remove data_expression

downloads-generation/data_expression/GENERATE.sh

-#!/bin/bash
-#
-# Download published gene expression data corresponding to some of our mass
-# spec datasets.
-#
-#
-set -e
-set -x
-
-DOWNLOAD_NAME=data_expression
-SCRATCH_DIR=${TMPDIR-/tmp}/mhcflurry-downloads-generation
-SCRIPT_ABSOLUTE_PATH="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/$(basename "${BASH_SOURCE[0]}")"
-SCRIPT_DIR=$(dirname "$SCRIPT_ABSOLUTE_PATH")
-
-mkdir -p "$SCRATCH_DIR"
-rm -rf "$SCRATCH_DIR/$DOWNLOAD_NAME"
-mkdir "$SCRATCH_DIR/$DOWNLOAD_NAME"
-
-# Send stdout and stderr to a logfile included with the archive.
-exec >  >(tee -ia "$SCRATCH_DIR/$DOWNLOAD_NAME/LOG.txt")
-exec 2> >(tee -ia "$SCRATCH_DIR/$DOWNLOAD_NAME/LOG.txt" >&2)
-
-date
-
-cd $SCRATCH_DIR/$DOWNLOAD_NAME
-
-# Many cell line sequencing data is available from:
-# Available from SRA [access required] at:
-# https://www.ebi.ac.uk/ega/studies/EGAS00001000610
-
-# CCLE as processed by expression atlas
-DATASET=expression-atlas-22460905
-mkdir $DATASET
-cd $DATASET
-#wget -q https://www.ebi.ac.uk/gxa/experiments-content/E-MTAB-2770/resources/ExperimentDownloadSupplier.RnaSeqBaseline/tpms.tsv
-ls -lh .
-cd ..
-
-# Human protein atlas
-DATASET=human-protein-atlas
-mkdir $DATASET
-cd $DATASET
-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=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 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"
-tar -cjf "$RESULT" *
-echo "Created archive: $RESULT"