diff query_microarray_datasets/GetDatasets.R @ 1:842f8effaf59 draft default tip

Deleted selected files
author taoufik
date Thu, 27 Dec 2018 06:56:28 -0500
parents cf862e6a6ddb
children
line wrap: on
line diff
--- a/query_microarray_datasets/GetDatasets.R	Thu Dec 27 05:54:24 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,27 +0,0 @@
-log_file=file("Query_Geo_Database.log", open = "wt")
-sink(log_file)
-sink(log_file, type = "out")
-suppressWarnings(suppressMessages(library("batch")))
-suppressWarnings(suppressMessages(library(GEOquery)))
-listArguments = parseCommandArgs(evaluate=FALSE)
-GeoCode=listArguments[["GeoCode"]]
-GeoCode=toupper(GeoCode)
-gethelp.df =tryCatch(eList <- getGEOSuppFiles(GeoCode), error = function(cond)"skip")
-if(is.null(gethelp.df)){
-  gethelp.df =tryCatch(eList <- getGEOSuppFiles(GeoCode), error = function(cond)"skip")
-}
-if(is.null(gethelp.df)){
-  print('GeoCode with no raw data, choose another code or retry.')
-}else{
-  if(is.data.frame(gethelp.df)==TRUE){
-    rawdata=rownames(eList)[grep('RAW',rownames(eList))][1]
-    untar(rawdata, exdir = 'CEL')
-  }else{
-    if(gethelp.df=="skip"){
-      print('Network Trouble Try Again Or Check your GeoCode')
-    }else{
-      print('GeoCode with no raw data, choose another code or retry.')
-    }
-  }
-}
-