def load(): # load appropriate data from GA4GH
callset_id = sample_id = session['sample_id']
variants, variantset_ids = ga4gh.search_variants(
GENOTYPES,
ga4gh.OKG,
callSetIds=[sample_id],
repo_id='google')
pid = session['patient']
uploads = []
for rsid, variant in variants:
coord = snps.COORDINATES[rsid]
interp = 'positive' if float(snps.DATA[rsid]['Risk']) > 1 else 'negative'
seq = {
'resourceType': 'Sequence',
'type': DNA,
'coordinate': [
{"start": coord['pos']-1,
"end": coord['pos'],
"chromosome": {'text': coord['chromosome']},
"genomeBuild": {'text': 'GRCh37'},
}],
'variation': {'text': rsid},
'species': {'text': 'H**o sapiens'},
"repository": [
{
"url": "https://www.googleapis.com/genomics/v1beta2",
"variantId": variantset_ids
}
]
}
uploads.append(gevent.spawn(upload_seq, seq, session['access_token']))
for g in uploads:
g.join()
return redirect('%s/Sequence' % config.API_BASE)
def get_snps(sample_id):
'''
return sequences mentioned in SNPData.csv
'''
variants = ga4gh.search_variants(GENOTYPES,
ga4gh.OKG,
callSetIds=[sample_id],
repo_id='google')
snps = {}
for rsid, variant in variants:
gts = [variant['referenceBases']]
gts.extend(variant['alternateBases'])
for call in variant['calls']:
if call.get('callSetId') != sample_id:
continue
snps[rsid] = [gts[i] for i in call['genotype']]
return jsonify(snps)
def get_snps(sample_id):
'''
return sequences mentioned in SNPData.csv
'''
variants = ga4gh.search_variants(
GENOTYPES,
ga4gh.OKG,
callSetIds=[sample_id],
repo_id='google')
snps = {}
for rsid, variant in variants:
gts = [variant['referenceBases']]
gts.extend(variant['alternateBases'])
for call in variant['calls']:
if call.get('callSetId') != sample_id:
continue
snps[rsid] = [gts[i] for i in call['genotype']]
return jsonify(snps)
def load(): # load appropriate data from GA4GH
callset_id = sample_id = session['sample_id']
variants, variantset_ids = ga4gh.search_variants(GENOTYPES,
ga4gh.OKG,
callSetIds=[sample_id],
repo_id='google')
pid = session['patient']
uploads = []
for rsid, variant in variants:
coord = snps.COORDINATES[rsid]
interp = 'positive' if float(
snps.DATA[rsid]['Risk']) > 1 else 'negative'
seq = {
'resourceType':
'Sequence',
'type':
DNA,
'coordinate': [{
"start": coord['pos'] - 1,
"end": coord['pos'],
"chromosome": {
'text': coord['chromosome']
},
"genomeBuild": {
'text': 'GRCh37'
},
}],
'variation': {
'text': rsid
},
'species': {
'text': 'H**o sapiens'
},
"repository": [{
"url": "https://www.googleapis.com/genomics/v1beta2",
"variantId": variantset_ids
}]
}
uploads.append(gevent.spawn(upload_seq, seq, session['access_token']))
for g in uploads:
g.join()
return redirect('%s/Sequence' % config.API_BASE)
def load(): # load appropriate data from GA4GH
callset_id = sample_id = session['sample_id']
variants, variantset_ids = ga4gh.search_variants(
GENOTYPES,
ga4gh.OKG,
callSetIds=[sample_id],
repo_id='google')
pid = session['patient']
uploads = []
for rsid, variant in variants:
coord = snps.COORDINATES[rsid]
interp = 'positive' if float(snps.DATA[rsid]['Risk']) > 1 else 'negative'
seq = {
'resourceType': 'Sequence',
'chromosome': {'text': coord['chromosome']},
'start': coord['pos']-1,
'end': coord['pos'],
'genomeBuild': {'text': 'GRCh37'},
'type': 'DNA',
'source': {'text': 'somatic'},
'patient': {'reference': '/Patient/%s' % pid},
'variation': {'text': rsid},
'species': {'text': 'H**o sapiens'},
'analysis': [{
'target': {'text': snps.DATA[rsid]['disease']},
'type': {'text': 'Disease Risk Analysis'},
'interpretation': {'text': interp},
'confidence': 'reviewing'
}],
'gaRepository': ga4gh.REPOSITORIES['google'],
'gaVariantSet': variantset_ids,
'gaCallSet': callset_id
}
uploads.append(gevent.spawn(upload_seq, seq, session['access_token']))
for g in uploads:
g.join()
return redirect('%s/Sequence' % config.API_BASE)
f = TabixFile('snps.sorted.txt.gz', parser=asTuple())
snp_table = {}
for row in f.fetch():
_, snp, chrom, pos = row
if snp in snps or snp in drug_info:
snp_table[snp] = {'chromosome': chrom, 'pos': int(pos)}
with open('snps.py', 'w') as dump:
dump.write(WARNING)
dump.write('COORDINATES = %s\n' % snp_table)
dump.write('DATA = %s\n' % snps)
dump.write('DRUG_INFO = %s\n' % drug_info)
print 'Data written to snps.py'
print 'Determining allele frequencies (using data from 1000 Genomes)'
genotypes = {snp: snp_data['Code'] for snp, snp_data in snps.iteritems()}
variants = list(
ga4gh.search_variants(genotypes, dataset=ga4gh.OKG, repo_id='google'))
# determine allele frequencies for different population
freqs = {
pop: ga4gh.get_frequencies(variants,
genotypes,
population=lambda call: populations.get(
call.get('callSetName')) == pop)
for pop in set(populations.values())
}
# allele frequencies for 1000 Genomes' whole population
freqs['1kg'] = ga4gh.get_frequencies(variants, genotypes)
with open('freq.py', 'w') as dump:
dump.write(WARNING)
dump.write('FREQUENCIES = %s\n' % freqs)
print 'Data written to freq.py.'
snp_table = {}
for row in f.fetch():
_, snp, chrom, pos = row
if snp in snps or snp in drug_info:
snp_table[snp] = {
'chromosome': chrom,
'pos': int(pos)
}
with open('snps.py', 'w') as dump:
dump.write(WARNING)
dump.write('COORDINATES = %s\n'% snp_table)
dump.write('DATA = %s\n'% snps)
dump.write('DRUG_INFO = %s\n'% drug_info)
print 'Data written to snps.py'
print 'Determining allele frequencies (using data from 1000 Genomes)'
genotypes = {snp: snp_data['Code'] for snp, snp_data in snps.iteritems()}
variants = list(ga4gh.search_variants(genotypes, dataset=ga4gh.OKG, repo_id='google'))
# determine allele frequencies for different population
freqs = {
pop: ga4gh.get_frequencies(
variants,
genotypes,
population=lambda call: populations.get(call.get('callSetName'))==pop)
for pop in set(populations.values())}
# allele frequencies for 1000 Genomes' whole population
freqs['1kg'] = ga4gh.get_frequencies(variants, genotypes)
with open('freq.py', 'w') as dump:
dump.write(WARNING)
dump.write('FREQUENCIES = %s\n'% freqs)
print 'Data written to freq.py.'
def load(): # load appropriate data from GA4GH
callset_id = sample_id = session['sample_id']
variants, variantset_ids = ga4gh.search_variants(GENOTYPES,
ga4gh.OKG,
callSetIds=[sample_id],
repo_id='google')
pid = session['patient']
uploads = []
for rsid, variant in variants:
coord = snps.COORDINATES[rsid]
interp = 'positive' if float(
snps.DATA[rsid]['Risk']) > 1 else 'negative'
seq = {
'resourceType':
'Sequence',
'chromosome': {
'text': coord['chromosome']
},
'start':
coord['pos'] - 1,
'end':
coord['pos'],
'genomeBuild': {
'text': 'GRCh37'
},
'type':
'DNA',
'source': {
'text': 'somatic'
},
'patient': {
'reference': '/Patient/%s' % pid
},
'variation': {
'text': rsid
},
'species': {
'text': 'H**o sapiens'
},
'analysis': [{
'target': {
'text': snps.DATA[rsid]['disease']
},
'type': {
'text': 'Disease Risk Analysis'
},
'interpretation': {
'text': interp
},
'confidence': 'reviewing'
}],
'gaRepository':
ga4gh.REPOSITORIES['google'],
'gaVariantSet':
variantset_ids,
'gaCallSet':
callset_id
}
uploads.append(gevent.spawn(upload_seq, seq, session['access_token']))
for g in uploads:
g.join()
return redirect('%s/Sequence' % config.API_BASE)
