diff options
Diffstat (limited to 'wqflask/base')
| -rwxr-xr-x | wqflask/base/data_set.py | 14 | ||||
| -rwxr-xr-x | wqflask/base/trait.py | 63 |
2 files changed, 62 insertions, 15 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index cd8c1ac1..fbe78d5d 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -318,12 +318,17 @@ class DatasetGroup(object): #determine default genotype object if self.incparentsf1 and genotype_1.type != "intercross": - self.genotype = genotype_2 + #self.genotype = genotype_2 + genotype = genotype_2 else: self.incparentsf1 = 0 - self.genotype = genotype_1 + #self.genotype = genotype_1 + genotype = genotype_1 - self.samplelist = list(self.genotype.prgy) + #self.samplelist = list(self.genotype.prgy) + self.samplelist = list(genotype.prgy) + + return genotype #class DataSets(object): @@ -624,7 +629,7 @@ class PhenotypeDataSet(DataSet): description = this_trait.pre_publication_description - this_trait.description_display = description + this_trait.description_display = description.strip() if not this_trait.year.isdigit(): this_trait.pubmed_text = "N/A" @@ -1084,6 +1089,7 @@ class MrnaAssayDataSet(DataSet): Strain.Name """ % (escape(trait), escape(self.name)) results = g.db.execute(query).fetchall() + print("RETRIEVED RESULTS HERE:", results) return results diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 731f99eb..712d9af5 100755 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -12,10 +12,13 @@ from base.data_set import create_dataset from dbFunction import webqtlDatabaseFunction from utility import webqtlUtil +from wqflask import app + +import simplejson as json from MySQLdb import escape_string as escape from pprint import pformat as pf -from flask import Flask, g +from flask import Flask, g, request def print_mem(stage=""): mem = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss @@ -43,7 +46,7 @@ class GeneralTrait(object): self.sequence = kw.get('sequence') # Blat sequence, available for ProbeSet self.data = kw.get('data', {}) - # Sets defaultst + # Sets defaults self.locus = None self.lrs = None self.pvalue = None @@ -63,6 +66,17 @@ class GeneralTrait(object): # So we could add a simple if statement to short-circuit this if necessary self.retrieve_info(get_qtl_info=get_qtl_info) self.retrieve_sample_data() + + + def jsonable(self): + """Return a dict suitable for using as json + + Actual turning into json doesn't happen here though""" + return dict(name=self.name, + dataset=self.dataset.name, + description=self.description_display, + mean=self.mean) + def get_info(self): """For lots of traits just use get_trait_info in dataset instead...that will be way @@ -154,7 +168,7 @@ class GeneralTrait(object): result.append(None) return result - def export_informative(self, incVar=0): + def export_informative(self, include_variance=0): """ export informative sample mostly used in qtl regression @@ -163,12 +177,12 @@ class GeneralTrait(object): samples = [] vals = [] the_vars = [] - for sample, value in self.data.items(): - if value.val != None: - if not incVar or value.var != None: - samples.append(sample) - vals.append(value.val) - the_vars.append(value.var) + 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 @@ -235,11 +249,19 @@ class GeneralTrait(object): # Todo: is this necessary? If not remove self.data.clear() + if self.dataset.group.parlist: + all_samples_ordered = (self.dataset.group.parlist + + self.dataset.group.f1list + + self.dataset.group.samplelist) + elif self.dataset.group.f1list: + all_samples_ordered = self.dataset.group.f1list + self.dataset.group.samplelist + else: + all_samples_ordered = self.dataset.group.samplelist + if results: for item in results: - #name, value, variance, num_cases = item + name, value, variance, num_cases = item if not samplelist or (samplelist and name in samplelist): - name = item[0] self.data[name] = webqtlCaseData(*item) #name, value, variance, num_cases) #def keys(self): @@ -608,3 +630,22 @@ class GeneralTrait(object): ZValue = 0.5*log((1.0+self.correlation)/(1.0-self.correlation)) ZValue = ZValue*sqrt(self.overlap-3) self.p_value = 2.0*(1.0 - reaper.normp(abs(ZValue))) + + + +@app.route("/trait/get_sample_data") +def get_sample_data(): + params = request.args + trait = params['trait'] + dataset = params['dataset'] + + trait_ob = GeneralTrait(name=trait, dataset_name=dataset) + + return json.dumps({key: value.value for key, value in trait_ob.data.iteritems() }) + + #jsonable_sample_data = {} + #for sample in trait_ob.data.iteritems(): + # jsonable_sample_data[sample] = trait_ob.data[sample].value + # + #return jsonable_sample_data +
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