Mercurial > repos > taoufik > microarrays
diff query_microarray_datasets/GetDatasets.R @ 1:842f8effaf59 draft default tip
Deleted selected files
author | taoufik |
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date | Thu, 27 Dec 2018 06:56:28 -0500 |
parents | cf862e6a6ddb |
children |
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--- 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.') - } - } -} -