Script to get Rv IDs from GO downloads

regulators/regs_from_GO.R

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+# Script to parse files downloaded from AmiGO for various GO categories
+#
+# Written by Joe Reistetter
+
+# GO categories:
+#   GO:0006950 : response to stress [188 gene products]
+
+#laptop
+setwd("~/schoolDB/Dropbox/thesis_work/data/regulators/")
+
+
+get_rv <- function(pipe_list){
+  #Extracts Rv ID from pipe-delimted list
+  ids <- unlist(strsplit(pipe_list, '|', fixed=T))
+  rv_id <- ids[grepl("Rv", ids, fixed=T)]
+  if (length(rv_id) > 1){
+    return(rv_id[2])
+  }
+  return(rv_id)
+}
+
+parse_GO <- function(go_path){
+  g.raw <- read.table(go_path, head=F, stringsAsFactors=F,
+                              quote="", sep="\t")
+
+  #Pull out two rows with name and pipe-delimited list of different gene IDs
+  g.cols <- g.raw[,c(3,11)]
+  colnames(g.cols) <- c("name", "id_list")
+
+  g.rv <- unique(sapply(g.cols$id_list, get_rv))
+  return(g.rv)
+}
+
+###################################
+#
+#     GO:0006950 : response to stress [188 gene products]
+#
+###################################
+
+g.6950.rv <- parse_GO("GO_0006950.txt")