Mercurial > repos > petrn > repeat_annotation_pipeline

comparison clean_rm_output.R @ 0:d14182506989 draft default tip

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"planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
author petrn
date Tue, 15 Feb 2022 16:44:31 +0000
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-1:000000000000 0:d14182506989
1 #!/usr/bin/env Rscript
2 suppressPackageStartupMessages(library(rtracklayer))
3 suppressPackageStartupMessages(library(parallel))
4
5
6 gff_cleanup = function(gff){
7 ## remove overlapin annotation track - assign new annot
8 gff_disjoin = disjoin(gff, with.revmap=TRUE)
9 ## append annotation:
10 gff_names = mclapply(as.list(gff_disjoin$revmap), FUN = function(x)gff$Name[x], mc.cores = 8)
11 gff_strands = mclapply(as.list(gff_disjoin$revmap), FUN = function(x)strand(gff[x]), mc.cores = 8)
12 new_annot = sapply(sapply(gff_names, unique), paste, collapse="|")
13 new_annot_uniq = unique(new_annot)
14 lca_annot = sapply(strsplit(new_annot_uniq, "|", fixed = TRUE), resolve_name)
15 names(lca_annot) = new_annot_uniq
16 new_annot_lca = lca_annot[new_annot]
17 #new_annot_lca = sapply(sapply(gff_names, unique), resolve_name)
18 strand_attribute = sapply(sapply(gff_strands, unique), paste, collapse="|")
19 gff_disjoin$strands=strand_attribute
20 gff_disjoin$source="RM"
21 gff_disjoin$type="repeat"
22 gff_disjoin$score=NA
23 gff_disjoin$phase=NA
24 gff_disjoin$Name=new_annot_lca
25 gff_disjoin$Original_names=new_annot
26 gff_disjoin$revmap=NULL
27 return(gff_disjoin)
28 }
29
30 resolve_name=function(x){
31 if (length(x)==1){
32 # no conflict
33 return(x)
34 } else{
35 y = sapply(x, strsplit, split="/", fixed = TRUE)
36 ny = table(unlist(sapply(y, function(x)paste(seq_along(x),x))))
37 if (max(ny)<length(x)){
38 return("Unknown")
39 }else{
40 k = which(ny==length(x))
41 r = max(as.numeric((gsub(" .+","",names(k)))))
42 out = paste(y[[1]][1:r], collapse="/")
43 return(out)
44 }
45 }
46 }
47
48 convert_names <- function(n, old_sep = "|" , new_sep = "\""){
49 # remove all characters which are new_sep with -
50 n_new = gsub(old_sep, new_sep,
51 gsub(new_sep,"-", n, fixed = TRUE),
52 fixed = TRUE)
53 return(n_new)
54 }
55
56
57 infile = commandArgs(T)[1]
58 outfile = commandArgs(T)[2]
59
60
61 ## infile = "./test_data/raw_rm.out"
62
63 rm_out = read.table(infile, as.is=TRUE, sep="", skip = 2, fill=TRUE, header=FALSE, col.names=paste0("V",1:16))
64
65 gff = GRanges(seqnames = rm_out$V5, ranges = IRanges(start = rm_out$V6, end=rm_out$V7))
66
67 # repeat class after # symbol - syntax 1
68 # detect separator
69 # if "|" is present replace "|" -> "/" and "/" -> "-"
70 if (any(grep("|", rm_out$V11))){
71 gff$Name <- convert_names(rm_out$V11, old_sep = "|", new_sep = "/")
72 message('replacing classification separator character "|" with "/"')
73 print(gff)
74 }else{
75 gff$Name <- rm_out$V11
76 }
77
78 ## is repeat type is specifies by double underscore:
79 ## then rm_out$V11 is unspecified
80 if (any(rm_out$V11 == "Unspecified")){
81 ## set Name from prefix
82 ## TODO
83 inc = rm_out$V11 == "Unspecified"
84 Name = gsub("__.+","",rm_out$V10)
85 # chanche Usnpsecified to new name
86 gff$Name[inc] = Name
87 }
88
89
90 ## join neighbors with the same annotation, disregard strand!
91 result <- unlist(reduce(split(gff, gff$Name)))
92
93 result$Name <- names(result)
94
95 result_clean = gff_cleanup(result)
96
97 ## TODO
98 ## identify conflicting annotation, replace by LCA but keep origin list of classifications
99
100 gff_out = sortSeqlevels(result_clean)
101 gff_out = sort(gff_out)
102 gff_out$type = "repeat_region"
103 gff_out$source = "RepeatMasker_parsed"
104 gff_out$ID=paste0(gff_out$Name, "_", seq_along(gff_out$Name))
105 export(gff_out, format = "gff3", con=outfile)
106
107