From 3bc4cc5037aff483be0f1c87e830c2cf87dc4baa Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Thu, 10 Oct 2019 12:15:00 -0400
Subject: [PATCH] update data_expression

---
 .../data_expression/GENERATE.sh               | 61 ++++++++++++++++---
 1 file changed, 51 insertions(+), 10 deletions(-)

diff --git a/downloads-generation/data_expression/GENERATE.sh b/downloads-generation/data_expression/GENERATE.sh
index c780b42f..5453b0dd 100755
--- a/downloads-generation/data_expression/GENERATE.sh
+++ b/downloads-generation/data_expression/GENERATE.sh
@@ -28,28 +28,69 @@ cd $SCRATCH_DIR/$DOWNLOAD_NAME
 # Available from SRA [access required] at:
 # https://www.ebi.ac.uk/ega/studies/EGAS00001000610
 
-# CCLE cell lines
-DATASET=ccle
+# CCLE as processed by expression atlas
+DATASET=expression-atlas-22460905
 mkdir $DATASET
 cd $DATASET
-wget -q https://data.broadinstitute.org/ccle/CCLE_RNAseq_rsem_genes_tpm_20180929.txt.gz
-wget -q https://data.broadinstitute.org/ccle/CCLE_miRNA_20181103.gct
+#wget -q https://www.ebi.ac.uk/gxa/experiments-content/E-MTAB-2770/resources/ExperimentDownloadSupplier.RnaSeqBaseline/tpms.tsv
+ls -lh .
 cd ..
 
-# B721.221
-DATASET=b721221
+# Human protein atlas
+DATASET=human-protein-atlas
 mkdir $DATASET
 cd $DATASET
-wget -q https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE93315&format=file
+wget -q https://www.proteinatlas.org/download/rna_celline.tsv.zip
+wget -q https://www.proteinatlas.org/download/rna_blood_cell_schmiedel.tsv.zip
+wget -q https://www.proteinatlas.org/download/rna_blood_cell_sample_tpm_m.tsv.zip
+wget -q https://www.proteinatlas.org/download/rna_tissue_gtex.tsv.zip
+for i in $(ls *.zip)
+do
+    unzip $i
+    rm $i
+done
+ls -lh .
 cd ..
 
-DATASET=pancan-xena
+#DATASET=HEK293
+#mkdir $DATASET
+#cd $DATASET
+#wget -q  "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE85161&format=file" -O GSE85161_RAW.tar
+#tar -xvf GSE85161_RAW.tar
+#rm GSE85161_RAW.tar
+#ls -lh .
+#cd ..
+
+# CCLE cell lines
+# Other source of CCLE information
+#DATASET=ccle
+#mkdir $DATASET
+#cd $DATASET
+#wget -q https://data.broadinstitute.org/ccle/CCLE_RNAseq_rsem_genes_tpm_20180929.txt.gz
+#wget -q https://data.broadinstitute.org/ccle/CCLE_miRNA_20181103.gct
+#cd ..
+
+# PBMC
+DATASET=pbmc
 mkdir $DATASET
 cd $DATASET
-wget -q https://pancanatlas.xenahubs.net/download/probeMap/hugo_gencode_good_hg19_V24lift37_probemap
-wget -q https://pancanatlas.xenahubs.net/download/EB++AdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.xena.gz
+wget -q ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107011/suppl/GSE107011_Processed_data_TPM.txt.gz
 cd ..
 
+# B721.221
+#DATASET=b721221
+#mkdir $DATASET
+#cd $DATASET
+#wget -q https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE93315&format=file
+#cd ..
+
+#DATASET=pancan-xena
+#mkdir $DATASET
+#cd $DATASET
+#wget -q https://pancanatlas.xenahubs.net/download/probeMap/hugo_gencode_good_hg19_V24lift37_probemap
+#wget -q https://pancanatlas.xenahubs.net/download/EB++AdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.xena.gz
+#cd ..
+
 cp $SCRIPT_ABSOLUTE_PATH .
 bzip2 LOG.txt
 RESULT="$SCRATCH_DIR/${DOWNLOAD_NAME}.$(date +%Y%m%d).tar.bz2"
-- 
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