def type(self, id=None):
ScoreRankHistogram = model.Stock_250kDB.ScoreRankHistogram
ScoreRankHistogramType = model.Stock_250kDB.ScoreRankHistogramType
query = ScoreRankHistogram.query
if id is None:
id = request.params.get('id', 1)
hist_type_id = id
extra_condition = 's.hist_type_id=%s'%hist_type_id
c.phenotype_info = hc.getPhenotypeInfo(ScoreRankHistogram.table.name, extra_condition)
c.list_info = hc.getListTypeInfo(ScoreRankHistogram.table.name, extra_condition)
c.hist_type = ScoreRankHistogramType.get(hist_type_id)
rows = query.filter_by(hist_type_id=hist_type_id).all()
data_matrix = numpy.zeros([len(c.list_info.list_type_id_ls), len(c.phenotype_info.phenotype_method_id_ls)], numpy.int)
data_matrix[:] = -1
counter = 0
for row in rows:
row_index = c.list_info.list_type_id2index[row.list_type_id]
col_index = c.phenotype_info.phenotype_method_id2index[row.phenotype_method_id]
data_matrix[row_index, col_index] = row.id
counter +=1
c.counter = counter
c.data_matrix = data_matrix
return render('/score_rank_histgram_type.html')
def getGeneListTypeLsGivenTypeAndPhenotypeMethodAndAnalysisMethod(): """ 2009-3-4 called by getGeneListTypeLsGivenTypeAndPhenotypeMethodAndAnalysisMethodJson() """ #if not affiliated_table_name: # affiliated_table_name = model.Stock_250kDB.CandidateGeneTopSNPTestRM.table.name #alias is 's' #extra_tables = ' %s c '%model.Stock_250kDB.ResultsMethod.table.name #extra_condition = 's.results_id=c.id and s.type_id=%s and c.call_method_id=%s and c.phenotype_method_id=%s and c.analysis_method_id=%s'%\ # (type_id, call_method_id, phenotype_method_id, analysis_method_id) list_info = hc.getListTypeInfo(affiliated_table_name=None, extra_condition=None, extra_tables=None) ls = [[0, u'No candidate gene list. (All SNPs)']] for i in range(len(list_info.list_type_id_ls)): id = list_info.list_type_id_ls[i] label = list_info.list_type_label_ls[i] ls.append([id, label]) return ls
def getGeneListTypeLsGivenTypeAndPhenotypeMethodAndAnalysisMethod(type_id, call_method_id, phenotype_method_id, analysis_method_id, affiliated_table_name=None): """ 2009-2-22 add argument affiliated_table_name (but not used) 2008-12-30 """ if not affiliated_table_name: affiliated_table_name = model.Stock_250kDB.CandidateGeneTopSNPTestRM.table.name #alias is 's' extra_tables = ' %s c '%model.Stock_250kDB.ResultsMethod.table.name extra_condition = 's.results_id=c.id and s.type_id=%s and c.call_method_id=%s and c.phenotype_method_id=%s and c.analysis_method_id=%s'%\ (type_id, call_method_id, phenotype_method_id, analysis_method_id) list_info = hc.getListTypeInfo(affiliated_table_name, extra_condition=extra_condition, extra_tables=extra_tables) ls = [] for i in range(len(list_info.list_type_id_ls)): id = list_info.list_type_id_ls[i] label = list_info.list_type_label_ls[i] ls.append([id, label]) return ls
def type(cls, id=None, TypeClass=model.Stock_250kDB.CandidateGeneTopSNPTestRMType, \
template='/display_top_snp_test_rm_type.html', \
phenotype_id_ls_str = '1-7,39-61,80-82,9-13,32-38,65-74', \
list_type_id_ls_str = '3,6,8,28,51,64,65,68,71,76,129,24,29,30,130,131',\
analysis_method_id_ls_str = '1,5,6,7',\
figure_type=1, call_method_id=17):
"""
2009-10-13
allow user to specify phenotype_id_ls_str and list_type_id_ls_str in URL
add figure_type argument:
1: candidate vs non-candidate ratio (in db beforehand)
2: 2D matrix-plot of pvalue for enrichment statistic. row is cutoff. column is distance between gene and SNP.
add call_method_id argument
add argument analysis_method_id_ls_str
2008-10-30
generalized so that DisplayResultsGene could call it
"""
ResultsMethod = model.Stock_250kDB.ResultsMethod
if id is None:
id = request.params.get('id', '1')
phenotype_id_ls_str = request.params.get('phenotype_id_ls_str', phenotype_id_ls_str) # 2009-10-13
list_type_id_ls_str = request.params.get('list_type_id_ls_str', list_type_id_ls_str) # 2009-10-13
analysis_method_id_ls_str = request.params.get('analysis_method_id_ls_str', analysis_method_id_ls_str) # 2009-10-13
c.figure_type = request.params.get('figure_type', figure_type) # 2009-10-13
call_method_id = request.params.get('call_method_id', call_method_id) # 2009-10-13
phenotype_id_ls = getListOutOfStr(phenotype_id_ls_str, data_type=str)
list_type_id_ls = getListOutOfStr(list_type_id_ls_str, data_type=str)
analysis_method_id_ls = getListOutOfStr(analysis_method_id_ls_str, data_type=int)
#extra_tables = ' %s c '%(CandidateGeneTopSNPTestRM.table.name)
extra_condition = 'p.id in (%s)'%(','.join(phenotype_id_ls))
c.phenotype_info = hc.getPhenotypeInfo(extra_condition=extra_condition, extra_tables=None)
#extra_condition = 's.type_id =%s'%id
extra_condition = 'p.id in (%s)'%(','.join(list_type_id_ls))
c.list_info = hc.getListTypeInfo(extra_condition=extra_condition)
data_matrix = []
no_of_rows = len(c.list_info.list_type_id_ls)
no_of_cols = len(c.phenotype_info.phenotype_method_id_ls)
for i in range(no_of_rows):
data_matrix.append([None]*no_of_cols)
c.type = TypeClass.get(id)
#2008-10-29 a faster way to come up the data_matrix but data is not guaranteed inside
rows = ResultsMethod.query.filter(ResultsMethod.phenotype_method_id.in_(map(int, phenotype_id_ls))).\
filter(ResultsMethod.analysis_method_id.in_(analysis_method_id_ls)).\
filter_by(call_method_id=call_method_id).\
order_by(ResultsMethod.analysis_method_id)
counter = 0
for row in rows:
col_index = c.phenotype_info.phenotype_method_id2index.get(row.phenotype_method_id)
if col_index is None:
continue
for list_type_id, row_index in c.list_info.list_type_id2index.iteritems():
if list_type_id>0:
if data_matrix[row_index][col_index] is None:
data_matrix[row_index][col_index] = []
data_matrix[row_index][col_index].append((row.id, row.analysis_method.short_name))
counter +=1
"""
rows = CandidateGeneTopSNPTestRM.query.filter_by(type_id=id)
for row in rows:
row_index = c.list_info.list_type_id2index[row.list_type_id]
col_index = c.phenotype_info.phenotype_method_id2index[row.result.phenotype_method_id]
if data_matrix[row_index][col_index] is None:
data_matrix[row_index][col_index] = Set()
data_matrix[row_index][col_index].add(row.results_id)
counter +=1
"""
c.counter = counter
c.data_matrix = data_matrix
return render(template)
