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Makefile
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create:
./db_create.py
./db_migrate.py
migrate:
./db_migrate
clean:
rm freq_api/*.pyc
rm freq_api/static/app.db
rm -rf freq_api/static/db_repository/
sample:
./db_fill_freqs.py freq_api/static/data/1000genomes/1000genomes.chr22.phase3.frq.strat.sample.gz 1000genomes_phase3
./db_fill_rsIDs.py freq_api/static/data/rsIDs/GRCh37/bed_chr_22.bed.sample.gz GRCh37
./db_fill_coordinates.py freq_api/static/data/1000genomes/1000genomes_phase3_coordinates.txt 1000genomes_phase3
serve:
python run.py
restart:
sudo service apache2 reload
sudo service apache2 restart
snp:
curl "http://127.0.0.1:5000/freq?dataset=1000genomes_phase3&pos=22:16050069"
snp2:
curl "http://127.0.0.1:5000/freq?dataset=1000genomes_phase3&pos=1:752566"
snp3:
curl "http://127.0.0.1:5000/freq?dataset=1000genomes_phase3&pos=22:16050607"
snp4:
curl "http://127.0.0.1:5000/freq?dataset=1000genomes_phase3&pos=22:27569979"
rsID:
curl "http://127.0.0.1:5000/freq?dataset=1000genomes_phase3&rsID=rs1056"
rsID2:
curl "http://127.0.0.1:5000/freq?dataset=1000genomes_phase3&rsID=rs587776127"
random:
curl "http://127.0.0.1:5000/freq?dataset=1000genomes_phase3&random=True"
fill_rsIDs:
./db_fill_rsIDs.py freq_api/static/data/rsIDs/hg18/snp130.txt.gz hg18
./db_fill_rsIDs.py freq_api/static/data/rsIDs/hg19/snp141.txt.gz hg19
1000genomes: 1000genomes_chr1 1000genomes_chr2 1000genomes_chr3 1000genomes_chr4 1000genomes_chr5 1000genomes_chr6 1000genomes_chr7 1000genomes_chr8 1000genomes_chr9 1000genomes_chr10 1000genomes_chr11 1000genomes_chr12 1000genomes_chr13 1000genomes_chr14 1000genomes_chr15 1000genomes_chr16 1000genomes_chr17 1000genomes_chr18 1000genomes_chr19 1000genomes_chr20 1000genomes_chr21 1000genomes_chr22
./db_fill_coordinates.py freq_api/static/data/1000genomes/1000genomes_phase3_coordinates.txt 1000genomes_phase3
1000genomes_chr1:
./db_fill_freqs.py freq_api/static/data/1000genomes/1000genomes.chr1.phase3.frq.strat.gz 1000genomes_phase3
./db_fill_rsIDs.py freq_api/static/data/rsIDs/GRCh37/bed_chr_1.bed.gz GRCh37
1000genomes_chr2:
./db_fill_freqs.py freq_api/static/data/1000genomes/1000genomes.chr2.phase3.frq.strat.gz 1000genomes_phase3
./db_fill_rsIDs.py freq_api/static/data/rsIDs/GRCh37/bed_chr_2.bed.gz GRCh37
1000genomes_chr3:
./db_fill_freqs.py freq_api/static/data/1000genomes/1000genomes.chr3.phase3.frq.strat.gz 1000genomes_phase3
./db_fill_rsIDs.py freq_api/static/data/rsIDs/GRCh37/bed_chr_3.bed.gz GRCh37
1000genomes_chr4:
./db_fill_freqs.py freq_api/static/data/1000genomes/1000genomes.chr4.phase3.frq.strat.gz 1000genomes_phase3
./db_fill_rsIDs.py freq_api/static/data/rsIDs/GRCh37/bed_chr_4.bed.gz GRCh37
1000genomes_chr5:
./db_fill_freqs.py freq_api/static/data/1000genomes/1000genomes.chr5.phase3.frq.strat.gz 1000genomes_phase3
./db_fill_rsIDs.py freq_api/static/data/rsIDs/GRCh37/bed_chr_5.bed.gz GRCh37
1000genomes_chr6:
./db_fill_freqs.py freq_api/static/data/1000genomes/1000genomes.chr6.phase3.frq.strat.gz 1000genomes_phase3
./db_fill_rsIDs.py freq_api/static/data/rsIDs/GRCh37/bed_chr_6.bed.gz GRCh37
1000genomes_chr7:
./db_fill_freqs.py freq_api/static/data/1000genomes/1000genomes.chr7.phase3.frq.strat.gz 1000genomes_phase3
./db_fill_rsIDs.py freq_api/static/data/rsIDs/GRCh37/bed_chr_7.bed.gz GRCh37
1000genomes_chr8:
./db_fill_freqs.py freq_api/static/data/1000genomes/1000genomes.chr8.phase3.frq.strat.gz 1000genomes_phase3
./db_fill_rsIDs.py freq_api/static/data/rsIDs/GRCh37/bed_chr_8.bed.gz GRCh37
1000genomes_chr9:
./db_fill_freqs.py freq_api/static/data/1000genomes/1000genomes.chr9.phase3.frq.strat.gz 1000genomes_phase3
./db_fill_rsIDs.py freq_api/static/data/rsIDs/GRCh37/bed_chr_9.bed.gz GRCh37
1000genomes_chr10:
./db_fill_freqs.py freq_api/static/data/1000genomes/1000genomes.chr10.phase3.frq.strat.gz 1000genomes_phase3
./db_fill_rsIDs.py freq_api/static/data/rsIDs/GRCh37/bed_chr_10.bed.gz GRCh37
1000genomes_chr11:
./db_fill_freqs.py freq_api/static/data/1000genomes/1000genomes.chr11.phase3.frq.strat.gz 1000genomes_phase3
./db_fill_rsIDs.py freq_api/static/data/rsIDs/GRCh37/bed_chr_11.bed.gz GRCh37
1000genomes_chr12:
./db_fill_freqs.py freq_api/static/data/1000genomes/1000genomes.chr12.phase3.frq.strat.gz 1000genomes_phase3
./db_fill_rsIDs.py freq_api/static/data/rsIDs/GRCh37/bed_chr_12.bed.gz GRCh37
1000genomes_chr13:
./db_fill_freqs.py freq_api/static/data/1000genomes/1000genomes.chr13.phase3.frq.strat.gz 1000genomes_phase3
./db_fill_rsIDs.py freq_api/static/data/rsIDs/GRCh37/bed_chr_13.bed.gz GRCh37
1000genomes_chr14:
./db_fill_freqs.py freq_api/static/data/1000genomes/1000genomes.chr14.phase3.frq.strat.gz 1000genomes_phase3
./db_fill_rsIDs.py freq_api/static/data/rsIDs/GRCh37/bed_chr_14.bed.gz GRCh37
1000genomes_chr15:
./db_fill_freqs.py freq_api/static/data/1000genomes/1000genomes.chr15.phase3.frq.strat.gz 1000genomes_phase3
./db_fill_rsIDs.py freq_api/static/data/rsIDs/GRCh37/bed_chr_15.bed.gz GRCh37
1000genomes_chr16:
./db_fill_freqs.py freq_api/static/data/1000genomes/1000genomes.chr16.phase3.frq.strat.gz 1000genomes_phase3
./db_fill_rsIDs.py freq_api/static/data/rsIDs/GRCh37/bed_chr_16.bed.gz GRCh37
1000genomes_chr17:
./db_fill_freqs.py freq_api/static/data/1000genomes/1000genomes.chr17.phase3.frq.strat.gz 1000genomes_phase3
./db_fill_rsIDs.py freq_api/static/data/rsIDs/GRCh37/bed_chr_17.bed.gz GRCh37
1000genomes_chr18:
./db_fill_freqs.py freq_api/static/data/1000genomes/1000genomes.chr18.phase3.frq.strat.gz 1000genomes_phase3
./db_fill_rsIDs.py freq_api/static/data/rsIDs/GRCh37/bed_chr_18.bed.gz GRCh37
1000genomes_chr19:
./db_fill_freqs.py freq_api/static/data/1000genomes/1000genomes.chr19.phase3.frq.strat.gz 1000genomes_phase3
./db_fill_rsIDs.py freq_api/static/data/rsIDs/GRCh37/bed_chr_19.bed.gz GRCh37
1000genomes_chr20:
./db_fill_freqs.py freq_api/static/data/1000genomes/1000genomes.chr20.phase3.frq.strat.gz 1000genomes_phase3
./db_fill_rsIDs.py freq_api/static/data/rsIDs/GRCh37/bed_chr_20.bed.gz GRCh37
1000genomes_chr21:
./db_fill_freqs.py freq_api/static/data/1000genomes/1000genomes.chr21.phase3.frq.strat.gz 1000genomes_phase3
./db_fill_rsIDs.py freq_api/static/data/rsIDs/GRCh37/bed_chr_21.bed.gz GRCh37
1000genomes_chr22:
./db_fill_freqs.py freq_api/static/data/1000genomes/1000genomes.chr22.phase3.frq.strat.gz 1000genomes_phase3
./db_fill_rsIDs.py freq_api/static/data/rsIDs/GRCh37/bed_chr_22.bed.gz GRCh37
22:
./db_fill_freqs.py freq_api/static/data/1000genomes/1000genomes.chr22.phase3.frq.strat.gz 1000genomes_phase3
./db_fill_rsIDs.py freq_api/static/data/rsIDs/GRCh37/bed_chr_22.bed.gz GRCh37
./db_fill_coordinates.py freq_api/static/data/1000genomes/1000genomes_phase3_coordinates.txt 1000genomes_phase3