def results(res, field, mark):
for doc in res:
index_id = doc['_id']
query = doc['_source'][field]
index = doc['_index']
output_formatter.output('%s\t%s\t%s' % (query, index_id, index),
output, True)
def sample_query(*argv):
if type(argv[0]) == list:
samples = argv[0]
else:
samples = argv
output_formatter.output('Query: %s' % ' '.join(samples), output, False)
try:
for samp in samples:
output_formatter.output(samp, output, True)
output_formatter.output(
'S_SAMPLEID\tS_SUBJECTID\tS_STUDYID\tALIASTYPE\tALIASID',
output, True)
sample = Sample()
sample.select(lv, S_SAMPLEID=samp)
sf = SampleFamily()
sf.select(lv, S_SAMPLEFAMILYID=sample.SAMPLEFAMILYID)
subject = Subject()
subject.select(lv, S_SUBJECTID=sf.SUBJECTID)
cohort = Cohort()
cohort.select(lv, SUBJECTID=subject.S_SUBJECTID)
aliases = SDIAlias.selectAll(lv, KEYID1=subject.S_SUBJECTID)
for alias in aliases:
output_formatter.output(
'%s\t%s\t%s\t%s' % (subject.S_SUBJECTID, cohort.STUDYID,
alias['ALIASTYPE'], alias['ALIASID']),
output, True)
except Exception as e:
print e
def redmine_query(*argv):
if type(argv[0]) == list:
keywords = argv[0]
else:
keywords = argv
output_formatter.output('Query: %s\n' % ' '.join(keywords), output, False)
output_formatter.output('ID\tCategory\tSubject\tPath', output, True)
for keyword in keywords:
try:
datasets = Issue.find(None,
None,
tracker='Dataset',
project_id=keyword)
datasets = json.loads(datasets[0].to_json())
for ds in datasets['issue']['issues']:
path = 'N/A'
for cf in ds.get('custom_fields', []):
if cf['name'] == 'URL':
path = cf['value']
category = 'N/A'
if 'category' in ds:
category = ds['category']['name']
output_formatter.output(
'%s\t%s\t"%s"\t(%s)' %
(ds['id'], category, ds['subject'], path), output, True)
except:
output_formatter.output('No results found for %s' % arg, output,
True)
def marker_query(*argv):
if type(argv[0]) == list:
markers = argv[0]
else:
markers = argv
output_formatter.output('Query: %s' % ' '.join(markers), output, False)
output_formatter.output('Marker\tIndex ID\tIndex', output, True)
for marker in markers:
docs = ['vcf_record']
q = {'query': {'bool': {'must': [{'match': {'id': marker}}]}}}
res = es.search(index=index, doc_type=docs, body=q)
res_filtered = strictCheck(res, 'id', marker)
results(res_filtered, 'id', 'marker')
def results(res):
data = []
for doc in res['hits']['hits']:
rsid = doc['_source']['id']
chrom = doc['_source']['chrom']
start = doc['_source']['start_pos']
alleles = doc['_source']['alleles']
ref = None
alts_list = []
for i in range(0,len(alleles)):
if len(alleles[i]) == 2:
ref = alleles[i].get('allele')
else:
alts_list.append(alleles[i].get('allele'))
alts = ''.join(alts_list)
ind = doc['_index']
output_formatter.output('%s\t%s:%s\t%s\t%s\t%s' % (rsid, chrom, start, ref, alts, ind), output, True)
def subject_query(*argv):
if type(argv[0]) == list:
subjects = argv[0]
else:
subjects = argv
output_formatter.output('Query: %s' % ' '.join(subjects), output, False)
output_formatter.output('Subject\tIndex ID\tIndex', output, False)
for subject in subjects:
docs = ['plink_fam_record']
q = {'query': {'bool': {'must': [{'match': {'subject_id': subject}}]}}}
res = es.search(index=index, doc_type=docs, body=q)
if strict:
res = strictCheck(res, 'subject_id', subject)
else:
res = res['hits']['hits']
results(res, 'subject_id', 'subjectID')
def marker_query(*argv):
if re.match('^rs\d+', argv[0]):
index = getCurrentIndex()
rsids = argv
else:
index = argv[0]
rsids = argv[1:]
output_formatter.output('Query: %s' % ' '.join(argv), output, False)
output_formatter.output('rs number\tlocation\treference allele\talternative allele\tindex', output, True)
for rsid in rsids:
q = {
'query': {
'bool': {
'must': [{'match': {'id': rsid}}]
}
}
}
res = es.search(index=index, size=10000, body=q)
results(res)
def keyword_query(*argv):
if type(argv[0]) == list:
keywords = argv[0]
else:
keywords = argv
output_formatter.output('Query: %s\n' % ' '.join(keywords), output, False)
output_formatter.output('ID\tType\tIndex\tPath', output, True)
for keyword in keywords:
indices = []
search_ind = []
for index in es.indices.get_alias("*"):
if keyword.lower() in index.lower():
res = es.search(index=index)
search_ind.append(res)
for result in search_ind:
for ind in result['hits']['hits']:
path = 'N/A'
if 'path' in ind:
path = ind['path']
output_formatter.output(
'%s\t%s\t"%s"\t(%s)' %
(ind['_id'], ind['_type'], ind['_index'], path), output,
True)
def subject_query(*argv):
if type(argv[0]) == list:
subjects = argv[0]
else:
subjects = argv
output_formatter.output('Query: %s' % ' '.join(subjects), output, False)
for sub in subjects:
try:
subject = Subject()
subject.select(lv, S_SUBJECTID=sub)
cohort = Cohort()
cohort.select(lv, SUBJECTID=sub)
output_formatter.output(sub, output, True)
for (k, v) in subject.__dict__.items():
output_formatter.output('%s\t%s' % (k, v), output, True)
for (k, v) in cohort.__dict__.items():
output_formatter.output('%s\t%s' % (k, v), output, True)
except Exception as e:
output_formatter.output(e, output, True)
def chrom_query(*argv):
if re.match('^\d:\d+', argv[0]):
index = getCurrentIndex()
locs = argv
else:
index = argv[0]
locs = argv[1:]
output_formatter.output('Query: %s' % ' '.join(argv), output, False)
output_formatter.output('rs number\tlocation\treference allele\talternative allele\tindex', output, True)
for loc in locs:
(chrom, position) = loc.split(':')
q = {
'query': {
'bool': {
'minimum_should_match': '1',
'must': [{'match': {'chrom': chrom}}],
'should': [{'match': {'start_pos': position}}]
}
}
}
res = es.search(index=index, size=10000, body=q)
return results(res)
def alias_query(*argv):
if type(argv[0]) == list:
aliases = argv[0]
else:
aliases = argv
output_formatter.output('Query: %s' % ' '.join(aliases), output, False)
for alias in aliases:
output_formatter.output(alias, output, True)
output_formatter.output('S_SAMPLEID\tS_SUBJECTID\tS_STUDYID', output,
True)
alias_list = SDIAlias().selectAll(lv, ALIASID=alias)
n = len(alias_list)
for a in alias_list:
sid = a['KEYID1'].strip()
study = a['KEYID2']
if sid.startswith('S-'):
s = Sample()
s.select(lv, S_SAMPLEID=sid)
sf = SampleFamily()
sf.select(lv, S_SAMPLEFAMILYID=s.SAMPLEFAMILYID)
subj = sf.SUBJECTID
elif sid.startswith('ST-'):
subj = sid
else:
raise ValueError(sid)
if not study or study == '(null)':
try:
coh = Cohort()
coh.select(lv, SUBJECTID=subj)
study = coh.STUDYID
except:
study = 'N/A'
output_formatter.output('%s\t%s\t%s' % (sid, subj, study), output,
True)
def bim_query(*argv):
if argv[0].endswith('.bim'):
index = getCurrentIndex()
bims = argv
else:
index = argv[0]
bims = argv[1:]
output_formatter.output('Query: %s' % ' '.join(argv), output, False)
for bim in bims:
rsids = numpy.genfromtxt(bim, dtype='str')[:,1].tolist()
output_formatter.output('%s' % bim, output, True)
output_formatter.output('rs number\tlocation\treference allele\talternative allele\tindex', output, True)
for rsid in rsids:
q = {
'query': {
'bool': {
'must': [{'match': {'id': rsid}}]
}
}
}
res = es.search(index=index, size=10000, body=q)
results(res)
