From 2520342c689233a82b70b5328a044add87169d84 Mon Sep 17 00:00:00 2001
From: Zachary Sloan
Date: Fri, 4 Jan 2013 17:09:27 -0600
Subject: Correct results are being returned from reaper for the marker
regression page
---
misc/notes.txt | 13 +-
misc/todo.txt | 3 +-
.../wqflask/marker_regression/marker_regression.py | 255 ++++++++++++---------
.../wqflask/templates/show_trait_edit_data.html | 4 +-
.../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>
@@ -134,6 +134,13 @@
</div>
</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"
--
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