diff options
| -rwxr-xr-x | wqflask/base/data_set.py | 2 | ||||
| -rwxr-xr-x | wqflask/base/mrna_assay_tissue_data.py | 5 | ||||
| -rwxr-xr-x | wqflask/wqflask/correlation/show_corr_results.py | 41 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/show_trait_calculate_correlations.html | 10 |
4 files changed, 22 insertions, 36 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 427fd991..d6a46c2e 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -1257,7 +1257,7 @@ class MrnaAssayDataSet(DataSet): Strain.Name """ % (escape(trait), escape(self.name)) results = g.db.execute(query).fetchall() - print("RETRIEVED RESULTS HERE:", results) + #print("RETRIEVED RESULTS HERE:", results) return results diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py index b2c0448a..54a7ce8e 100755 --- a/wqflask/base/mrna_assay_tissue_data.py +++ b/wqflask/base/mrna_assay_tissue_data.py @@ -40,7 +40,6 @@ class MrnaAssayTissueData(object): # with highest mean value # Due to the limit size of TissueProbeSetFreezeId table in DB, # performance of inner join is acceptable.MrnaAssayTissueData(gene_symbols=symbol_list) - #print("len(gene_symbols): ", len(gene_symbols)) if len(gene_symbols) == 0: query += '''Symbol!='' and Symbol Is Not Null group by Symbol) as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol @@ -49,9 +48,11 @@ class MrnaAssayTissueData(object): else: in_clause = db_tools.create_in_clause(gene_symbols) + #ZS: This was in the query, not sure why: http://docs.python.org/2/library/string.html?highlight=lower#string.lower + query += ''' Symbol in {} group by Symbol) as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol - and t.Mean = x.maxmean;http://docs.python.org/2/library/string.html?highlight=lower#string.lower + and t.Mean = x.maxmean; '''.format(in_clause) results = g.db.execute(query).fetchall() diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index af8bb2ab..2612857f 100755 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -112,19 +112,19 @@ class CorrelationResults(object): self.p_range_lower = float(start_vars['p_range_lower']) self.p_range_upper = float(start_vars['p_range_upper']) - if ('min_loc_chr' in start_vars and - 'max_loc_chr' in start_vars and + if ('loc_chr' in start_vars and 'min_loc_mb' in start_vars and 'max_loc_mb' in start_vars): - self.min_location_chr = start_vars['min_loc_chr'] - self.max_location_chr = start_vars['max_loc_chr'] + self.location_chr = start_vars['loc_chr'] if start_vars['min_loc_mb'].isdigit(): self.min_location_mb = start_vars['min_loc_mb'] else: - self.min_location_mb = 0 + self.min_location_mb = None if start_vars['max_loc_mb'].isdigit(): self.max_location_mb = start_vars['max_loc_mb'] + else: + self.max_location_mb = None self.get_formatted_corr_type() self.return_number = int(start_vars['corr_return_results']) @@ -149,7 +149,6 @@ class CorrelationResults(object): if corr_samples_group == 'samples_other': primary_samples = [x for x in primary_samples if x not in ( self.dataset.group.parlist + self.dataset.group.f1list)] - print("primary_samples:", primary_samples) self.process_samples(start_vars, self.this_trait.data.keys(), primary_samples) self.target_dataset = data_set.create_dataset(start_vars['corr_dataset']) @@ -185,16 +184,12 @@ class CorrelationResults(object): if self.dataset.type == "ProbeSet" or self.dataset.type == "Geno": #ZS: Convert min/max chromosome to an int for the location range option - min_chr_as_int = 1 - max_chr_as_int = 30 #Just to make sure all are included if user inputs nothing + range_chr_as_int = None for order_id, chr_info in self.dataset.species.chromosomes.chromosomes.iteritems(): - if chr_info.name == self.min_location_chr: - min_chr_as_int = order_id - if chr_info.name == self.max_location_chr: - max_chr_as_int = order_id + if chr_info.name == self.location_chr: + range_chr_as_int = order_id for _trait_counter, trait in enumerate(self.correlation_data.keys()[:self.return_number]): - print("trait name:", trait) trait_object = GeneralTrait(dataset=self.target_dataset, name=trait, get_qtl_info=True) if self.dataset.type == "ProbeSet" or self.dataset.type == "Geno": @@ -207,15 +202,15 @@ class CorrelationResults(object): if (float(self.correlation_data[trait][0]) >= self.p_range_lower and float(self.correlation_data[trait][0]) <= self.p_range_upper): - if ((self.dataset.type == "ProbeSet" or self.dataset.type == "Geno") and - (self.min_expr != None and float(trait_object.mean) >= self.min_expr) and - chr_as_int >= min_chr_as_int and - chr_as_int <= max_chr_as_int) : - + if self.dataset.type == "ProbeSet" or self.dataset.type == "Geno": - if (chr_as_int == min_chr_as_int and float(trait_object.mb) < float(self.min_location_mb)): + if (self.min_expr != None) and (float(trait_object.mean) < self.min_expr): + continue + elif range_chr_as_int != None and (chr_as_int != range_chr_as_int): + continue + elif (self.min_location_mb != None) and (float(trait_object.mb) < float(self.min_location_mb)): continue - elif (chr_as_int == max_chr_as_int and float(trait_object.mb) > float(self.max_location_mb)): + elif (self.max_location_mb != None) and (float(trait_object.mb) > float(self.max_location_mb)): continue (trait_object.sample_r, @@ -501,8 +496,6 @@ class CorrelationResults(object): FROM GeneIDXRef WHERE rat='%s'""" % escape(gene_id) - print("GENE_ID QUERY: ", query) - result = g.db.execute(query).fetchone() if result != None: mouse_gene_id = result.mouse @@ -513,13 +506,9 @@ class CorrelationResults(object): FROM GeneIDXRef WHERE human='%s'""" % escape(gene_id) - print("GENE_ID QUERY: ", query) - result = g.db.execute(query).fetchone() if result != None: mouse_gene_id = result.mouse - - print("mouse_geneid:", mouse_gene_id) return mouse_gene_id diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html index 3203c0c4..68cc8b18 100755 --- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html +++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html @@ -82,15 +82,11 @@ <div class="form-group"> <label class="col-xs-1 control-label">Location</label> <div class="col-xs-4 controls"> - <span style="margin:10px;"> - Min Chr: <input name="min_loc_chr" value="" type="text" class="form-control" style="width: 50px; display: inline;"> - Mb: <input name="min_loc_mb" value="" type="text" class="form-control" style="width: 50px; display: inline;"> + <span> + Chr: <input name="loc_chr" value="" type="text" class="form-control" style="width: 50px; display: inline;"> + Mb: <input name="min_loc_mb" value="" type="text" class="form-control" style="width: 50px; display: inline;"> to <input name="max_loc_mb" value="" type="text" class="form-control" style="width: 50px; display: inline;"> </span> <br> - <span style="margin:10px;"> - Max Chr: <input name="max_loc_chr" value="" type="text" class="form-control" style="width: 50px; display: inline;"> - Mb: <input name="max_loc_mb" value="" type="text" class="form-control" style="width: 50px; display: inline;"> - </span> </div> </div> {% endif %} |