|
0
|
1 log_file=file("Query_Geo_Database.log", open = "wt")
|
|
|
2 sink(log_file)
|
|
|
3 sink(log_file, type = "out")
|
|
|
4 suppressWarnings(suppressMessages(library("batch")))
|
|
|
5 suppressWarnings(suppressMessages(library(GEOquery)))
|
|
|
6 listArguments = parseCommandArgs(evaluate=FALSE)
|
|
|
7 GeoCode=listArguments[["GeoCode"]]
|
|
|
8 GeoCode=toupper(GeoCode)
|
|
|
9 gethelp.df =tryCatch(eList <- getGEOSuppFiles(GeoCode), error = function(cond)"skip")
|
|
|
10 if(is.null(gethelp.df)){
|
|
|
11 gethelp.df =tryCatch(eList <- getGEOSuppFiles(GeoCode), error = function(cond)"skip")
|
|
|
12 }
|
|
|
13 if(is.null(gethelp.df)){
|
|
|
14 print('GeoCode with no raw data, choose another code or retry.')
|
|
|
15 }else{
|
|
|
16 if(is.data.frame(gethelp.df)==TRUE){
|
|
|
17 rawdata=rownames(eList)[grep('RAW',rownames(eList))][1]
|
|
|
18 untar(rawdata, exdir = 'CEL')
|
|
|
19 }else{
|
|
|
20 if(gethelp.df=="skip"){
|
|
|
21 print('Network Trouble Try Again Or Check your GeoCode')
|
|
|
22 }else{
|
|
|
23 print('GeoCode with no raw data, choose another code or retry.')
|
|
|
24 }
|
|
|
25 }
|
|
|
26 }
|
|
|
27
|
