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annotate sleuth.R @ 3:172091d47f5a draft default tip

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planemo upload for repository https://github.com/youyuh48/galaxy-sleuth/tree/master/ commit 8d9ff6181e933951e015e67f1719588bab2b3ab5-dirty
author youyuh48
date Tue, 12 Jun 2018 17:58:47 -0400
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3
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1 #!/usr/bin/env Rscript
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2
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3 # A command-line interface to sleuth for use with Galaxy This script modified
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4 # from https://github.com/pachterlab/bears_analyses/blob/master/sleuth.R
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5 # https://github.com/nturaga/bioc-galaxy-integration/blob/master/README.md
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6
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7 ## Command to run tool:
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8 ## Rscript sleuth.R --indir test-rscript --metadata test-rscript/metadata.txt
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9 ## --full_model '~condition' --reduced_model '~1'
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10 ## --gene_anno_name 'hsapiens_gene_ensembl'
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11
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12 # setup R error handling to go to stderr
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13 options(show.error.messages = F, error = function() {
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14 cat(geterrmessage(), file = stderr())
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15 q("no", 1, F)
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16 })
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17
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18 # we need that to not crash galaxy with an UTF8 error on German LC settings.
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19 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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20
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21 library("getopt")
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22 library("tools")
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23 options(stringAsFactors = FALSE, useFancyQuotes = FALSE)
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24 args <- commandArgs(trailingOnly = TRUE)
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25
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26 # get options, using the spec as defined by the enclosed list.
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27 spec <- matrix(c(
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28 "quiet", "q", 0, "logical",
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29 "help", "h", 0, "logical",
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30 "indir", "i", 1, "character",
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31 "metadata", "m", 1, "character",
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32 "full_model", "f", 1, "character",
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33 "reduced_model", "r", 1, "character",
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34 "gene_anno_name", "a", 2, "character"),
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35 byrow = TRUE, ncol = 4)
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36 opt <- getopt(spec)
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37
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38 # if help was asked for print a friendly message and exit with a non-zero error
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39 # code
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40 if (!is.null(opt$help)) {
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41 cat(getopt(spec, usage = TRUE))
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42 q(status = 1)
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43 }
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44
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45 # enforce the following required arguments
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46 if (is.null(opt$indir)) {
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47 cat("'indir' is required\n")
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48 q(status = 1)
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49 }
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50 if (is.null(opt$metadata)) {
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51 cat("'metadata' is required\n")
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52 q(status = 1)
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53 }
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54 if (is.null(opt$full_model)) {
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55 cat("'full_model' is required\n")
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56 q(status = 1)
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57 }
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58 if (is.null(opt$reduced_model)) {
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59 cat("'reduced_model' is required\n")
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60 q(status = 1)
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61 }
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62
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63 verbose <- if (is.null(opt$quiet)) {
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64 TRUE
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65 } else {
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66 FALSE
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67 }
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68
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69 suppressPackageStartupMessages({
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70 library("sleuth")
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71 library("biomaRt")
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72 })
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73
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74 s2c <- read.table(file.path(opt$metadata), header = TRUE, stringsAsFactors = FALSE)
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75 run_dirs <- s2c$sample
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76 kal_dirs <- c()
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77
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78 for (dir in run_dirs) {
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79 kal_dirs <- c(kal_dirs, file.path(opt$indir, dir, "kallisto"))
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80 }
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81
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82 s2c <- dplyr::mutate(s2c, path = kal_dirs)
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83
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84 if (!is.null(opt$gene_anno_name)) {
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85 mart <- biomaRt::useMart(biomart = "ensembl", dataset = opt$gene_anno_name)
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86 t2g <- biomaRt::getBM(attributes = c("ensembl_transcript_id", "ensembl_gene_id",
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87 "external_gene_name"), mart = mart)
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88 t2g <- dplyr::rename(t2g, target_id = ensembl_transcript_id, ens_gene = ensembl_gene_id,
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89 ext_gene = external_gene_name)
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90 so <- sleuth_prep(s2c, as.formula(opt$full_model), target_mapping = t2g, read_bootstrap_tpm = TRUE,
172091d47f5a planemo upload for repository https://github.com/youyuh48/galaxy-sleuth/tree/master/ commit 8d9ff6181e933951e015e67f1719588bab2b3ab5-dirty
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91 extra_bootstrap_summary = TRUE)
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92 } else {
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93 so <- sleuth_prep(s2c, as.formula(opt$full_model), read_bootstrap_tpm = TRUE,
172091d47f5a planemo upload for repository https://github.com/youyuh48/galaxy-sleuth/tree/master/ commit 8d9ff6181e933951e015e67f1719588bab2b3ab5-dirty
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94 extra_bootstrap_summary = TRUE)
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95 }
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96 so <- sleuth_fit(so, as.formula(opt$full_model), "full")
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97 so <- sleuth_fit(so, as.formula(opt$reduced_model), "reduced")
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98 so <- sleuth_lrt(so, "reduced", "full")
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99 sleuth_deploy(so, opt$indir)
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100
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101 cat("Successfully finished script.\n")