diff options
| -rw-r--r-- | wqflask/base/data_set.py | 6 | ||||
| -rw-r--r-- | wqflask/base/trait.py | 46 | ||||
| -rwxr-xr-x | wqflask/base/webqtlCaseData.py | 3 | ||||
| -rw-r--r--[-rwxr-xr-x] | wqflask/base/webqtlConfig.py | 0 | ||||
| -rw-r--r-- | wqflask/wqflask/heatmap/heatmap.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression.py | 28 | ||||
| -rw-r--r--[-rwxr-xr-x] | wqflask/wqflask/show_trait/show_trait.py | 9 |
7 files changed, 34 insertions, 60 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 053b45fc..4953e728 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -711,7 +711,7 @@ class PhenotypeDataSet(DataSet): def retrieve_sample_data(self, trait): query = """ SELECT - Strain.Name, PublishData.value, PublishSE.error, NStrain.count + Strain.Name, PublishData.value, PublishSE.error, NStrain.count, Strain.Name2 FROM (PublishData, Strain, PublishXRef, PublishFreeze) left join PublishSE on @@ -803,7 +803,7 @@ class GenotypeDataSet(DataSet): def retrieve_sample_data(self, trait): query = """ SELECT - Strain.Name, GenoData.value, GenoSE.error, GenoData.Id + Strain.Name, GenoData.value, GenoSE.error, GenoData.Id, Sample.Name2 FROM (GenoData, GenoFreeze, Strain, Geno, GenoXRef) left join GenoSE on @@ -1031,7 +1031,7 @@ class MrnaAssayDataSet(DataSet): def retrieve_sample_data(self, trait): query = """ SELECT - Strain.Name, ProbeSetData.value, ProbeSetSE.error, ProbeSetData.Id + Strain.Name, ProbeSetData.value, ProbeSetSE.error, ProbeSetData.Id, Strain.Name2 FROM (ProbeSetData, ProbeSetFreeze, Strain, ProbeSet, ProbeSetXRef) left join ProbeSetSE on diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index af22b5a1..05ee3d96 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -180,13 +180,15 @@ class GeneralTrait(object): samples = [] vals = [] the_vars = [] + sample_aliases = [] for sample_name, sample_data in self.data.items(): if sample_data.value != None: if not include_variance or sample_data.variance != None: samples.append(sample_name) vals.append(sample_data.value) the_vars.append(sample_data.variance) - return samples, vals, the_vars + sample_aliases.append(sample_data.name2) + return samples, vals, the_vars, sample_aliases # @@ -230,7 +232,7 @@ class GeneralTrait(object): if results: for item in results: - name, value, variance, num_cases = item + name, value, variance, num_cases, name2 = item if not samplelist or (samplelist and name in samplelist): self.data[name] = webqtlCaseData(*item) #name, value, variance, num_cases) @@ -308,46 +310,6 @@ class GeneralTrait(object): if isinstance(trait_info[i], basestring): holder = unicode(trait_info[i], "utf8", "ignore") setattr(self, field, holder) -<<<<<<< HEAD - - description_string = unicode(str(self.description).strip(codecs.BOM_UTF8), 'utf-8') - target_string = unicode(str(self.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8') - - if len(description_string) > 1 and description_string != 'None': - description_display = description_string - else: - description_display = self.symbol - - if (len(description_display) > 1 and description_display != 'N/A' and - len(target_string) > 1 and target_string != 'None'): - description_display = description_display + '; ' + target_string.strip() - - # Save it for the jinja2 template - self.description_display = description_display - - #XZ: trait_location_value is used for sorting - trait_location_repr = 'N/A' - trait_location_value = 1000000 - - if self.chr and self.mb: - #Checks if the chromosome number can be cast to an int (i.e. isn't "X" or "Y") - #This is so we can convert the location to a number used for sorting - trait_location_value = convert_location_to_value(self.chr, self.mb) - #try: - # trait_location_value = int(self.chr)*1000 + self.mb - #except ValueError: - # if self.chr.upper() == 'X': - # trait_location_value = 20*1000 + self.mb - # else: - # trait_location_value = (ord(str(self.chr).upper()[0])*1000 + - # self.mb) - - #ZS: Put this in function currently called "convert_location_to_value" - self.location_repr = 'Chr%s: %.6f' % (self.chr, float(self.mb)) - self.location_value = trait_location_value - -======= ->>>>>>> e0c5c1aae3aaaa1d81bcec36835a97e169dcc2e2 if self.dataset.type == 'Publish': self.confidential = 0 diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py index 42763aed..99a34866 100755 --- a/wqflask/base/webqtlCaseData.py +++ b/wqflask/base/webqtlCaseData.py @@ -29,8 +29,9 @@ print("Mr. Mojo Risin 2") class webqtlCaseData(object): """one case data in one trait""" - def __init__(self, name, value=None, variance=None, num_cases=None): + def __init__(self, name, value=None, variance=None, num_cases=None, name2=None): self.name = name + self.name2 = name2 # Other name (for traits like BXD65a) self.value = value # Trait Value self.variance = variance # Trait Variance self.num_cases = num_cases # Number of individuals/cases diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index 0358bcbf..0358bcbf 100755..100644 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py index 2445b37f..19c330eb 100644 --- a/wqflask/wqflask/heatmap/heatmap.py +++ b/wqflask/wqflask/heatmap/heatmap.py @@ -136,7 +136,7 @@ class Heatmap(object): this_trait = trait_db[0] #this_db = trait_db[1] genotype = self.dataset.group.read_genotype_file() - samples, values, variances = this_trait.export_informative() + samples, values, variances, sample_aliases = this_trait.export_informative() trimmed_samples = [] trimmed_values = [] diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index 08f422f0..9cd02bd1 100644 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -56,11 +56,21 @@ class MarkerRegression(object): self.samples = [] # Want only ones with values self.vals = [] - + + #for sample in self.this_trait.data.keys(): for sample in self.dataset.group.samplelist: - value = start_vars['value:' + sample] - self.samples.append(str(sample)) - self.vals.append(value) + in_trait_data = False + for item in self.this_trait.data: + if self.this_trait.data[item].name2 == sample: + value = start_vars['value:' + self.this_trait.data[item].name] + self.samples.append(self.this_trait.data[item].name) + self.vals.append(value) + in_trait_data = True + break + if not in_trait_data: + value = start_vars['value:' + sample] + self.samples.append(sample) + self.vals.append(value) self.mapping_method = start_vars['method'] if start_vars['manhattan_plot'] == "True": @@ -641,15 +651,17 @@ class MarkerRegression(object): if self.manhattan_plot != True: genotype = genotype.addinterval() - samples, values, variances = self.this_trait.export_informative() - + samples, values, variances, sample_aliases = self.this_trait.export_informative() + trimmed_samples = [] trimmed_values = [] for i in range(0, len(samples)): - if samples[i] in self.dataset.group.samplelist: - trimmed_samples.append(samples[i]) + if self.this_trait.data[samples[i]].name2 in self.dataset.group.samplelist: + trimmed_samples.append(sample_aliases[i]) trimmed_values.append(values[i]) + #print("THE SAMPLES:", trimmed_samples) + if self.num_perm < 100: self.suggestive = 0 self.significant = 0 diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 074c78bf..76651cbf 100755..100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -1184,17 +1184,16 @@ class ShowTrait(object): all_samples_ordered = self.dataset.group.all_samples_ordered() primary_sample_names = list(all_samples_ordered) - - print("self.dataset.group", pf(self.dataset.group.__dict__)) - print("-*- primary_samplelist is:", pf(primary_sample_names)) - + other_sample_names = [] for sample in this_trait.data.keys(): + if (this_trait.data[sample].name2 in primary_sample_names) and (this_trait.data[sample].name not in primary_sample_names): + primary_sample_names.append(this_trait.data[sample].name) + primary_sample_names.remove(this_trait.data[sample].name2) if sample not in all_samples_ordered: all_samples_ordered.append(sample) other_sample_names.append(sample) - print("species:", self.dataset.group.species) if self.dataset.group.species == "human": primary_sample_names += other_sample_names |