From 5223eab99184d7d6508a7328065d05a5b1ffec48 Mon Sep 17 00:00:00 2001
From: rioualen <claire.rioualen@inserm.fr>
Date: Thu, 2 Jun 2016 14:38:01 +0200
Subject: [PATCH] added temporary notes

---
 scripts/snakefiles/rules/download_from_GEO.rules | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

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)