diff --git a/scripts/snakefiles/rules/download_from_GEO.rules b/scripts/snakefiles/rules/download_from_GEO.rules index b8732624..1cda841c 100644 --- a/scripts/snakefiles/rules/download_from_GEO.rules +++ b/scripts/snakefiles/rules/download_from_GEO.rules @@ -21,6 +21,20 @@ rule download_sra: """ +## TODO ! download function + +## 1. Get SRR ids from GSE id + +library(GEOquery) +gse <- getGEO('GSE20870') # retrieves a GEO list set for your SRA id. +## see what is in there: +show(gse) +# There are 2 sets of samples for that ID +## what you want is table a with SRR to download and some sample information: +## lets see what the first set contains: +df <- as.data.frame(gse[[1]]) +write.csv(df, file="test.csv") +head(df)