Mercurial > repos > iuc > ribowaltz_plot

annotate ribowaltz.R @ 1:e25d81465c23 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit 416063685092b818a398e00d5027f7fe742230f1
author iuc
date Mon, 23 Oct 2023 12:10:37 +0000
parents 8e903cb3f919
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8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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diff changeset
1 # setup R error handling to go to stderr
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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2 options(show.error.messages = FALSE, error = function() {
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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3 cat(geterrmessage(), file = stderr())
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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4 q("no", 1, FALSE)
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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5 })
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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6
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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7 # we need that to not crash galaxy with an UTF8 error on German LC settings.
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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8 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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9 library("getopt")
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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10 options(stringAsFactors = FALSE, useFancyQuotes = FALSE)
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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11 args <- commandArgs(trailingOnly = TRUE)
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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12
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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13 # get options, using the spec as defined by the enclosed list.
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
iuc
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14 # we read the options from the default: commandArgs(TRUE).
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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15 spec <- matrix(c(
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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16 "quiet", "q", 0, "logical",
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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17 "help", "h", 0, "logical",
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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18 "bamdir", "b", 1, "character",
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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19 "gtffile", "g", 1, "character",
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20 "codon_coverage_info", "Y", 1, "character",
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21 "cds_coverage_info", "Z", 1, "character",
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22 "psite_info_rdata", "O", 0, "character",
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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23 "refseq_sep", "s", 0, "character",
1
e25d81465c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit 416063685092b818a398e00d5027f7fe742230f1
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24 "indel_threshold", "t", 0, "integer",
0
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25 "params_duplicate_filterting", "d", 0, "character",
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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26 "params_peridiocity_filterting", "l", 0, "character",
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27 "params_custom_filterting", "c", 0, "character",
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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28 "params_psite_additional", "p", 0, "character",
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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29 "params_coverage_additional", "C", 0, "character"
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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30 ), byrow = TRUE, ncol = 4)
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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31 opt <- getopt(spec)
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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32
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33 # if help was asked for print a friendly message
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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34 # and exit with a non-zero error code
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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35 if (!is.null(opt$help)) {
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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36 cat(getopt(spec, usage = TRUE))
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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37 q(status = 1)
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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38 }
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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39
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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40 verbose <- is.null(opt$quiet)
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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41
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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42 library("riboWaltz")
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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43
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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44 # create annotation data table
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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45 annotation_dt <- create_annotation(opt$gtffile)
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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46
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47 sep <- opt$refseq_sep
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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48 if (opt$refseq_sep == "") {
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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49 sep <- NULL
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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50 }
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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51 # convert alignments in BAM files into list of data tables
1
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52 reads_list <- bamtolist(bamfolder = opt$bamdir, annotation = annotation_dt, refseq_sep = sep, indel_threshold = opt$indel_threshold)
0
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53
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54 library("jsonlite")
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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55 # remove duplicate reads
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56 if (!is.null(opt$params_duplicate_filterting)) {
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57 json_duplicate_filterting <- fromJSON(opt$params_duplicate_filterting)
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58 reads_list <- duplicates_filter(
8e903cb3f919 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit ff002df702f544829d1b500ac4b517c1e70ad14d
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59 data = reads_list,
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60 extremity = json_duplicate_filterting$extremity,
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61 keep = json_duplicate_filterting$keep
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62 )
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63 }
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64
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65 # selection of read lengths - periodicity filtering
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66 if (!is.null(opt$params_peridiocity_filterting)) {
1
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67 json_peridiocity_filterting <- fromJSON(opt$params_peridiocity_filterting)
e25d81465c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit 416063685092b818a398e00d5027f7fe742230f1
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68 reads_list <- length_filter(
e25d81465c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit 416063685092b818a398e00d5027f7fe742230f1
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69 data = reads_list,
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70 length_filter_mode = "periodicity",
e25d81465c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit 416063685092b818a398e00d5027f7fe742230f1
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71 periodicity_threshold = json_peridiocity_filterting$periodicity_threshold
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72 )
0
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73 }
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74 # selection of read lengths - length range filtering
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75 if (!is.null(opt$params_custom_filterting)) {
1
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76 json_custom_filterting <- fromJSON(opt$params_custom_filterting)
e25d81465c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz commit 416063685092b818a398e00d5027f7fe742230f1
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77 reads_list <- length_filter(
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78 data = reads_list,
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79 length_filter_mode = "custom",
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80 length_range = json_custom_filterting$length_range
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81 )
0
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82 }
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83
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84 # compute P-site offset
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85 json_psite_additional <- fromJSON(opt$params_psite_additional)
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86 psite_offset <- psite(
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87 reads_list,
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88 start = json_psite_additional$use_start,
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89 flanking = json_psite_additional$flanking,
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90 extremity = json_psite_additional$psite_extrimity,
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91 plot = TRUE,
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92 cl = json_psite_additional$cl,
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93 plot_format = "pdf",
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94 plot_dir = "plots"
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95 )
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96 psite_offset
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97
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98 reads_psite_list <- psite_info(reads_list, psite_offset)
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99 reads_psite_list
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100 # write a separate P-site offset info table for each sample
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101 for (sample in names(reads_psite_list)) {
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102 write.table(
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103 reads_psite_list[[sample]],
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104 file = paste(sample, "psite_info.tsv", sep = "_"),
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105 sep = "\t", row.names = FALSE, quote = FALSE
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106 )
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107 print(paste(sample, "psite_info.tsv", sep = "_"))
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108 }
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109
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110 # write R object to a file
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111 if (!is.null(opt$psite_info_rdata)) {
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112 save(reads_psite_list, annotation_dt, file = opt$psite_info_rdata)
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113 }
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114
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115 json_coverage_additional <- fromJSON(opt$params_coverage_additional)
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116 # codon coverage
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117 codon_coverage_out <- codon_coverage(
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118 reads_psite_list,
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119 annotation_dt,
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120 psite = json_coverage_additional$psites_per_region,
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121 min_overlap = json_coverage_additional$min_overlap
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122 )
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123 write.table(codon_coverage_out, file = opt$codon_coverage_info, sep = "\t", row.names = FALSE, quote = FALSE)
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124
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125 # CDS coverage
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126 cds_coverage_out <- cds_coverage(
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127 reads_psite_list,
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128 annotation_dt,
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129 start_nts = json_coverage_additional$start_nts,
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130 stop_nts = json_coverage_additional$stop_nts
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131 )
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132 write.table(cds_coverage_out, file = opt$cds_coverage_info, sep = "\t", row.names = FALSE, quote = FALSE)