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34393ef | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 | DATA_DIR=$(cat machine_configure.json |grep data_dir|awk -F ': "' '{print $2}'|awk -F '",' '{print $1}')
if [ ! -d ${DATA_DIR} ]; then
echo "=============================================================="
echo " "
echo ${DATA_DIR} does not exist! Redirect to ./data
echo " "
echo "=============================================================="
DATA_DIR=$(pwd)/data
fi
cd ${DATA_DIR}
## download the ribosome profiling datasest
# RP-muscle
wget https://raw.githubusercontent.com/zzz2010/5UTR_Optimizer/master/data/df_counts_and_len.TE_sorted.Muscle.with_annot.txt
# RP-293T
wget https://raw.githubusercontent.com/zzz2010/5UTR_Optimizer/master/data/df_counts_and_len.TE_sorted.HEK_Andrev2015.with_annot.txt
# RP-PC3
wget https://raw.githubusercontent.com/zzz2010/5UTR_Optimizer/master/data/df_counts_and_len.TE_sorted.pc3.with_annot.txt
# ref
wget https://raw.githubusercontent.com/zzz2010/5UTR_Optimizer/master/data/gencode_v17_5utr_15bpcds.fa
## download the Massively parallel report assay datasets
# MPA_U
wget ftp.ncbi.nlm.nih.gov/geo/samples/GSM3130nnn/GSM3130435/suppl/GSM3130435_egfp_unmod_1.csv.gz
# MPA_H
wget ftp.ncbi.nlm.nih.gov/geo/samples/GSM3130nnn/GSM3130443/suppl/GSM3130443_designed_library.csv.gz
# MPA_V
wget ftp.ncbi.nlm.nih.gov/geo/samples/GSM4084nnn/GSM4084997/suppl/GSM4084997_varying_length_25to100.csv.gz
## dowlaod the yeast dataset
wget ftp.ncbi.nlm.nih.gov/geo/samples/GSM2793nnn/GSM2793752/suppl/GSM2793752_Random_UTRs.csv.gz
gzip -d *.gz
echo "Finished ! All data ready~"
echo "Please step to the pre-proccessing" |