Mercurial > repos > galaxyp > custom_pro_db

annotate customProDB.R @ 2:2cba79e6037e draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
author galaxyp
date Wed, 17 May 2017 20:23:39 -0400
parents ad130eaa3a05
children bc08158abf77
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1 #!/usr/bin/env Rscript
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3 initial.options <- commandArgs(trailingOnly = FALSE)
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4 script_parent_dir <- dirname(sub("--file=", "", initial.options[grep("--file=", initial.options)]))
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6 ## begin warning handler
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7 withCallingHandlers({
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9 library(methods) # Because Rscript does not always do this
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11 options('useFancyQuotes' = FALSE)
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13 suppressPackageStartupMessages(library("optparse"))
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14 suppressPackageStartupMessages(library("RGalaxy"))
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17 option_list <- list()
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19 option_list$bam <- make_option('--bam', type='character')
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20 option_list$bai <- make_option('--bai', type='character')
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21 option_list$vcf <- make_option('--vcf', type='character')
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22 option_list$exon_anno <- make_option('--exon_anno', type='character')
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23 option_list$proteinseq <- make_option('--proteinseq', type='character')
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24 option_list$procodingseq <- make_option('--procodingseq', type='character')
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25 option_list$ids <- make_option('--ids', type='character')
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26 option_list$dbsnpinCoding <- make_option('--dbsnpinCoding', type='character')
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27 option_list$cosmic <- make_option('--cosmic', type='character')
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28 option_list$annotationFromHistory <- make_option('--annotationFromHistory', type='logical', action="store_true", default=FALSE)
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29 option_list$rpkmCutoff <- make_option('--rpkmCutoff', type='character')
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30 option_list$outputIndels <- make_option('--outputIndels', type='logical', action="store_true", default=FALSE)
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31 #option_list$outputNovelJunctions <- make_option('--outputNovelJunctions', type='logical', action="store_true", default=FALSE)
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32 #option_list$bedFile <- make_option('--bedFile', type='character')
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33 #option_list$bsGenome <- make_option('--bsGenome', type='character')
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34 option_list$outputRData <- make_option('--outputRData', type='logical', action="store_true", default=FALSE)
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35 option_list$outputSQLite <- make_option('--outputSQLite', type='logical', action="store_true", default=FALSE)
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38 opt <- parse_args(OptionParser(option_list=option_list))
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41 customProDB <- function(
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42 bam_file = GalaxyInputFile(required=TRUE),
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43 bai_file = GalaxyInputFile(required=TRUE),
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44 vcf_file = GalaxyInputFile(required=TRUE),
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45 exon_anno_file = GalaxyInputFile(required=TRUE),
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46 proteinseq_file = GalaxyInputFile(required=TRUE),
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47 procodingseq_file = GalaxyInputFile(required=TRUE),
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48 ids_file = GalaxyInputFile(required=TRUE),
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49 dbsnpinCoding_file = GalaxyInputFile(required=FALSE),
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50 cosmic_file = GalaxyInputFile(required=FALSE),
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51 annotationFromHistory = GalaxyLogicalParam(required=FALSE),
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52 rpkmCutoff = GalaxyNumericParam(required=TRUE),
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53 outputIndels = GalaxyLogicalParam(required=FALSE),
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54 outputRData = GalaxyLogicalParam(required=FALSE),
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55 outputSQLite = GalaxyLogicalParam(required=FALSE)
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56 #,outputNovelJunctions = GalaxyLogicalParam(required=FALSE)
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57 #,bedFile = GalaxyInputFile(required=FALSE)
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58 #,bsGenome = GalaxyCharacterParam(required=FALSE)
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59 )
0
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60 {
1
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61 old <- options(stringsAsFactors = FALSE, gsubfn.engine = "R")
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62 on.exit(options(old), add = TRUE)
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63
0
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64 file.symlink(exon_anno_file, paste(getwd(), "exon_anno.RData", sep="/"))
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65 file.symlink(proteinseq_file, paste(getwd(), "proseq.RData", sep="/"))
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66 file.symlink(procodingseq_file, paste(getwd(), "procodingseq.RData", sep="/"))
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67 file.symlink(ids_file, paste(getwd(), "ids.RData", sep="/"))
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68
1
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69 load(exon_anno_file)
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70 load(proteinseq_file)
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71 load(procodingseq_file)
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72 load(ids_file)
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73
0
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74 if (length(dbsnpinCoding_file) > 0)
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75 {
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76 file.symlink(dbsnpinCoding_file, paste(getwd(), "dbsnpinCoding.RData", sep="/"))
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77 labelrsid = TRUE
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78 load(dbsnpinCoding_file)
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79 }
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80 else
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81 {
1
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82 dbsnpinCoding = NULL
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83 labelrsid = FALSE
0
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84 }
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85
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86 if (length(cosmic_file) > 0)
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87 {
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88 file.symlink(cosmic_file, paste(getwd(), "cosmic.RData", sep="/"))
1
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89 use_cosmic = TRUE
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90 load(cosmic_file)
0
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91 }
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92 else
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93 {
1
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94 cosmic = NULL
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95 use_cosmic = FALSE
0
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96 }
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97
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98 bamLink = "input.bam"
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99 file.symlink(bam_file, bamLink)
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100 file.symlink(bai_file, paste(bamLink, ".bai", sep=""))
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101
1
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102 # load customProDB from GitHub (NOTE: downloading the zip is faster than cloning the repo with git2r or devtools::install_github)
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103 download.file("https://github.com/chambm/customProDB/archive/master.zip", "customProDB.zip", quiet=TRUE)
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104 unzip("customProDB.zip")
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105 devtools::load_all("customProDB-master")
0
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106
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107 easyRun(bamFile=bamLink, vcfFile=vcf_file, annotation_path=getwd(),
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108 rpkm_cutoff=rpkmCutoff, outfile_path=".", outfile_name="output",
1
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109 nov_junction=FALSE, INDEL=outputIndels,
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110 lablersid=labelrsid, COSMIC=use_cosmic)
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111
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112 # save variant annotations to an RData file (needed by proBAMr)
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113 if (outputRData || outputSQLite)
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114 {
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115 variantAnnotation = getVariantAnnotation(vcf_file, ids, exon, proteinseq, procodingseq, dbsnpinCoding, cosmic)
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116 if (outputRData) save(variantAnnotation, file="output.rdata")
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117 }
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118
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119 if (outputSQLite)
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120 {
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121 # create protein-centric variant annotation table (needed by Galaxy-P viewer MVP)
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122 varproseq = unique(rbind(variantAnnotation$snvproseq, variantAnnotation$indelproseq))
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123 ref_vs_var_seq = sqldf::sqldf("SELECT reference.pro_name, variant.pro_name AS var_pro_name, reference.peptide AS ref_seq, variant.peptide AS var_seq
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124 FROM proteinseq reference, varproseq variant
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125 WHERE reference.tx_name=variant.tx_name
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126 GROUP BY variant.pro_name")
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127 getCigarishString = function(ref, var)
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128 {
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129 a = Biostrings::pairwiseAlignment(ref, var)
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130 d = gsub("[A-Z]", "=", Biostrings::compareStrings(a@pattern, a@subject))
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131 r = rle(strsplit(d, "")[[1]])
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132 gsub("-", "D", gsub("\\+", "I", gsub("\\?", "X", paste0(r$lengths, r$values, collapse=""))))
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133 }
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134 ref_vs_var_seq$cigar = mapply(FUN=getCigarishString, ref_vs_var_seq$ref_seq, ref_vs_var_seq$var_seq, USE.NAMES=FALSE)
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135 ref_vs_var_seq$annotation = substring(ref_vs_var_seq$var_pro_name, stringr::str_length(ref_vs_var_seq$pro_name)+2)
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136
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137 variant_annotation_sqlite = dbConnect(RSQLite::SQLite(), "output_variant_annotation.sqlite")
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138 dbWriteTable(variant_annotation_sqlite,
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139 "variant_annotation",
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140 sqldf::sqldf("SELECT var_pro_name, pro_name, cigar, annotation FROM ref_vs_var_seq"))
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141 DBI::dbExecute(variant_annotation_sqlite, "CREATE INDEX variant_annotation_var_pro_name ON variant_annotation (var_pro_name)")
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142
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143 # save genomic mapping to a SQLite file (needed by Galaxy-P viewer MVP)
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144 exon$cds_start = as.integer(exon$cds_start)
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145 exon$cds_end = as.integer(exon$cds_end)
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146 genomic_mapping_sqlite = dbConnect(RSQLite::SQLite(), "output_genomic_mapping.sqlite")
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147 varprocoding = unique(rbind(variantAnnotation$snvprocoding, variantAnnotation$indelprocoding))
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148 dbWriteTable(genomic_mapping_sqlite,
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149 "genomic_mapping",
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150 sqldf::sqldf("SELECT exon.gene_name, exon.tx_name, varprocoding.pro_name, cds_start, cds_end,
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151 chromosome_name AS chr_name, cds_chr_start, cds_chr_end, exon.strand
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152 FROM exon, varprocoding
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153 WHERE exon.tx_id=varprocoding.tx_id AND cds_chr_start > 0
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154 GROUP BY exon.tx_id, rank
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155 UNION
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156 SELECT gene_name, tx_name, pro_name, cds_start, cds_end,
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157 chromosome_name AS chr_name, cds_chr_start, cds_chr_end, exon.strand
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158 FROM exon
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159 WHERE cds_chr_start > 0
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160 GROUP BY tx_id, rank"))
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161 DBI::dbExecute(genomic_mapping_sqlite, "CREATE INDEX genomic_mapping_pro_name ON genomic_mapping (pro_name)")
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162 }
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163
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164 invisible(NULL)
0
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165 }
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166
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167
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168 params <- list()
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169 for(param in names(opt))
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170 {
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171 if (!param == "help")
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172 params[param] <- opt[param]
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173 }
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174
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175 setClass("GalaxyRemoteError", contains="character")
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176 wrappedFunction <- function(f)
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177 {
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178 tryCatch(do.call(f, params),
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179 error=function(e) new("GalaxyRemoteError", conditionMessage(e)))
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180 }
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181
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182
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183 suppressPackageStartupMessages(library(RGalaxy))
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184 do.call(customProDB, params)
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185
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186 ## end warning handler
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187 }, warning = function(w) {
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188 cat(paste("Warning:", conditionMessage(w), "\n"))
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189 invokeRestart("muffleWarning")
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190 })