Download necessary data for Trait-o-matic core

trait_data.sh

sudo mkdir /var/trait
sudo wget http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/hg18.2bit -O /var/trait/hg18.2bit

cd

# dbSNP (only two tables)
wget ftp://ftp.ncbi.nih.gov:21/snp/organisms/human_9606/database/organism_data/OmimVarLocusIdSNP.bcp.gz
wget ftp://ftp.ncbi.nih.gov:21/snp/organisms/human_9606/database/organism_data/b129/b129_SNPChrPosOnRef_36_3.bcp.gz
gunzip OmimVarLocusIdSNP.bcp.gz
gunzip b129_SNPChrPosOnRef_36_3.bcp.gz

# HapMap
wget -r -l1 --no-parent http://ftp.hapmap.org/frequencies/2009-02_phaseII+III/forward/non-redundant/
rm -f ftp.hapmap.org/frequencies/2009-02_phaseII+III/forward/non-redundant/index.*
gunzip ftp.hapmap.org/frequencies/2009-02_phaseII+III/forward/non-redundant/allele_*
# -- load HapMap data immediately (this may take several hours in the background)
sudo python /usr/share/trait/hapmap_load_database.py ftp.hapmap.org/frequencies/2009-02_phaseII+III/forward/non-redundant/allele_* &

# morbidmap/OMIM
wget ftp://ftp.ncbi.nih.gov/repository/OMIM/morbidmap -O morbidmap.txt

# OMIM
wget ftp://ftp.ncbi.nih.gov/repository/OMIM/omim.txt.Z -O omim.txt.Z
gunzip omim.txt.Z
python /usr/share/trait/omim_print_variants.py omim.txt > omim.tsv

# refFlat/UCSC
wget http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/refFlat.txt.gz -O refFlat.txt.gz
gunzip refFlat.txt.gz

# snp/UCSC
wget http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/snp129.txt.gz -O snp129.txt.gz
gunzip snp129.txt.gz
# -- load these data immediately (note the use of password)
mysql -uupdater -pshakespeare -e "USE caliban; LOAD DATA LOCAL INFILE '~/snp129.txt' INTO TABLE snp129 FIELDS TERMINATED BY '\t' LINES TERMINATED BY '\n';"

# SNPedia (retrieval may take up to 30 min with no visual response)
python /usr/share/trait/snpedia.py > snpedia.txt
# -- clean up some descriptive text
sed -i'.bak'  's/ (None)//' snpedia.txt
awk 'BEGIN { FS = "\t" }; ($5 !~ /(^normal)|(^\?)/ || $5 ~ /;/)' snpedia.txt > snpedia.filtered.txt
python /usr/share/trait/snpedia_print_genotypes.py snpedia.filtered.txt > snpedia.tsv