diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/correlation/show_corr_results.py | 37 |
1 files changed, 23 insertions, 14 deletions
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 298a3559..6175dc7e 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -101,11 +101,12 @@ class CorrelationResults(object): 'min_loc_mb' in start_vars and 'max_loc_mb' in start_vars): + self.location_type = get_string(start_vars, 'location_type') self.location_chr = get_string(start_vars, 'loc_chr') self.min_location_mb = get_int(start_vars, 'min_loc_mb') self.max_location_mb = get_int(start_vars, 'max_loc_mb') else: - self.location_chr = self.min_location_mb = self.max_location_mb = None + self.location_type = self.location_chr = self.min_location_mb = self.max_location_mb = None self.get_formatted_corr_type() self.return_number = int(start_vars['corr_return_results']) @@ -173,23 +174,25 @@ class CorrelationResults(object): self.correlation_data = collections.OrderedDict(sorted(list(self.correlation_data.items()), key=lambda t: -abs(t[1][0]))) - if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno": - #ZS: Convert min/max chromosome to an int for the location range option - range_chr_as_int = None - for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()): - if 'loc_chr' in start_vars: - if chr_info.name == self.location_chr: - range_chr_as_int = order_id + + #ZS: Convert min/max chromosome to an int for the location range option + range_chr_as_int = None + for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()): + if 'loc_chr' in start_vars: + if chr_info.name == self.location_chr: + range_chr_as_int = order_id for _trait_counter, trait in enumerate(list(self.correlation_data.keys())[:self.return_number]): trait_object = create_trait(dataset=self.target_dataset, name=trait, get_qtl_info=True, get_sample_info=False) if not trait_object: continue - if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno": - #ZS: Convert trait chromosome to an int for the location range option - chr_as_int = 0 - for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()): + chr_as_int = 0 + for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()): + if self.location_type == "highest_lod": + if chr_info.name == trait_object.locus_chr: + chr_as_int = order_id + else: if chr_info.name == trait_object.chr: chr_as_int = order_id @@ -199,9 +202,15 @@ class CorrelationResults(object): if (self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Publish") and bool(trait_object.mean): if (self.min_expr != None) and (float(trait_object.mean) < self.min_expr): continue - if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno": - if range_chr_as_int != None and (chr_as_int != range_chr_as_int): + + if range_chr_as_int != None and (chr_as_int != range_chr_as_int): + continue + if self.location_type == "highest_lod": + if (self.min_location_mb != None) and (float(trait_object.locus_mb) < float(self.min_location_mb)): + continue + if (self.max_location_mb != None) and (float(trait_object.locus_mb) > float(self.max_location_mb)): continue + else: if (self.min_location_mb != None) and (float(trait_object.mb) < float(self.min_location_mb)): continue if (self.max_location_mb != None) and (float(trait_object.mb) > float(self.max_location_mb)): |