Mercurial > repos > galaxyp > psm_to_sam

comparison PSM2SAM.R @ 1:34f9e847dd4e draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit cf9086847f3153e28b697b5f4b0da1a677eb165a-dirty
author galaxyp
date Thu, 12 Nov 2015 18:11:28 -0500
parents c506e5dac2bb
children ce09f1a1bbad
comparison
equal deleted inserted replaced
0:c506e5dac2bb 1:34f9e847dd4e
1 #!/usr/bin/env Rscript 1 #!/usr/bin/env Rscript
2
3 initial.options <- commandArgs(trailingOnly = FALSE)
4 script_parent_dir <- dirname(sub("--file=", "", initial.options[grep("--file=", initial.options)]))
2 5
3 ## begin warning handler 6 ## begin warning handler
4 withCallingHandlers({ 7 withCallingHandlers({
5 8
6 library(methods) # Because Rscript does not always do this 9 library(methods) # Because Rscript does not always do this
34 procodingseq_file = GalaxyInputFile(), 37 procodingseq_file = GalaxyInputFile(),
35 header_file = GalaxyInputFile(), 38 header_file = GalaxyInputFile(),
36 XScolumn = GalaxyCharacterParam(required=TRUE), 39 XScolumn = GalaxyCharacterParam(required=TRUE),
37 OutputFile = GalaxyOutput("proSAM","sam")) 40 OutputFile = GalaxyOutput("proSAM","sam"))
38 { 41 {
39 if (length(exon_anno_file) == 0) { exon_anno_file = "/export/src/tools-galaxyp-chambm/tools/bumbershoot/psm_to_sam/tool-data/exon_anno.RData" } 42 if (length(exon_anno_file) == 0) { exon_anno_file = paste(script_parent_dir, "tool-data/exon_anno.RData", sep="/") }
40 if (length(proteinseq_file) == 0) { proteinseq_file = "/export/src/tools-galaxyp-chambm/tools/bumbershoot/psm_to_sam/tool-data/proseq.RData" } 43 if (length(proteinseq_file) == 0) { proteinseq_file = paste(script_parent_dir, "tool-data/proseq.RData", sep="/") }
41 if (length(procodingseq_file) == 0) { procodingseq_file = "/export/src/tools-galaxyp-chambm/tools/bumbershoot/psm_to_sam/tool-data/procodingseq.RData" } 44 if (length(procodingseq_file) == 0) { procodingseq_file = paste(script_parent_dir, "tool-data/procodingseq.RData", sep="/") }
42 if (length(header_file) == 0) { header_file = "/export/src/tools-galaxyp-chambm/tools/bumbershoot/psm_to_sam/tool-data/header_refseq_hg19.txt" } 45 if (length(header_file) == 0) { header_file = paste(script_parent_dir, "tool-data/header_refseq_hg19.txt", sep="/") }
43 46
44 if (!file.exists(header_file)) { gstop("failed to read header file") } 47 if (!file.exists(header_file)) { gstop("failed to read header file") }
45 if (file.exists(OutputFile)) 48 if (file.exists(OutputFile))
46 { 49 {
47 if (file.info(OutputFile)$size > 0) { gstop("output file already exists") } 50 if (file.info(OutputFile)$size > 0) { gstop("output file already exists") }
61 suppressPackageStartupMessages(library(Biostrings)) 64 suppressPackageStartupMessages(library(Biostrings))
62 65
63 options(stringsAsFactors=FALSE) 66 options(stringsAsFactors=FALSE)
64 67
65 scoreName = XScolumn 68 scoreName = XScolumn
66 columnName = gsub(":", "_", scoreName) 69 columnName = gsub("[^A-Z0-9]", "_", scoreName)
67 70
68 passedPSM <- tryCatch({ 71 passedPSM <- tryCatch({
69 #read.delim(passedPSM_file, row.names=1) 72 #read.delim(passedPSM_file, row.names=1)
70 suppressPackageStartupMessages(library(RSQLite)) 73 suppressPackageStartupMessages(library(RSQLite))
71 drv <- dbDriver("SQLite") 74 drv <- dbDriver("SQLite")