diff options
| -rw-r--r-- | misc/notes.txt | 13 | ||||
| -rw-r--r-- | misc/todo.txt | 3 | ||||
| -rwxr-xr-x | wqflask/wqflask/marker_regression/marker_regression.py | 255 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait_edit_data.html | 4 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait_mapping_tools.html | 13 |
5 files changed, 173 insertions, 115 deletions
diff --git a/misc/notes.txt b/misc/notes.txt index b0c0762c..306cadeb 100644 --- a/misc/notes.txt +++ b/misc/notes.txt @@ -57,12 +57,6 @@ unset SSH_ASKPASS =========================================== -Python stuff: - -Classes should always inherit "object" - -=========================================== - htop: Gives information on processes, cpu/memory load, etc dstat: Also gives various system information, resource usage, etc df: Reports file system disk space usage @@ -78,4 +72,11 @@ ps -ax - View processes kill (process #) +=========================================== + +Python stuff: + +Classes should always inherit "object" +To iterate through dictionary items: for X, Y in MyDictionary.items(): + diff --git a/misc/todo.txt b/misc/todo.txt index 60655a71..1d781b13 100644 --- a/misc/todo.txt +++ b/misc/todo.txt @@ -1,3 +1,2 @@ -- Check about using trait id instead of trait name in queries in data_set.py - +- Ask Rob about potentially recoding qtlreaper - Ask Rob about Probe/cellid traits
\ 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 ed01a3fa..30860376 100755 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -52,7 +52,36 @@ class MarkerRegression(object): #if not self.openMysql(): # return + print("start_vars are: ", pf(start_vars)) + self.dataset = create_dataset(start_vars['dataset_name']) + self.num_perm = int(start_vars['num_perm']) + + # Passed in by the form (user might have edited) + #samples = start_vars['allsamples'].split() + + self.samples = [] # Want only ones with values + self.vals = [] + self.variances = [] + + self.dataset.group.read_genotype_file() + self.genotype = self.dataset.group.genotype + + for sample in self.dataset.group.samplelist: + value = start_vars['value:' + sample] + variance = start_vars['variance:' + sample] + if variance.strip().lower() == 'x': + variance = 0 + else: + variance = float(variance) + if value.strip().lower() != 'x': + self.samples.append(str(sample)) + self.vals.append(float(value)) + self.variances.append(variance) + + print("self.samples is:", pf(self.samples)) + print("self.vals is:", pf(self.vals)) + print("self.variances is:", pf(self.variances)) #self.initializeParameters(start_vars) @@ -162,111 +191,114 @@ class MarkerRegression(object): #if fd.parentsf14regression and fd.genotype_2: # _genotype = fd.genotype_2 #else: - genotype = self.dataset.group.read_genotype_file() - print("[black]:", genotype) + #print("[black]:", self.genotype) - _strains, _vals, _vars, N = fd.informativeStrains(_genotype.prgy, weightedRegression) + #_strains, _vals, _vars, N = fd.informativeStrains(_genotype.prgy, weightedRegression) - if fd.identification: - heading2 = HT.Paragraph('Trait ID: %s' % fd.identification) - heading2.__setattr__("class","subtitle") - self.dict['title'] = '%s: Genome Association' % fd.identification - else: - heading2 = "" - self.dict['title'] = 'Genome Association' - - if fd.traitInfo: - symbol,chromosome,MB = string.split(fd.traitInfo,'\t') - heading3 = HT.Paragraph('[ ',HT.Strong(HT.Italic('%s' % symbol,id="green")),' on Chr %s @ %s Mb ]' % (chromosome,MB)) - else: - heading3 = "" - - if N < webqtlConfig.KMININFORMATIVE: - heading = "Genome Association" - detail = ['Fewer than %d strain data were entered for %s data set. No mapping attempted.' % (webqtlConfig.KMININFORMATIVE, fd.RISet)] - self.error(heading=heading,detail=detail) - return - else: - heading = HT.Paragraph('Trait Data Entered for %s Set' % fd.RISet) - heading.__setattr__("class","title") - - datadiv = HT.TD(heading, heading2,heading3, width='45%',valign='top', align='left', bgColor='#eeeeee') - resultstable,tblobj,bottomInfo = self.GenReport(ChrNameOrderIdDict,fd, _genotype, _strains, _vals, _vars) - #resultstable = self.GenReport(fd, _genotype, _strains, _vals, _vars) - - # creat object for result table for sort function - objfile = open('%s.obj' % (webqtlConfig.TMPDIR+filename), 'wb') - cPickle.dump(tblobj, objfile) - objfile.close() + #if fd.identification: + # heading2 = HT.Paragraph('Trait ID: %s' % fd.identification) + # heading2.__setattr__("class","subtitle") + # self.dict['title'] = '%s: Genome Association' % fd.identification + #else: + # heading2 = "" + # self.dict['title'] = 'Genome Association' - sortby = ("Index", "up") - reportTable =HT.Div(webqtlUtil.genTableObj(tblobj=tblobj, file=filename, sortby=sortby, tableID = "sortable", addIndex = "0"), Id="sortable") + #if fd.traitInfo: + # symbol, chromosome, MB = string.split(fd.traitInfo,'\t') + # heading3 = HT.Paragraph('[ ',HT.Strong(HT.Italic('%s' % symbol,id="green")),' on Chr %s @ %s Mb ]' % (chromosome,MB)) + #else: + # heading3 = "" - descriptionTable = HT.TableLite(border=0, cellpadding=0, cellspacing=0) - descriptionTable.append(HT.TR(HT.TD(reportTable, colspan=3))) - descriptionTable.append(HT.TR(HT.TD(HT.BR(),HT.BR()))) - descriptionTable.append(bottomInfo) + ### Todo in 2013: Don't allow marker regression in show trait page when number of samples + ### with values < 5 - self.traitList=_vals - - ##########################plot####################### - - ################################################################ - # Generate Chr list and Retrieve Length Information - ################################################################ - self.genotype= _genotype - self.ChrList = [("All", -1)] - - for i, indChr in enumerate(self.genotype): - self.ChrList.append((indChr.name, i)) - - self.cursor.execute(""" - Select - Length from Chr_Length, InbredSet - where - Chr_Length.SpeciesId = InbredSet.SpeciesId AND - InbredSet.Name = '%s' AND - Chr_Length.Name in (%s) - Order by - OrderId - """ % (fd.RISet, string.join(map(lambda X: "'%s'" % X[0], self.ChrList[1:]), ", "))) - - self.ChrLengthMbList = self.cursor.fetchall() - self.ChrLengthMbList = map(lambda x: x[0]/1000000.0, self.ChrLengthMbList) - self.ChrLengthMbSum = reduce(lambda x, y:x+y, self.ChrLengthMbList, 0.0) - if self.ChrLengthMbList: - self.MbGraphInterval = self.ChrLengthMbSum/(len(self.ChrLengthMbList)*12) #Empirical Mb interval - else: - self.MbGraphInterval = 1 + #if N < webqtlConfig.KMININFORMATIVE: + # heading = "Genome Association" + # detail = ['Fewer than %d strain data were entered for %s data set. No mapping attempted.' % (webqtlConfig.KMININFORMATIVE, fd.RISet)] + # self.error(heading=heading,detail=detail) + # return + #else: + # heading = HT.Paragraph('Trait Data Entered for %s Set' % fd.RISet) + # heading.__setattr__("class","title") + + #datadiv = HT.TD(heading, heading2,heading3, width='45%',valign='top', align='left', bgColor='#eeeeee') + #resultstable,tblobj,bottomInfo = self.GenReport(ChrNameOrderIdDict,fd, _genotype, _strains, _vals, _vars) + resultstable, tblobj, bottomInfo = self.gen_data() + #resultstable = self.GenReport(fd, _genotype, _strains, _vals, _vars) + + # creat object for result table for sort function + objfile = open('%s.obj' % (webqtlConfig.TMPDIR+filename), 'wb') + cPickle.dump(tblobj, objfile) + objfile.close() + + sortby = ("Index", "up") + reportTable =HT.Div(webqtlUtil.genTableObj(tblobj=tblobj, file=filename, sortby=sortby, tableID = "sortable", addIndex = "0"), Id="sortable") + + descriptionTable = HT.TableLite(border=0, cellpadding=0, cellspacing=0) + descriptionTable.append(HT.TR(HT.TD(reportTable, colspan=3))) + descriptionTable.append(HT.TR(HT.TD(HT.BR(),HT.BR()))) + descriptionTable.append(bottomInfo) + + self.traitList=_vals + + ##########################plot####################### + + ################################################################ + # Generate Chr list and Retrieve Length Information + ################################################################ + self.genotype= _genotype + self.ChrList = [("All", -1)] + + for i, indChr in enumerate(self.genotype): + self.ChrList.append((indChr.name, i)) + + self.cursor.execute(""" + Select + Length from Chr_Length, InbredSet + where + Chr_Length.SpeciesId = InbredSet.SpeciesId AND + InbredSet.Name = '%s' AND + Chr_Length.Name in (%s) + Order by + OrderId + """ % (fd.RISet, string.join(map(lambda X: "'%s'" % X[0], self.ChrList[1:]), ", "))) + + self.ChrLengthMbList = self.cursor.fetchall() + self.ChrLengthMbList = map(lambda x: x[0]/1000000.0, self.ChrLengthMbList) + self.ChrLengthMbSum = reduce(lambda x, y:x+y, self.ChrLengthMbList, 0.0) + if self.ChrLengthMbList: + self.MbGraphInterval = self.ChrLengthMbSum/(len(self.ChrLengthMbList)*12) #Empirical Mb interval + else: + self.MbGraphInterval = 1 - self.ChrLengthCMList = [] - for i, _chr in enumerate(self.genotype): - self.ChrLengthCMList.append(_chr[-1].cM - _chr[0].cM) - self.ChrLengthCMSum = reduce(lambda x, y:x+y, self.ChrLengthCMList, 0.0)# used for calculate plot scale + self.ChrLengthCMList = [] + for i, _chr in enumerate(self.genotype): + self.ChrLengthCMList.append(_chr[-1].cM - _chr[0].cM) + self.ChrLengthCMSum = reduce(lambda x, y:x+y, self.ChrLengthCMList, 0.0)# used for calculate plot scale - self.GraphInterval = self.MbGraphInterval #Mb + self.GraphInterval = self.MbGraphInterval #Mb - # begin: common part with human data - intCanvas = pid.PILCanvas(size=(self.graphWidth,self.graphHeight)) - gifmap = self.plotIntMapping(fd, intCanvas, startMb = self.startMb, endMb = self.endMb, showLocusForm= "") - filename= webqtlUtil.genRandStr("Itvl_") - intCanvas.save(os.path.join(webqtlConfig.IMGDIR, filename), format='png') - intImg=HT.Image('/image/'+filename+'.png', border=0, usemap='#WebQTLImageMap') + # begin: common part with human data + intCanvas = pid.PILCanvas(size=(self.graphWidth,self.graphHeight)) + gifmap = self.plotIntMapping(fd, intCanvas, startMb = self.startMb, endMb = self.endMb, showLocusForm= "") + filename= webqtlUtil.genRandStr("Itvl_") + intCanvas.save(os.path.join(webqtlConfig.IMGDIR, filename), format='png') + intImg=HT.Image('/image/'+filename+'.png', border=0, usemap='#WebQTLImageMap') - ################################################################ - # footnote goes here - ################################################################ - btminfo = HT.Paragraph(Id="smallsize") #Small('More information about this graph is available here.') + ################################################################ + # footnote goes here + ################################################################ + btminfo = HT.Paragraph(Id="smallsize") #Small('More information about this graph is available here.') - if (self.additiveChecked): - btminfo.append(HT.BR(), 'A positive additive coefficient (', HT.Font('green', color='green'), ' line) indicates that %s alleles increase trait values. In contrast, a negative additive coefficient (' % fd.ppolar, HT.Font('red', color='red'), ' line) indicates that %s alleles increase trait values.' % fd.mpolar) + if (self.additiveChecked): + btminfo.append(HT.BR(), 'A positive additive coefficient (', HT.Font('green', color='green'), ' line) indicates that %s alleles increase trait values. In contrast, a negative additive coefficient (' % fd.ppolar, HT.Font('red', color='red'), ' line) indicates that %s alleles increase trait values.' % fd.mpolar) - TD_LR = HT.TR(HT.TD(HT.Blockquote(gifmap,intImg, HT.P()), bgColor='#eeeeee', height = 200)) + TD_LR = HT.TR(HT.TD(HT.Blockquote(gifmap,intImg, HT.P()), bgColor='#eeeeee', height = 200)) - self.dict['body'] = str(datadiv)+str(TD_LR)+str(resultstable)+str(HT.TR(HT.TD(descriptionTable))) + self.dict['body'] = str(datadiv)+str(TD_LR)+str(resultstable)+str(HT.TR(HT.TD(descriptionTable))) - # end: common part with human data + # end: common part with human data @@ -410,18 +442,37 @@ class MarkerRegression(object): return rv, tblobj,bottomInfo - def GenReport(self, ChrNameOrderIdDict,fd, _genotype, _strains, _vals, _vars= []): - 'Create an HTML division which reports any loci which are significantly associated with the submitted trait data.' + #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): - qtlresults = _genotype.regression(strains = _strains, trait = _vals, variance = _vars) - LRSArray = _genotype.permutation(strains = _strains, trait = _vals, variance = _vars, nperm=fd.nperm) - else: - qtlresults = _genotype.regression(strains = _strains, trait = _vals) - LRSArray = _genotype.permutation(strains = _strains, trait = _vals,nperm=fd.nperm) - - self.qtlresults.append(qtlresults) + #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_") diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html index 9023b34d..84c606b9 100644 --- a/wqflask/wqflask/templates/show_trait_edit_data.html +++ b/wqflask/wqflask/templates/show_trait_edit_data.html @@ -120,7 +120,7 @@ {# Todo: Add IDs #} <td class="column_name-Value"> - <input type="text" data-value="{{ sample.display_value }}" name="{{ sample.name }}" + <input type="text" data-value="{{ sample.display_value }}" name="{{ 'value:' + sample.name }}" class="trait_value_input edit_sample_value" value="{{ sample.display_value }}" size=8 maxlength=8 @@ -134,7 +134,7 @@ {# Todo: Add IDs #} <td class="column_name-SE"> - <input type="text" data-value="{{ sample.display_variance }}" name=""{{ 'V' + sample.name}}" + <input type="text" data-value="{{ sample.display_variance }}" name="{{ 'variance:' + sample.name}}" class="trait_value_input edit_sample_se" value="{{ sample.display_variance }}" size=8 maxlength=8 diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index 72b152fa..0bdefb5a 100644 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -20,7 +20,7 @@ <label for="chromosome" class="control-label">Chromosome</label> <div class="controls"> <select name="chromosome"> - {% for name, value in dataset.species.chromosomes %} + {% for name, value in dataset.species.chromosomes.chromosomes.items() %} <option value="{{ value }}">{{ name }}</option> {% endfor %} </select> @@ -30,7 +30,7 @@ <div class="control-group"> <label for="mapping_permutations" class="control-label">Permutations (n)</label> <div class="controls"> - <input name="num_permutations" value="2000" type="text" /> + <input name="num_perm" value="2000" type="text" /> </div> </div> @@ -125,7 +125,7 @@ No </label> </div> - </div> + </div> <div class="control-group"> <label for="suggestive_lrs" class="control-label" title="Control Locus">LRS greater than</label> @@ -135,6 +135,13 @@ </div> <div class="control-group"> + <label for="marker_reg_permutations" class="control-label">Permutations (n)</label> + <div class="controls"> + <input name="num_perm" value="2000" type="text" /> + </div> + </div> + + <div class="control-group"> <div class="controls"> <button class="btn btn-inverse submit_special" data-url="/marker_regression" |