diff options
| -rw-r--r-- | wqflask/base/species.py | 22 | ||||
| -rwxr-xr-x | wqflask/wqflask/marker_regression/marker_regression.py | 66 |
2 files changed, 30 insertions, 58 deletions
diff --git a/wqflask/base/species.py b/wqflask/base/species.py index 1fd76772..85f076ca 100644 --- a/wqflask/base/species.py +++ b/wqflask/base/species.py @@ -13,7 +13,8 @@ class TheSpecies(object): self.dataset = dataset print("self.dataset is:", pf(self.dataset.__dict__)) self.chromosomes = Chromosomes(self.dataset.group.name) - + self.genome_length = self.chromosomes.get_genome_length() + #@property #def chromosomes(self): # chromosomes = [("All", -1)] @@ -31,7 +32,7 @@ class TheSpecies(object): class Chromosomes(object): def __init__(self, group_name): self.chromosomes = collections.OrderedDict() - + results = g.db.execute(""" Select Chr_Length.Name, Length from Chr_Length, InbredSet @@ -46,3 +47,20 @@ class Chromosomes(object): self.chromosomes[item.Name] = item.Length print("self.chromosomes:", self.chromosomes) + + + def get_mb_length(self): + """Gets the chromosome length in megabases""" + + mb_lengths = chr_length/1000000.0 for name, chr_length in self.chromosomes + + return mb_lengths + + def get_genome_length(self): + """Gets the sum of each chromosome's length""" + + genome_length = 0 + for name, value in self.chromosomes.items(): + genome_length += value + + return genome_length
\ No newline at end of file diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index ace76411..0aad4e54 100755 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -67,11 +67,9 @@ class MarkerRegression(object): self.dataset.group.read_genotype_file() self.genotype = self.dataset.group.genotype - assert start_vars['display_all_vars'] in ('True', 'False') + assert start_vars['display_all_lrs'] in ('True', 'False') self.display_all_lrs = True if start_vars['display_all_lrs'] == 'True' else False - print("self.display_all_lrs is:", pf(self.display_all_lrs)) - for sample in self.dataset.group.samplelist: value = start_vars['value:' + sample] variance = start_vars['variance:' + sample] @@ -314,6 +312,7 @@ class MarkerRegression(object): """ Initializes all of the MarkerRegressionPage class parameters, acquiring most values from the formdata (fd) + """ ################################### # manhattam plot parameters @@ -448,70 +447,23 @@ class MarkerRegression(object): return rv, tblobj,bottomInfo - #def GenReport(self, ChrNameOrderIdDict,fd, _genotype, _strains, _vals, _vars= []): def gen_data(self): """Todo: Fill this in here""" - #'Create an HTML division which reports any loci which are significantly associated with the submitted trait data.' - + #calculate QTL for each trait - #self.qtlresults = [] - #if webqtlUtil.ListNotNull(_vars): - - #strains = - #vals = - #variances = - - #if any(self.variances): - # self.qtl_results = self.genotype.regression(strains = self.samples, - # trait = self.vals, - # variance = self.variances) - # self.lrs_array = self.genotype.permutation(strains = self.samples, - # trait = self.vals, - # variance = self.variances, - # nperm = self.num_perm) - #else: self.qtl_results = self.genotype.regression(strains = self.samples, trait = self.vals) self.lrs_array = self.genotype.permutation(strains = self.samples, trait = self.vals, nperm=self.num_perm) - #print("[yellow] self.__dict__ is:", pf(self.__dict__)) - - #self.qtlresults.append(qtlresults) - - #filename= webqtlUtil.genRandStr("GenomeAsscociation_") - - - - # set suggestive, significant and highly significant LRS - #if fd.suggestive == None: - #self.suggestive = self.lrs_array[int(self.num_perm*0.37-1)] - ##else: - ## fd.suggestive = float(fd.suggestive) - ##if fd.significance == None: - #self.significance = self.lrs_array[int(self.num_perm*0.95-1)] - ##else: - ## fd.significance = float(fd.significance) - # - ##self.significance =fd.significance - ##self.suggestive = fd.suggestive - #self.highlysignificant = LRSArray[int(fd.nperm*0.99-1)] - self.lrs_thresholds = Bunch( suggestive = self.lrs_array[int(self.num_perm*0.37-1)], significant = self.lrs_array[int(self.num_perm*0.95-1)], - highly_significant = self.lrs_array[int(fd.nperm*0.99-1)] + highly_significant = self.lrs_array[int(self.num_perm*0.99-1)] ) - - #disp_all_lrs = False - #if fd.formdata.getvalue('displayAllLRS'): - # disp_all_lrs = True - - #if not self.disp_all_lrs: - - if self.disp_all_lrs: + if self.display_all_lrs: filtered_results = self.qtl_results else: suggestive_results = [] @@ -587,7 +539,9 @@ class MarkerRegression(object): # report = HT.Blockquote(HT.Font('No association ',color="#FF0000"),HT.Font('with a likelihood ratio statistic greater than %3.1f was found. Here are the top 10 LRSs.' % fd.suggestive,color="#000000")) #else: # report = HT.Blockquote('The following loci in the %s data set have associations with the above trait data.\n' % fd.RISet, HT.P()) - report.__setattr__("class","normalsize") + + + #report.__setattr__("class","normalsize") #fpText = open('%s.txt' % (webqtlConfig.TMPDIR+filename), 'wb') #fpText.write('Suggestive LRS =%3.2f\n'%self.suggestive) @@ -610,11 +564,11 @@ class MarkerRegression(object): #for ncol, item in enumerate(headerList): # reportHeaderRow.append(THCell(HT.TD(item, Class=headerStyle, valign='bottom',nowrap='ON'),text=item, idx=ncol)) - for marker in filtered: + for marker in filtered_results: if marker.lrs > webqtlConfig.MAXLRS: marker.lrs = webqtlConfig.MAXLRS - self.filtered = filtered + self.filtered_results = filtered_results #if fd.genotype.type == 'intercross': # ncol =len(headerList) |