def getPhenotypeInfo(self, db, where_condition):
"""
2008-08-29
add -1 as a separator into phenotype_method_id_ls and others
"""
sys.stderr.write("Getting phenotype method info ...")
rows = db.metadata.bind.execute("select distinct r.phenotype_method_id, p.biology_category_id from %s p, %s and p.id=r.phenotype_method_id order by p.biology_category_id, r.phenotype_method_id"\
%(PhenotypeMethod.table.name, where_condition))
phenotype_method_id_ls = []
phenotype_method_id2index = {}
phenotype_method_label_ls = []
prev_biology_category_id = None
no_of_separators = 0
for row in rows:
if prev_biology_category_id == None:
prev_biology_category_id = row.biology_category_id
elif row.biology_category_id != prev_biology_category_id:
prev_biology_category_id = row.biology_category_id
#add a blank phenotype id as separator
no_of_separators += 1
phenotype_method_id2index[-no_of_separators] = len(
phenotype_method_id_ls)
phenotype_method_id_ls.append(-no_of_separators)
phenotype_method_label_ls.append('')
phenotype_method_id2index[row.phenotype_method_id] = len(
phenotype_method_id_ls)
phenotype_method_id_ls.append(row.phenotype_method_id)
pm = PhenotypeMethod.get(row.phenotype_method_id)
phenotype_method_label_ls.append('%s_%s' % (pm.id, pm.short_name))
phenotype_info = PassingData()
phenotype_info.phenotype_method_id2index = phenotype_method_id2index
phenotype_info.phenotype_method_id_ls = phenotype_method_id_ls
phenotype_info.phenotype_method_label_ls = phenotype_method_label_ls
sys.stderr.write("Done.\n")
return phenotype_info
def getPhenotypeInfo(self, db, where_condition):
"""
2008-08-29
add -1 as a separator into phenotype_method_id_ls and others
"""
sys.stderr.write("Getting phenotype method info ...")
rows = db.metadata.bind.execute("select distinct r.phenotype_method_id, p.biology_category_id from %s p, %s and p.id=r.phenotype_method_id order by p.biology_category_id, r.phenotype_method_id"\
%(PhenotypeMethod.table.name, where_condition))
phenotype_method_id_ls = []
phenotype_method_id2index = {}
phenotype_method_label_ls = []
prev_biology_category_id = None
no_of_separators = 0
for row in rows:
if prev_biology_category_id == None:
prev_biology_category_id = row.biology_category_id
elif row.biology_category_id!=prev_biology_category_id:
prev_biology_category_id = row.biology_category_id
#add a blank phenotype id as separator
no_of_separators += 1
phenotype_method_id2index[-no_of_separators] = len(phenotype_method_id_ls)
phenotype_method_id_ls.append(-no_of_separators)
phenotype_method_label_ls.append('')
phenotype_method_id2index[row.phenotype_method_id] = len(phenotype_method_id_ls)
phenotype_method_id_ls.append(row.phenotype_method_id)
pm = PhenotypeMethod.get(row.phenotype_method_id)
phenotype_method_label_ls.append('%s_%s'%(pm.id, pm.short_name))
phenotype_info = PassingData()
phenotype_info.phenotype_method_id2index = phenotype_method_id2index
phenotype_info.phenotype_method_id_ls = phenotype_method_id_ls
phenotype_info.phenotype_method_label_ls = phenotype_method_label_ls
sys.stderr.write("Done.\n")
return phenotype_info
def getResultsMethodIDInfo(self, db, call_method_id_ls, min_distance, get_closest, min_MAF):
"""
2008-09-05
use results_by_gene.id as main result id
"""
sys.stderr.write("Gettiing ResultsMethodIDInfo ...")
results_method_id_info = PassingData()
results_method_id_ls = []
results_method_id2index = {}
results_method_id_label_ls = []
rows = db.metadata.bind.execute("select distinct rg.id, rg.results_method_id, r.analysis_method_id, r.phenotype_method_id, \
p.biology_category_id from %s rg, %s r, %s p \
where rg.results_method_id=r.id and p.id=r.phenotype_method_id and r.call_method_id in (%s) \
and rg.min_distance=%s and rg.get_closest=%s and rg.min_MAF>=%s-0.0001 and rg.min_MAF<=%s+0.0001 \
order by p.biology_category_id, r.phenotype_method_id, r.analysis_method_id"%(ResultsByGene.table.name, \
ResultsMethod.table.name, PhenotypeMethod.table.name, repr(call_method_id_ls)[1:-1], min_distance, get_closest, min_MAF, min_MAF))
prev_phenotype_method_id = None
prev_biology_category_id = None
no_of_separators = 0
for row in rows:
if prev_biology_category_id==None:
prev_biology_category_id = row.biology_category_id
elif row.biology_category_id!=prev_biology_category_id:
prev_biology_category_id = row.biology_category_id
no_of_separators += 1
results_method_id2index[-no_of_separators] = len(results_method_id_ls)
results_method_id_ls.append(-no_of_separators)
results_method_id_label_ls.append('')
if prev_phenotype_method_id == None:
prev_phenotype_method_id = row.phenotype_method_id
elif row.phenotype_method_id!=prev_phenotype_method_id:
prev_phenotype_method_id = row.phenotype_method_id
#add a blank phenotype id as separator
no_of_separators += 1
results_method_id2index[-no_of_separators] = len(results_method_id_ls)
results_method_id_ls.append(-no_of_separators)
results_method_id_label_ls.append('')
results_method_id2index[row.id] = len(results_method_id_ls)
results_method_id_ls.append(row.id)
am = AnalysisMethod.get(row.analysis_method_id)
pm = PhenotypeMethod.get(row.phenotype_method_id)
results_method_id_label_ls.append('%s_%s_%s'%(am.short_name, pm.short_name, pm.id))
results_method_id_info.results_method_id_ls = results_method_id_ls
results_method_id_info.results_method_id2index = results_method_id2index
results_method_id_info.results_method_id_label_ls = results_method_id_label_ls
sys.stderr.write("%s results. Done.\n"%(len(results_method_id_ls)))
return results_method_id_info
def findPhenotypeMethodGivenName(self, phenotype_name, db):
"""
2009-7-30
find/create the db phenotype entry given phenotype_name
"""
session = db.session
if phenotype_name: #if the short name is given, forget about phenotype_id
if phenotype_name in self.phenotype_name2pm:
return self.phenotype_name2pm.get(phenotype_name)
pm = PhenotypeMethod.query.filter_by(
short_name=phenotype_name).first() #try search the db first.
if not pm:
pm = PhenotypeMethod(short_name=phenotype_name)
session.save(pm)
session.flush()
if self.report:
sys.stderr.write("phenotype ID for %s is %s." %
(phenotype_name, pm.id))
self.phenotype_name2pm[phenotype_name] = pm
return pm
