offset < offset, max_offset, offset)
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65 gr <- GRanges(seqnames = sapply(gx, function(x)x$seqnames[1]), IRanges(start = S - offset_adjusted, end = S + offset2))
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66 return(gr)
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67 }
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68
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69 get_ranges_right <- function(gx, offset = OFFSET, offset2 = 300) {
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70 E <- sapply(gx, function(x)max(x$end))
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71 max_offset <- sapply(gx, function(x)max(x$downstream_domain)) - E
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72 offset_adjusted <- ifelse(max_offset < offset, max_offset, offset)
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73 gr <- GRanges(seqnames = sapply(gx, function(x)x$seqnames[1]), IRanges(start = E - offset2, end = E + offset_adjusted))
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74 return(gr)
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75 }
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76
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77 firstTG <- function(ss) {
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78 x <- matchPattern("TG", ss)
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79 if (length(x) == 0) {
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80 return(0)
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81 }else {
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82 return(min(start(x)))
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83 }
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84 }
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85
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86 lastCA <- function(ss) {
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87 x <- matchPattern("CA", ss)
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88 if (length(x) == 0) {
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89 return(0)
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90 }else {
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91 return(max(start(x)))
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92 }
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93 }
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94
2
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95
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96
0
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97 trim2TGAC <- function(bl) {
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98 for (i in 1:nrow(bl)) {
2
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99 cons <- consensusString(c(bl$qseq[i], bl$sseq[i]), ambiguityMap="?")
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100 tg_P <- firstTG(cons)
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101 ca_P <- lastCA(cons)
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102 e_dist <- bl$length[i] - ca_P
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103 max_dist = 50 # was 25
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104 no_match <- any(tg_P == 0, ca_P == 0)
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105 if (!no_match &
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106 tg_P < max_dist &
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107 e_dist < max_dist) {
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108 ## trim alignment
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109 bl[i,] <- trim_blast_table(bl[i,], tg_P, e_dist - 1)
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110 }
2
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111
0
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112 }
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113 return(bl)
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114 }
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115
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116 trim_blast_table <- function(b, T1, T2) {
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117 b$qstart <- b$qstart + T1
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118 b$sstart <- b$sstart + T1
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119 b$qend <- b$qend - T2
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120 b$send <- b$send - T2
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121 b$sseq <- substring(b$sseq, T1, b$length - T2)
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122 b$qseq <- substring(b$qseq, T1, b$length - T2)
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123 b$length <- nchar(b$sseq)
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124 return(b)
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125 }
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126
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127 blast_all2all <- function(seqs, db=NULL, ncpus=1, word_size=20, perc_identity=90, max_target_seq = 5000, task = "megablast", additional_params= ""){
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128 if (ncpus == 1){
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129 query <- list(seqs)
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130 }else{
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131 query <-split(seqs, round(seq(1,ncpus,length.out = length(seqs))))
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132 }
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133 if(is.null(db)){
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134 # search against itself
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135 db <- seqs
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136 }
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137 qf <-tempfile(fileext=paste0("_",1:ncpus,".fasta"))
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138 outf <-tempfile(fileext=paste0("_",1:ncpus,".csv"))
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139 dbf <- tempfile()
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140 script <- tempfile()
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141 writeXStringSet(db, dbf)
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142 mapply(query, qf, FUN = writeXStringSet)
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143 cols <- "qaccver saccver pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen slen"
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144 cmd_db <- paste("makeblastdb -dbtype nucl -in ", dbf)
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145 cmd_blast <- paste("blastn -task ", task, " -word_size", word_size,
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146 "-outfmt \"6 ", cols, "\" ",
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147 "-perc_identity", perc_identity, " -min_raw_gapped_score 500",
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148 "-max_target_seqs", max_target_seq, additional_params,
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149 "-query", qf, "-db", dbf, "-out", outf,
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150 "&"
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151 )
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152
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153 # TODO - inspect only forward strand??
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154 system(cmd_db)
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155 cmd_all <- paste(paste(cmd_blast,collapse="\n"),"\nwait")
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156 cat(cmd_all, file = script)
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157 system(paste("sh ", script))
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158
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159 bl_list <- lapply(outf, read.table, stringsAsFactors = FALSE, col.names = unlist(strsplit(cols, " ")), sep="\t", comment.char = "")
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160 bl_table <- do.call(rbind, bl_list)
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161 unlink(qf)
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162 #unlink(outf)
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163 unlink(dbf)
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164 unlink(script)
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165 return(bl_table)
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166 }
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167
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168 identify_conflicts <- function (bl){
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169 QL <- gsub(".+[|]", "", bl$qaccver)
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170 SL <- gsub(".+[|]", "", bl$saccver)
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171 id_with_conflict <- unique(c(bl$qaccver[QL != SL],bl$saccver[QL != SL]))
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172 id_ok <- setdiff(unique(c(bl$qaccver,bl$saccver)), id_with_conflict)
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173 single_hit <- sapply(
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174 sapply(
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175 split(bl$qaccver, bl$saccver), unique
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176 ), length) == 1
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177 id_with_no_hits <- names(single_hit)[single_hit] # except hit to itself
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178 return(list(
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179 ok = id_ok,
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180 conflict = id_with_conflict,
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181 no_hit = id_with_no_hits)
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182 )
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183 }
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184
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185
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186 analyze_TE <- function(seqs, ncpus = 10, word_size = 20){
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187 blt <- blast_all2all(seqs, ncpus = ncpus, word_size = word_size, perc_identity = 90)
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188 te_conflict_info <- identify_conflicts(blt)
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189 blt_te_ok <- blast_table_subset(blt, te_conflict_info$ok)
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190 te_ok_lineages <- split(blt_te_ok,
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191 gsub(
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192 ".+[|]",
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193 "",
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194 blt_te_ok$qaccver))
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195 gr_representative <- GRangesList(mclapply(te_ok_lineages,
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196 FUN = get_representative_ranges,
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197 mc.cores = ncpus
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198 ))
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199 seqs_representative <- getSeq(seqs, Reduce(c, gr_representative))
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200 names(seqs_representative) <- seqnames(Reduce(c, gr_representative))
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201 # TODO - add swithin group verification here, ! exclude self hits!!
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202
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203 return(
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204 list(
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205 seqs_representative = seqs_representative,
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206 te_conflict_info = te_conflict_info,
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207 gr_representative = gr_representative,
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208 blast = blt
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209 )
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210 )
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211 }
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212
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213 query_coverage <- function(blt){
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214 blt <- blt[blt$qaccver != blt$saccver,]
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215 Q_lengths <- blt$qlen[!duplicated(blt$qaccver)]
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216 names(Q_lengths) <- blt$qaccver[!duplicated(blt$qaccver)]
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217 gr <- GRanges(seqnames = blt$qaccver, seqlengths = Q_lengths,
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218 IRanges(start = blt$qstart, end = blt$qend))
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219 return(coverage(gr))
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220 }
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221
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222 multiplicity_of_te <- function(blt){
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223 # exclude self to self hits and calculate coverage + mean_multiplicity of TE
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224 # assuption is that TE which are 'identical' to other TE from the same lineage are
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225 # likely correct
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226 blt_no_self <- blt[blt$qaccver != blt$saccver,]
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227 cvr <- query_coverage(blt_no_self)
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228 L <- sapply(cvr, function(x) sum(width(x)))
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229 C1 <- sapply(cvr, function(x) sum(as.numeric(runValue(x) >= 1) * runLength(x)))
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230 multiplicity <- sapply(cvr, function(x) sum(as.numeric(runValue(x)) * runLength(x)))/L
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231 data.frame(L = L, C1 = C1, multiplicity = multiplicity )
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232 }
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233
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234 verify_based_on_multiplicity <- function(TE_info, min_coverage=0.99, min_multiplicity=3){
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235 blt <- TE_info$blast[TE_info$blast$qaccver %in% TE_info$te_conflict_info$ok,]
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236 mp <- multiplicity_of_te(blt)
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237 id_ok_mp_verified <- rownames(mp)[mp$C1/mp$L > min_coverage & mp$multiplicity >= min_multiplicity]
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238 return(list(multiplicity = mp,
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239 id_ok_mp_verified = id_ok_mp_verified))
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240
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241 }
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242
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243 compare_TE_datasets <- function(Q, S, word_size = 20, min_coverage = 0.95, ncpus=10){
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244 blt <- blast_all2all(seqs = Q, db = S, ncpus = ncpus, word_size = word_size)
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245 QL <- gsub(".+[|]", "", blt$qaccver)
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246 SL <- gsub(".+[|]", "", blt$saccver)
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247 id_with_conflict <- unique(c(blt$qaccver[QL != SL]))
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248 id_ok <- setdiff(unique(blt$qaccver), id_with_conflict)
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249 # check coverage hits
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250 blt_ok <- blt[blt$qaccver %in% id_ok,]
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251 Q_lengths <- blt_ok$qlen[!duplicated(blt_ok$qaccver)]
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252 names(Q_lengths) <- blt_ok$qaccver[!duplicated(blt_ok$qaccver)]
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253 gr <- GRanges(seqnames = blt_ok$qaccver, seqlengths = Q_lengths,
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254 IRanges(start = blt_ok$qstart, end = blt_ok$qend))
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255 cvr <- coverage(gr)
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256 L <- sapply(cvr, function(x) sum(width(x)))
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257 C1 <- sapply(cvr, function(x) sum(as.numeric(runValue(x) >= 1) * runLength(x)))
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258 Max_uncovered <- sapply(cvr, function(x){
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259 if(any(runValue(x)==0)){
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260 return(max(runLength(x)[runValue(x) == 0]))
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261 }else{
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262 return(0)
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263 }
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264 })
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265
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266 # verified based on hit to reference - S
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267 C1_prop <- C1/L
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268 pass <- (C1_prop >= min_coverage & Max_uncovered < 500)
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269 if (any(pass)){
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270 id_ok_verified <- names(C1_prop)
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271 }else {
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272 id_ok_verified <- NULL
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273 }
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274 return(list(id_with_conflict = id_with_conflict,
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275 id_ok = id_ok,
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276 id_ok_verified = id_ok_verified
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277 ))
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278 }
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279
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280
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281
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282 blast_table_subset <- function(bl,id){
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283 return(bl[bl$qaccver %in% id & bl$saccver %in% id,, drop = FALSE])
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284 }
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285
3
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286 get_representative_ranges <- function(bl, min_length = 200, min_identity = 98){
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287 bl <- bl[bl$pident>=min_identity, , drop=FALSE]
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288 bl <- bl[bl$pident>=min_identity & bl$length >= min_length, , drop=FALSE]
0
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289 score <- sort(unlist(by(bl$bitscore, bl$qaccver, sum, simplify = FALSE)),
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290 decreasing = TRUE)
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291 L <- bl$qlen[!duplicated(bl$qaccver)]
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292 names(L) <- bl$qaccver[!duplicated(bl$qaccver)]
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293 gr <- GRanges(seqnames = bl$qaccver,
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294 IRanges(start = bl$qstart, end = bl$qend),
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295 seqlengths = L,
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296 subject = bl$saccver,
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297 sstart = ifelse(bl$send < bl$sstart, bl$send, bl$sstart),
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298 send = ifelse(bl$send > bl$sstart, bl$send, bl$sstart))
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299 SN <- levels(seqnames(gr))
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300 inc <- rep(TRUE, length(gr))
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301 MSK <- GRangesList()
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302 for (i in names(score)){
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303 inc[gr$subject %in% i] <- FALSE
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304 gr_part <- gr[seqnames(gr) %in% i & inc]
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305 MSK[[i]] <- GRanges(seqnames = factor(gr_part$subject, levels = SN),
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306 IRanges(start = gr_part$sstart, end = gr_part$send),
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307 seqlengths = L
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308 )
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309 }
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310 gout <- unlist(MSK)
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311
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312 full_gr <- GRanges(seqnames = factor(SN, levels = SN),
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313 IRanges(start = rep(1,length(L)),
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314 end = L)
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315 )
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316 unmasked_gr <- GenomicRanges::setdiff(full_gr, gout)
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317 return(unmasked_gr[width(unmasked_gr) >= min_length])
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318 }
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319
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320 expected_diversity <- function(seqs, niter=100, km = 6){
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321 L <- nchar(seqs)
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322 R <- matrix(ncol = niter, nrow = length(seqs))
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323 for (i in 1:niter){
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324 seqs_rnd <- DNAStringSet(sapply(L, function(n) paste(sample(c("A", "C", "T", "G"), n, replace=TRUE), collapse="")))
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325 R[,i] <- seq_diversity(seqs_rnd, km = km)$richness
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326 }
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327 R
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328
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329 }
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330
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331 seq_diversity <- function (seqs, km=6){
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332 K <- oligonucleotideFrequency(seqs, width=km)>0
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333 P <- t(K)/rowSums(K)
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334 # shannon index
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335 SI <- apply(P, 2, function(x) {x1 <- x[x>0]; -sum(x1*log(x1))})
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336 # richness
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337 R <- rowSums(K)
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338 list(richness=R, shannon_index=SI)
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339 }
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340
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341
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342
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343 blast <- function(s1, s2) {
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344 tmp1 <- tempfile()
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345 tmp2 <- tempfile()
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346 tmp_out <- tempfile()
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347 writeXStringSet(DNAStringSet(s1), tmp1)
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348 writeXStringSet(DNAStringSet(s2), tmp2)
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349 # alternative blast:
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350 cmd <- paste("blastn -task blastn -word_size 7 -dust no -gapextend 1 -gapopen 2 -reward 1 -penalty -1",
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351 " -query ", tmp1, ' -subject ', tmp2, ' -strand plus ',
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352 '-outfmt "6 qaccver saccver pident length mismatch gapopen qstart qend sstart send evalue bitscore qseq sseq"',
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353 ' -out', tmp_out)
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354
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355 system(cmd)
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356 out_raw <- read.table(tmp_out, as.is = TRUE, sep = "\t",
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357 col.names = strsplit("qaccver saccver pident length mismatch gapopen qstart qend sstart send evalue bitscore qseq sseq", split = ' ')[[1]])
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358
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359 if (nrow(out_raw) == 0) {
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360 return(out_raw)
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361 }
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362 out <- trim2TGAC(out_raw)
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363 # remove alingment shorted that
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364 out <- out[out$length > 100,]
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365 if (nrow(out) == 0) {
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366 return(out)
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367 }
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368 ## filter for TGCA
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369 TG_L <- substring(out$qseq, 1, 2) == "TG"
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370 TG_R <- substring(out$sseq, 1, 2) == "TG"
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371 CA_L <- substring(out$qseq, out$length - 1, out$length) == "CA"
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372 CA_R <- substring(out$sseq, out$length - 1, out$length) == "CA"
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373 cond <- TG_L & TG_R & CA_L & CA_R
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374 out <- out[cond, , drop = FALSE]
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375 unlink(tmp1)
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376 unlink(tmp2)
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377 unlink(tmp_out)
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378 # TODO - detele all temp files!
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379 # unlink(tmp1, tmp2, tmp_out)
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380 return(out)
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381 }
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382
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383 get_correct_coordinates <- function(b) {
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384 do.call(rbind, strsplit(b$qaccver, split = "_"))
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385 }
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386
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387 evaluate_ltr <- function(GR, GRL, GRR, blast_line, Lseq, Rseq) {
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388 LTR_L <- makeGRangesFromDataFrame(data.frame(seqnames = seqnames(GR),
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389 start = start(GRL) + blast_line$qstart - 2,
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390 end = start(GRL) + blast_line$qend - 1))
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391 LTR_R <- makeGRangesFromDataFrame(data.frame(seqnames = seqnames(GR),
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392 start = start(GRR) + blast_line$sstart - 2,
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393 end = start(GRR) + blast_line$send - 1))
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394
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395 TSD_L <- makeGRangesFromDataFrame(data.frame(seqnames = seqnames(GR),
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396 start = start(GRL) + blast_line$qstart - 3:10,
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397 end = start(GRL) + blast_line$qstart - 3))
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398 TSD_R <- makeGRangesFromDataFrame(data.frame(seqnames = seqnames(GR),
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399 start = start(GRR) + blast_line$send,
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400 end = start(GRR) + blast_line$send + 0:7))
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401
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402 TSD_L_seq <- DNAStringSet(substring(Lseq, blast_line$qstart - 2:9, blast_line$qstart - 2))
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403 TSD_R_seq <- DNAStringSet(substring(Rseq, blast_line$send + 1, blast_line$send + 1:8))
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404
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405 matching_tsd <- TSD_R_seq == TSD_L_seq
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406 matching_tsd[1:3] <- FALSE # remove short tsd
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407 p <- which(matching_tsd)
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408 if (length(p) > 0) {
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409 TSD_Length <- max(p)
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410 TSD_sequence <- TSD_L_seq[TSD_Length]
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411 TSD_position <- append(TSD_R[TSD_Length], TSD_L[TSD_Length])
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412 }else {
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413 TSD_Length <- 0
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414 TSD_sequence <- ""
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415 TSD_position <- NA
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416 }
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417
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418 TE_Length <- end(LTR_R) - start(LTR_L)
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419 LTR_Identity <- blast_line$pident
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420 out <- list(TSD_position = TSD_position, TSD_sequence = TSD_sequence, TSD_Length = TSD_Length,
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421 LTR_R_position = LTR_R, LTR_L_position = LTR_L, TE_Length = TE_Length, LTR_Identity = LTR_Identity)
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422 return(out)
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423 }
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424
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diff changeset
425 get_best_ltr <- function(x) {
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petr-novak
parents:
diff changeset
426 tsd_ok <- sapply(x, function(k)k$TSD_Length > 3)
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petr-novak
parents:
diff changeset
427 te_length_ok <- sapply(x, function(k)k$TE_Length < 30000)
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petr-novak
parents:
diff changeset
428 ltr_length_ok <- sapply(x, function(k)width(k$LTR_R_position) >= 100 & width(k$LTR_L_position) >= 100)
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petr-novak
parents:
diff changeset
429 if (sum(tsd_ok & te_length_ok & ltr_length_ok) >= 1) {
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petr-novak
parents:
diff changeset
430 # return the first one (best bitscore)
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petr-novak
parents:
diff changeset
431 return(x[tsd_ok & te_length_ok][1])
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petr-novak
parents:
diff changeset
432 }
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petr-novak
parents:
diff changeset
433 if (any(te_length_ok & ltr_length_ok)) {
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petr-novak
parents:
diff changeset
434 return(x[te_length_ok & ltr_length_ok][1])
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petr-novak
parents:
diff changeset
435 }else {
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petr-novak
parents:
diff changeset
436 return(NULL)
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petr-novak
parents:
diff changeset
437 }
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petr-novak
parents:
diff changeset
438 }
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petr-novak
parents:
diff changeset
439
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petr-novak
parents:
diff changeset
440 get_te_gff3 <- function(g, ID) {
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petr-novak
parents:
diff changeset
441 D <- makeGRangesFromDataFrame(g$domain, keep.extra.columns = TRUE)
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petr-novak
parents:
diff changeset
442 sn <- seqnames(D)[1]
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petr-novak
parents:
diff changeset
443 S <- strand(D)[1]
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petr-novak
parents:
diff changeset
444 TE <- GRanges(seqnames = sn,
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petr-novak
parents:
diff changeset
445 IRanges(start = start(g$ltr_info[[1]]$LTR_L_position),
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petr-novak
parents:
diff changeset
446 end = end(g$ltr_info[[1]]$LTR_R_position)), strand = S)
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petr-novak
parents:
diff changeset
447 TE$type <- "transposable_element"
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petr-novak
parents:
diff changeset
448 TE$ID <- ID
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petr-novak
parents:
diff changeset
449
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petr-novak
parents:
diff changeset
450 if (as.character(S) == "+") {
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petr-novak
parents:
diff changeset
451 LTR_5 <- g$ltr_info[[1]]$LTR_L
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petr-novak
parents:
diff changeset
452 LTR_3 <- g$ltr_info[[1]]$LTR_R
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petr-novak
parents:
diff changeset
453 }else {
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petr-novak
parents:
diff changeset
454 LTR_3 <- g$ltr_info[[1]]$LTR_L
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petr-novak
parents:
diff changeset
455 LTR_5 <- g$ltr_info[[1]]$LTR_R
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petr-novak
parents:
diff changeset
456 }
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petr-novak
parents:
diff changeset
457 LTR_5$LTR <- '5LTR'
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petr-novak
parents:
diff changeset
458 LTR_3$LTR <- '3LTR'
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petr-novak
parents:
diff changeset
459 LTR_5$type <- "long_terminal_repeat"
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petr-novak
parents:
diff changeset
460 LTR_3$type <- "long_terminal_repeat"
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petr-novak
parents:
diff changeset
461 strand(LTR_3) <- S
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petr-novak
parents:
diff changeset
462 strand(LTR_5) <- S
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petr-novak
parents:
diff changeset
463 LTR_3$Parent <- ID
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petr-novak
parents:
diff changeset
464 LTR_5$Parent <- ID
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petr-novak
parents:
diff changeset
465 LTR_3$Final_Classification <- D$Final_Classification[1]
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petr-novak
parents:
diff changeset
466 LTR_5$Final_Classification <- D$Final_Classification[1]
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petr-novak
parents:
diff changeset
467 LTR_5$LTR_Identity <- g$ltr_info[[1]]$LTR_Identity
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petr-novak
parents:
diff changeset
468 LTR_3$LTR_Identity <- g$ltr_info[[1]]$LTR_Identity
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petr-novak
parents:
diff changeset
469
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petr-novak
parents:
diff changeset
470 TE$LTR_Identity <- g$ltr_info[[1]]$LTR_Identity
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petr-novak
parents:
diff changeset
471 TE$LTR5_length <- width(LTR_5)
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petr-novak
parents:
diff changeset
472 TE$LTR3_length <- width(LTR_3)
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petr-novak
parents:
diff changeset
473
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petr-novak
parents:
diff changeset
474 if (is.na(g$ltr_info[[1]]$TSD_position)[1]) {
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petr-novak
parents:
diff changeset
475 # no TSD found
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petr-novak
parents:
diff changeset
476 TSD <- NULL
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petr-novak
parents:
diff changeset
477 TE$TSD <- 'not_found'
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petr-novak
parents:
diff changeset
478 }else {
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petr-novak
parents:
diff changeset
479 TSD <- g$ltr_info[[1]]$TSD_position
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petr-novak
parents:
diff changeset
480 TSD$type <- "target_site_duplication"
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petr-novak
parents:
diff changeset
481 TSD$Parent <- ID
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petr-novak
parents:
diff changeset
482 TE$TSD <- as.character(g$ltr_info[[1]]$TSD_sequence)
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petr-novak
parents:
diff changeset
483 }
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petr-novak
parents:
diff changeset
484
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petr-novak
parents:
diff changeset
485 TE$Final_Classification <- D$Final_Classification[1]
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petr-novak
parents:
diff changeset
486
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petr-novak
parents:
diff changeset
487 D$Parent <- ID
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petr-novak
parents:
diff changeset
488 out <- c(TE, LTR_3, LTR_5, D, TSD)
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petr-novak
parents:
diff changeset
489 return(out)
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petr-novak
parents:
diff changeset
490 }
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petr-novak
parents:
diff changeset
491
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petr-novak
parents:
diff changeset
492 get_TE <- function(Lseq, Rseq, domains_gff, GR, GRL, GRR) {
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petr-novak
parents:
diff changeset
493 xx <- blast(Lseq, Rseq)
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petr-novak
parents:
diff changeset
494 if (nrow(xx) == 0) {
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petr-novak
parents:
diff changeset
495 return(NULL)
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petr-novak
parents:
diff changeset
496 }else {
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petr-novak
parents:
diff changeset
497 ltr_tmp <- list()
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petr-novak
parents:
diff changeset
498 for (j in 1:nrow(xx)) {
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petr-novak
parents:
diff changeset
499 ltr_tmp[[j]] <- evaluate_ltr(GR, GRL, GRR, xx[j, , drop = FALSE], Lseq, Rseq)
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petr-novak
parents:
diff changeset
500 }
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petr-novak
parents:
diff changeset
501 ltr <- get_best_ltr(ltr_tmp)
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petr-novak
parents:
diff changeset
502 if (length(ltr) == 0) {
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petr-novak
parents:
diff changeset
503 return(NULL)
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petr-novak
parents:
diff changeset
504 ## add good ltr
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petr-novak
parents:
diff changeset
505 }else {
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petr-novak
parents:
diff changeset
506 return(list(domain = domains_gff, ltr_info = ltr, blast_out = xx))
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petr-novak
parents:
diff changeset
507 }
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petr-novak
parents:
diff changeset
508 }
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petr-novak
parents:
diff changeset
509 }
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petr-novak
parents:
diff changeset
510
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petr-novak
parents:
diff changeset
511 add_pbs <- function(te, s, trna_db) {
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petr-novak
parents:
diff changeset
512 ltr5 <- te[which(te$LTR == "5LTR")]
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petr-novak
parents:
diff changeset
513 STRAND <- as.character(strand(te)[1])
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petr-novak
parents:
diff changeset
514 if (STRAND == "+") {
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petr-novak
parents:
diff changeset
515 pbs_gr <- GRanges(seqnames(ltr5), IRanges(start = end(ltr5) + 1, end = end(ltr5) + 31))
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petr-novak
parents:
diff changeset
516 pbs_s <- reverseComplement(getSeq(s, pbs_gr))
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petr-novak
parents:
diff changeset
517 }else {
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petr-novak
parents:
diff changeset
518 pbs_gr <- GRanges(seqnames(ltr5), IRanges(end = start(ltr5) - 1, start = start(ltr5) - 30))
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petr-novak
parents:
diff changeset
519 pbs_s <- getSeq(s, pbs_gr)
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petr-novak
parents:
diff changeset
520 }
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petr-novak
parents:
diff changeset
521
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petr-novak
parents:
diff changeset
522 names(pbs_s) <- "pbs_region"
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petr-novak
parents:
diff changeset
523 # find trna match
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petr-novak
parents:
diff changeset
524 tmp <- tempfile()
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petr-novak
parents:
diff changeset
525 tmp_out <- tempfile()
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petr-novak
parents:
diff changeset
526 writeXStringSet(DNAStringSet(pbs_s), tmp)
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petr-novak
parents:
diff changeset
527 # alternative blast:
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petr-novak
parents:
diff changeset
528 cmd <- paste("blastn -task blastn -word_size 7 -dust no -perc_identity 100",
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petr-novak
parents:
diff changeset
529 " -query ", tmp, ' -db ', trna_db, ' -strand plus ',
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petr-novak
parents:
diff changeset
530 '-outfmt "6 qaccver saccver pident length mismatch gapopen qstart qend sstart send evalue bitscore qseq sseq"',
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petr-novak
parents:
diff changeset
531 ' -out', tmp_out)
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petr-novak
parents:
diff changeset
532
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petr-novak
parents:
diff changeset
533 system(cmd)
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petr-novak
parents:
diff changeset
534 pbs_exact_gr <- NULL
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petr-novak
parents:
diff changeset
535 out_raw <- read.table(tmp_out, as.is = TRUE, sep = "\t",
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petr-novak
parents:
diff changeset
536 col.names = strsplit(
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petr-novak
parents:
diff changeset
537 "qaccver saccver pident length mismatch gapopen qstart qend sstart send evalue bitscore qseq sseq",
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petr-novak
parents:
diff changeset
538 split = ' ')[[1]])
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petr-novak
parents:
diff changeset
539 if (nrow(out_raw) > 0) {
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petr-novak
parents:
diff changeset
540 cca <- grepl("CCA$", out_raw$qseq)
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petr-novak
parents:
diff changeset
541 to_end <- out_raw$send == 23 # align to end of sequence
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petr-novak
parents:
diff changeset
542 max_dist <- out_raw$qend > 25 # max 5 bp from ltr
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petr-novak
parents:
diff changeset
543 min_length <- out_raw$length >= 10
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petr-novak
parents:
diff changeset
544 out_pass <- out_raw[cca & to_end & max_dist & min_length,]
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petr-novak
parents:
diff changeset
545 if (nrow(out_pass) > 0) {
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petr-novak
parents:
diff changeset
546 trna_id <- out_pass$saccver[1]
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petr-novak
parents:
diff changeset
547 if (STRAND == "+") {
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petr-novak
parents:
diff changeset
548 S <- end(ltr5) + 32 - out_pass$qend[1]
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petr-novak
parents:
diff changeset
549 E <- end(ltr5) + 32 - out_pass$qstart[1]
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petr-novak
parents:
diff changeset
550 }else {
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petr-novak
parents:
diff changeset
551 S <- start(ltr5) - 31 + out_pass$qstart[1]
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petr-novak
parents:
diff changeset
552 E <- start(ltr5) - 31 + out_pass$qend[1]
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petr-novak
parents:
diff changeset
553 }
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petr-novak
parents:
diff changeset
554 pbs_exact_gr <- GRanges(seqnames(ltr5), IRanges(start = S, end = E))
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petr-novak
parents:
diff changeset
555 pbs_exact_gr$trna_id <- trna_id
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petr-novak
parents:
diff changeset
556 pbs_exact_gr$Length <- out_pass$Length
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petr-novak
parents:
diff changeset
557 strand(pbs_exact_gr) <- STRAND
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petr-novak
parents:
diff changeset
558 pbs_exact_gr$type <- 'primer_binding_site'
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petr-novak
parents:
diff changeset
559 pbs_exact_gr$Parent <- te[1]$ID
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petr-novak
parents:
diff changeset
560 te$trna_id <- c(trna_id, rep(NA, length(te) - 1))
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petr-novak
parents:
diff changeset
561
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petr-novak
parents:
diff changeset
562 }
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petr-novak
parents:
diff changeset
563 }
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petr-novak
parents:
diff changeset
564 te <- append(te, pbs_exact_gr)
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petr-novak
parents:
diff changeset
565 unlink(tmp)
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petr-novak
parents:
diff changeset
566 unlink(tmp_out)
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petr-novak
parents:
diff changeset
567 return(te)
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petr-novak
parents:
diff changeset
568 }
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petr-novak
parents:
diff changeset
569
2
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petr-novak
parents: 0
diff changeset
570
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petr-novak
parents: 0
diff changeset
571 get_te_rank <- function (gr){
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petr-novak
parents: 0
diff changeset
572 DL_id <- gr$ID[gr$type == "transposable_element" &
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petr-novak
parents: 0
diff changeset
573 gr$TSD == "not_found" &
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petr-novak
parents: 0
diff changeset
574 is.na(gr$trna_id)]
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petr-novak
parents: 0
diff changeset
575 DLT_id <- gr$ID[gr$type == "transposable_element" &
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petr-novak
parents: 0
diff changeset
576 gr$TSD != "not_found" &
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petr-novak
parents: 0
diff changeset
577 is.na(gr$trna_id)]
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petr-novak
parents: 0
diff changeset
578 DLTP_id <- gr$ID[gr$type == "transposable_element" &
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petr-novak
parents: 0
diff changeset
579 gr$TSD != "not_found" &
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petr-novak
parents: 0
diff changeset
580 !is.na(gr$trna_id)]
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petr-novak
parents: 0
diff changeset
581 DLP_id <- gr$ID[gr$type == "transposable_element" &
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petr-novak
parents: 0
diff changeset
582 gr$TSD == "not_found" &
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petr-novak
parents: 0
diff changeset
583 !is.na(gr$trna_id)]
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petr-novak
parents: 0
diff changeset
584 Rank <- character(length(gr))
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petr-novak
parents: 0
diff changeset
585 ID <- unlist(ifelse(is.na(gr$ID), gr$Parent, gr$ID))
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petr-novak
parents: 0
diff changeset
586
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petr-novak
parents: 0
diff changeset
587 Rank[ID %in% DL_id] <- "DL"
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petr-novak
parents: 0
diff changeset
588 Rank[ID %in% DLT_id] <- "DLT"
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petr-novak
parents: 0
diff changeset
589 Rank[ID %in% DLP_id] <- "DLP"
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petr-novak
parents: 0
diff changeset
590 Rank[ID %in% DLTP_id] <- "DLTP"
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petr-novak
parents: 0
diff changeset
591 return(Rank)
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petr-novak
parents: 0
diff changeset
592 }
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petr-novak
parents: 0
diff changeset
593
0
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petr-novak
parents:
diff changeset
594 get_te_statistics <- function(gr, RT) {
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petr-novak
parents:
diff changeset
595 DOMAINS_LTR <- gr[gr$type == "transposable_element" &
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petr-novak
parents:
diff changeset
596 gr$TSD == "not_found" &
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petr-novak
parents:
diff changeset
597 is.na(gr$trna_id)]
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petr-novak
parents:
diff changeset
598 DOMAINS_LTR_TSD <- gr[gr$type == "transposable_element" &
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petr-novak
parents:
diff changeset
599 gr$TSD != "not_found" &
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petr-novak
parents:
diff changeset
600 is.na(gr$trna_id)]
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petr-novak
parents:
diff changeset
601 DOMAINS_LTR_TSD_PBS <- gr[gr$type == "transposable_element" &
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petr-novak
parents:
diff changeset
602 gr$TSD != "not_found" &
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petr-novak
parents:
diff changeset
603 !is.na(gr$trna_id)]
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petr-novak
parents:
diff changeset
604 DOMAINS_LTR_PBS <- gr[gr$type == "transposable_element" &
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petr-novak
parents:
diff changeset
605 gr$TSD == "not_found" &
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
606 !is.na(gr$trna_id)]
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petr-novak
parents:
diff changeset
607
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
608 all_class <- names(sort(table(RT$Final_Classification), decreasing = TRUE))
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petr-novak
parents:
diff changeset
609 RT_domain <- as.integer(table(factor(RT$Final_Classification, levels = all_class)))
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petr-novak
parents:
diff changeset
610 DL <- as.integer(table(factor(DOMAINS_LTR$Final_Classification, levels = all_class)))
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petr-novak
parents:
diff changeset
611 DLT <- as.integer(table(factor(DOMAINS_LTR_TSD$Final_Classification, levels = all_class)))
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petr-novak
parents:
diff changeset
612 DLTP <- as.integer(table(factor(DOMAINS_LTR_TSD_PBS$Final_Classification, levels = all_class)))
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petr-novak
parents:
diff changeset
613 DLP <- as.integer(table(factor(DOMAINS_LTR_PBS$Final_Classification, levels = all_class)))
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petr-novak
parents:
diff changeset
614 out <- data.frame(RT_domain = RT_domain,
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petr-novak
parents:
diff changeset
615 DOMAINS_LTR = DL,
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petr-novak
parents:
diff changeset
616 DOMAINS_LTR_TSD = DLT,
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petr-novak
parents:
diff changeset
617 DOMAINS_LTR_PBS = DLP,
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petr-novak
parents:
diff changeset
618 DOMAINS_LTR_TSD_PBS = DLTP,
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petr-novak
parents:
diff changeset
619 row.names = all_class
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petr-novak
parents:
diff changeset
620 )
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petr-novak
parents:
diff changeset
621 total <- colSums(out)
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petr-novak
parents:
diff changeset
622 out <- rbind(out, Total = total)
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petr-novak
parents:
diff changeset
623 return(out)
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petr-novak
parents:
diff changeset
624 }
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petr-novak
parents:
diff changeset
625
3
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petr-novak
parents: 2
diff changeset
626 getSeqNamed <- function(s, gr, name = NULL) {
0
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petr-novak
parents:
diff changeset
627 spart <- getSeq(s, gr)
3
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petr-novak
parents: 2
diff changeset
628 if (is.null(name)){
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petr-novak
parents: 2
diff changeset
629 id1 <- paste0(seqnames(gr), '_', start(gr), "_", end(gr))
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petr-novak
parents: 2
diff changeset
630 }else{
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petr-novak
parents: 2
diff changeset
631 id1 <- mcols(gr)[,name]
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petr-novak
parents: 2
diff changeset
632 }
0
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
633 id2 <- gr$Final_Classification
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petr-novak
parents:
diff changeset
634 names(spart) <- paste0(id1, "#", id2)
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petr-novak
parents:
diff changeset
635 spart
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petr-novak
parents:
diff changeset
636 }
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petr-novak
parents:
diff changeset
637
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petr-novak
parents:
diff changeset
638 get_TE_id <- function (gr){
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petr-novak
parents:
diff changeset
639 gr_te <- gr[gr$type == "transposable_element"]
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petr-novak
parents:
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640 ID <- gr_te$ID
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petr-novak
parents:
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641 A <- paste0(seqnames(gr_te), '_', start(gr_te), "_", end(gr_te))
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petr-novak
parents:
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642 B <- gr_te$Final_Classification
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petr-novak
parents:
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643 names(ID) <- paste0(A, "#", B)
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petr-novak
parents:
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644
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petr-novak
parents:
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645 }
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petr-novak
parents:
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646
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petr-novak
parents:
diff changeset
647 get_te_sequences <- function(gr, s) {
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petr-novak
parents:
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648 # return list of biostrings
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petr-novak
parents:
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649 DOMAINS_LTR <- gr[gr$type == "transposable_element" &
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petr-novak
parents:
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650 gr$TSD == "not_found" &
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petr-novak
parents:
diff changeset
651 is.na(gr$trna_id)]
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petr-novak
parents:
diff changeset
652 DOMAINS_LTR_TSD <- gr[gr$type == "transposable_element" &
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petr-novak
parents:
diff changeset
653 gr$TSD != "not_found" &
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petr-novak
parents:
diff changeset
654 is.na(gr$trna_id)]
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petr-novak
parents:
diff changeset
655 DOMAINS_LTR_TSD_PBS <- gr[gr$type == "transposable_element" &
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petr-novak
parents:
diff changeset
656 gr$TSD != "not_found" &
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petr-novak
parents:
diff changeset
657 !is.na(gr$trna_id)]
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petr-novak
parents:
diff changeset
658 DOMAINS_LTR_PBS <- gr[gr$type == "transposable_element" &
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petr-novak
parents:
diff changeset
659 gr$TSD == "not_found" &
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petr-novak
parents:
diff changeset
660 !is.na(gr$trna_id)]
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petr-novak
parents:
diff changeset
661 s_DL <- getSeqNamed(s, DOMAINS_LTR)
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petr-novak
parents:
diff changeset
662 s_DLT <- getSeqNamed(s, DOMAINS_LTR_TSD)
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petr-novak
parents:
diff changeset
663 s_DLP <- getSeqNamed(s, DOMAINS_LTR_PBS)
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petr-novak
parents:
diff changeset
664 s_DLTP <- getSeqNamed(s, DOMAINS_LTR_TSD_PBS)
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petr-novak
parents:
diff changeset
665 return(DNAStringSetList(
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petr-novak
parents:
diff changeset
666 DL = s_DL,
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petr-novak
parents:
diff changeset
667 DLT = s_DLT,
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petr-novak
parents:
diff changeset
668 DLP = s_DLP,
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petr-novak
parents:
diff changeset
669 DLTP = s_DLTP
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petr-novak
parents:
diff changeset
670 ))
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petr-novak
parents:
diff changeset
671
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petr-novak
parents:
diff changeset
672 }
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petr-novak
parents:
diff changeset
673
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petr-novak
parents:
diff changeset
674 cd_hit_est <- function(seqs, min_identity = 0.9, word_size = 10, ncpu = 2){
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petr-novak
parents:
diff changeset
675 # runs cd-hi-est and return table with cluster membership, and size and if reads was repesentative
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petr-novak
parents:
diff changeset
676 # input sequences must be in the same orientation!!!
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petr-novak
parents:
diff changeset
677 sfile <- tempfile()
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petr-novak
parents:
diff changeset
678 fasta_out <- tempfile()
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petr-novak
parents:
diff changeset
679 clstr <- paste0(fasta_out,".clstr")
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petr-novak
parents:
diff changeset
680 # cdhit is triming names!!
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petr-novak
parents:
diff changeset
681 ori_names <- names(seqs)
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petr-novak
parents:
diff changeset
682 names(seqs) <- seq_along(seqs)
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petr-novak
parents:
diff changeset
683 writeXStringSet(seqs, sfile)
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petr-novak
parents:
diff changeset
684 cmd <- paste("cd-hit-est",
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petr-novak
parents:
diff changeset
685 "-i", sfile,
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petr-novak
parents:
diff changeset
686 "-o", fasta_out,
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petr-novak
parents:
diff changeset
687 "-c", min_identity,
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petr-novak
parents:
diff changeset
688 "-n", word_size,
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petr-novak
parents:
diff changeset
689 "-T", ncpu,
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petr-novak
parents:
diff changeset
690 "-r", 0)
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petr-novak
parents:
diff changeset
691 system(cmd)
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petr-novak
parents:
diff changeset
692 cls_raw <- grep("^>", readLines(clstr), invert = TRUE, value = TRUE)
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petr-novak
parents:
diff changeset
693 unlink(fasta_out)
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petr-novak
parents:
diff changeset
694 unlink(clstr)
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petr-novak
parents:
diff changeset
695 index <- gsub("\t.+","",cls_raw)
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petr-novak
parents:
diff changeset
696 id <- as.numeric(gsub("[.].+","",
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petr-novak
parents:
diff changeset
697 gsub(".+>", "", cls_raw))
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petr-novak
parents:
diff changeset
698 )
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petr-novak
parents:
diff changeset
699 is_representative <- id %in% id[grep("[*]$",cls_raw)]
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petr-novak
parents:
diff changeset
700 membership <- cumsum(index=="0")
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petr-novak
parents:
diff changeset
701 cluster_size <- tabulate(membership)[membership]
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petr-novak
parents:
diff changeset
702 # reorder
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petr-novak
parents:
diff changeset
703 ord <- order(id)
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petr-novak
parents:
diff changeset
704 cls_info <- data.frame(
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petr-novak
parents:
diff changeset
705 seq_id = ori_names,
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petr-novak
parents:
diff changeset
706 membership = membership[ord],
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petr-novak
parents:
diff changeset
707 cluster_size = cluster_size[ord],
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petr-novak
parents:
diff changeset
708 is_representative = is_representative[ord]
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petr-novak
parents:
diff changeset
709 )
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petr-novak
parents:
diff changeset
710 return(cls_info)
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petr-novak
parents:
diff changeset
711 }
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petr-novak
parents:
diff changeset
712