def orderListTypeAnalysisMethodID(self, list_type_id_ls, analysis_method_id_ls):
"""
2008-08-29
deal with separator (list_type_id=-1) in list_type_id_ls
"""
sys.stderr.write("Orderinig list type id and analysis_method id ... ")
list_type_id_analysis_method_id_ls = []
list_type_id_analysis_method_id2index = {}
list_type_analysis_method_label_ls = []
no_of_separators = 0
for list_type_id in list_type_id_ls:
if list_type_id==-1: #separator
no_of_separators += 1
tup = (-no_of_separators,-1)
list_type_id_analysis_method_id2index[tup] = len(list_type_id_analysis_method_id_ls)
list_type_id_analysis_method_id_ls.append(tup)
list_type_analysis_method_label_ls.append('')
continue
list_type_short_name = GeneListType.get(list_type_id).short_name
for analysis_method_id in analysis_method_id_ls:
analysis_method_short_name = AnalysisMethod.get(analysis_method_id).short_name
tup = (list_type_id, analysis_method_id)
list_type_id_analysis_method_id2index[tup] = len(list_type_id_analysis_method_id_ls)
list_type_id_analysis_method_id_ls.append(tup)
list_type_analysis_method_label_ls.append('%s_%s_%s'%(analysis_method_short_name, list_type_short_name, list_type_id))
return_data = PassingData()
return_data.list_type_id_analysis_method_id_ls = list_type_id_analysis_method_id_ls
return_data.list_type_id_analysis_method_id2index = list_type_id_analysis_method_id2index
return_data.list_type_analysis_method_label_ls = list_type_analysis_method_label_ls
sys.stderr.write("Done.\n")
return return_data
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 orderListTypeAnalysisMethodID(self, list_type_id_ls,
analysis_method_id_ls):
"""
2008-08-29
deal with separator (list_type_id=-1) in list_type_id_ls
"""
sys.stderr.write("Orderinig list type id and analysis_method id ... ")
list_type_id_analysis_method_id_ls = []
list_type_id_analysis_method_id2index = {}
list_type_analysis_method_label_ls = []
no_of_separators = 0
for list_type_id in list_type_id_ls:
if list_type_id == -1: #separator
no_of_separators += 1
tup = (-no_of_separators, -1)
list_type_id_analysis_method_id2index[tup] = len(
list_type_id_analysis_method_id_ls)
list_type_id_analysis_method_id_ls.append(tup)
list_type_analysis_method_label_ls.append('')
continue
list_type_short_name = GeneListType.get(list_type_id).short_name
for analysis_method_id in analysis_method_id_ls:
analysis_method_short_name = AnalysisMethod.get(
analysis_method_id).short_name
tup = (list_type_id, analysis_method_id)
list_type_id_analysis_method_id2index[tup] = len(
list_type_id_analysis_method_id_ls)
list_type_id_analysis_method_id_ls.append(tup)
list_type_analysis_method_label_ls.append(
'%s_%s_%s' % (analysis_method_short_name,
list_type_short_name, list_type_id))
return_data = PassingData()
return_data.list_type_id_analysis_method_id_ls = list_type_id_analysis_method_id_ls
return_data.list_type_id_analysis_method_id2index = list_type_id_analysis_method_id2index
return_data.list_type_analysis_method_label_ls = list_type_analysis_method_label_ls
sys.stderr.write("Done.\n")
return return_data
