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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit d287d5688e57f4154d5875789e0cd4d5c87f11ce
author iuc
date Thu, 03 Oct 2024 22:35:41 +0000
parents 9083012a0abf
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9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
iuc
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1 library("getopt")
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
iuc
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2 suppressPackageStartupMessages(library("rtracklayer"))
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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3 library(GenomicRanges)
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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4 library("BREW3R.r")
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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5
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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6 options(stringAsFactors = FALSE, useFancyQuotes = FALSE)
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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7 args <- commandArgs(trailingOnly = TRUE)
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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8 # - Column 1: the long flag name. A multi-character string.
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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9 # - Column 2: short flag alias of Column 1. A single-character string.
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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10 # - Column 3: Argument mask of the flag. An integer.
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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11 # Possible values: 0=no argument, 1=required argument, 2=optional argument.
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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12 # - Column 4: Data type to which the flag's argument shall be cast using
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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13 # storage.mode(). A multi-character string. This only considered for same-row
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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14 # Column 3 values of 1,2. Possible values: logical, integer, double, complex,
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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15 # character. If numeric is encountered then it will be converted to double.
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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16 # - Column 5 (optional): A brief description of the purpose of the option.
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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17 spec <- matrix(c(
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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18 "help", "h", 0, "logical", "display help",
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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19 "gtf_to_extend", "i", 1, "character", "input gtf file to be extended on 3'",
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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20 "gtf_to_overlap", "g", 1, "character",
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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21 "input gtf file that will be used to extend",
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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22 "output", "o", 1, "character", "output extended gtf",
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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23 "sup_output", "s", 1, "character",
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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24 "supplementary output file with resolution of overlaps",
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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25 "no_add", "n", 0, "logical", "do not add new exons",
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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26 "exclude_pattern", "e", 1, "character", "do not extend genes with names matching this pattern",
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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27 "filter_unstranded", "f", 0, "logical",
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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28 "remove unstranded intervals from gtf_to_overlap which overlap intervals from gtf_to_extend of both strands",
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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29 "quiet", "q", 0, "logical", "decrease verbosity",
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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30 "verbose", "v", 0, "logical", "increase verbosity"
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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31 ), byrow = TRUE, ncol = 5)
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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32 opt <- getopt(spec)
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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33
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34 # if help was asked for print a friendly message
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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35 # and exit with a non-zero error code
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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36 if (!is.null(opt$help)) {
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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37 cat(getopt(spec, usage = TRUE))
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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38 q(status = 1)
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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39 }
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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40
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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41 # Check all required arguments
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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42 if (is.null(opt$gtf_to_extend)) {
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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43 stop("--gtf_to_extend is required")
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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44 }
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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45 if (is.null(opt$gtf_to_overlap)) {
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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46 stop("--gtf_to_overlap is required")
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47 }
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48 if (is.null(opt$output)) {
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49 stop("--output is required")
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50 }
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51
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52 # Check incompatible arguments
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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53 if (!is.null(opt$quiet) && !is.null(opt$verbose)) {
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54 stop("quiet and verbose are mutually exclusive options")
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55 }
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56
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57 # Adjust verbosity
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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58 if (!is.null(opt$quiet)) {
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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59 options(rlib_message_verbosity = "quiet")
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60 }
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61
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62 if (!is.null(opt$verbose)) {
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63 options(BREW3R.r.verbose = "progression")
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64 }
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65
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66 # Load gtfs as GenomicRanges
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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67 input_gr_to_extend <- rtracklayer::import(opt$gtf_to_extend, format = "gtf")
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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68 input_gr_template <- rtracklayer::import(opt$gtf_to_overlap, format = "gtf")
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69
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70 # Save CDS info
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71 input_gr_CDS <- subset(input_gr_to_extend, type == "CDS")
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72
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73 # Filter the template if needed
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74 if (!is.null(opt$filter_unstranded)) {
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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75 # Find intervals without strand information in template
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76 unstranded.intervals <- which(strand(input_gr_template) == "*")
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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77 if (length(unstranded.intervals) > 0) {
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78 # Check if they overlap genes from input with different strands
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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79 # First compute the overlap
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80 ov <- suppressWarnings(
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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81 as.data.frame(findOverlaps(
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82 input_gr_template[unstranded.intervals],
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83 input_gr_to_extend
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84 ))
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85 )
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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86 # Add the strand information
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87 ov$strand <- as.factor(strand(input_gr_to_extend))[ov$subjectHits]
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88 # Simplify the dataframe to get only the strand info
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89 ov.simple <- unique(ov[, c("queryHits", "strand")])
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90 # If the queryHits is duplicated it means there are different strands
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91 multi.strand.query <- ov.simple$queryHits[duplicated(ov.simple$queryHits)]
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92 to.remove <- unstranded.intervals[multi.strand.query]
9083012a0abf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit fa525468780f3dea175da15852b1b8c17e1a80d3
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93 # Remove these potentially error-prone intervals from the template
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94 if (length(to.remove) > 0) {
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95 input_gr_template <- input_gr_template[-to.remove]
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96 }
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97 }
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98 }
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99
2
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100 if (is.null(input_gr_to_extend$exon_id)) {
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101 is.exon <- which(input_gr_to_extend$type == "exon")
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102 input_gr_to_extend$exon_id <- NA
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103 input_gr_to_extend$exon_id[is.exon] <- paste0(
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104 "EXON",
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105 sprintf(
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106 "%010d",
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107 1:length(is.exon)
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108 )
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109 )
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110 }
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111
0
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112 # Run BREW3R.r main function
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113 if (length(input_gr_template) > 0) {
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114 new_gr_exons <- extend_granges(
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115 input_gr_to_extend = input_gr_to_extend,
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116 input_gr_to_overlap = input_gr_template,
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117 add_new_exons = is.null(opt$no_add),
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118 overlap_resolution_fn = opt$sup_output
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119 )
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120 } else {
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121 new_gr_exons <- subset(input_gr_to_extend, type == "exon")
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122 }
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123 # Prevent extension using pattern
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124 if (!is.null(opt$exclude_pattern)) {
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125 input_gr_pattern <- subset(
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126 input_gr_to_extend,
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127 type == "exon" & grepl(opt$exclude_pattern, gene_name)
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128 )
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129 new_gr_no_pattern <- subset(
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130 new_gr_exons,
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131 !grepl(opt$exclude_pattern, gene_name)
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132 )
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133 new_gr_exons <- c(new_gr_no_pattern, input_gr_pattern)
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134 }
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135
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136 # Recompose with CDS
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137 new_gr <- c(new_gr_exons, input_gr_CDS)
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138
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139 # Export
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140 rtracklayer::export.gff(sort(new_gr, ignore.strand = TRUE), opt$output)