diff options
Diffstat (limited to 'wqflask')
| -rwxr-xr-x | wqflask/wqflask/correlation/show_corr_results.py | 39 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/show_trait_calculate_correlations.html | 14 |
2 files changed, 49 insertions, 4 deletions
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 6a120325..63a7a555 100755 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -110,6 +110,17 @@ class CorrelationResults(object): self.min_expr = float(start_vars['min_expr']) self.p_range_lower = float(start_vars['p_range_lower']) self.p_range_upper = float(start_vars['p_range_upper']) + self.min_location_chr = start_vars['min_loc_chr'] + self.max_location_chr = start_vars['max_loc_chr'] + if start_vars['min_loc_mb'].isdigit(): + self.min_location_mb = start_vars['min_loc_mb'] + else: + self.min_location_mb = 0 + if start_vars['max_loc_mb'].isdigit(): + self.max_location_mb = start_vars['max_loc_mb'] + else: + self.max_location_mb = 1000 + self.max_location = [start_vars['max_loc_chr'], start_vars['max_loc_mb']] self.get_formatted_corr_type() self.return_number = int(start_vars['corr_return_results']) @@ -167,15 +178,35 @@ class CorrelationResults(object): key=lambda t: -abs(t[1][0]))) + #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 + 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 + 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) - print("trait_object.mean:", trait_object.mean) - print("self.min_expr:", self.min_expr) - print("self.p_range_upper:", self.p_range_upper) + + #ZS: Convert trait chromosome to an int for the location range option + chr_as_int = 0 + for order_id, chr_info in self.dataset.species.chromosomes.chromosomes.iteritems(): + if chr_info.name == trait_object.chr: + chr_as_int = order_id + if (float(trait_object.mean) > self.min_expr and float(self.correlation_data[trait][0]) > self.p_range_lower and - float(self.correlation_data[trait][0]) < self.p_range_upper): + float(self.correlation_data[trait][0]) < self.p_range_upper and + chr_as_int >= min_chr_as_int and + chr_as_int <= max_chr_as_int): + + if (chr_as_int == min_chr_as_int 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)): + continue (trait_object.sample_r, trait_object.sample_p, diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html index cefe9763..65b9d08e 100755 --- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html +++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html @@ -80,6 +80,20 @@ </div> </div> <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> + <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> + <div class="form-group"> <label class="col-xs-1 control-label">Range</label> <div class="col-xs-3 controls"> <input name="p_range_lower" value="" type="hidden"> |