Created IndChromosome class in species.py and wrote functions for

chromosome-related attributes

Began to try and pass qtlreaper results as js_data to use when
drawing graphs

3 files changed, 119 insertions, 56 deletions

diff --git a/wqflask/base/species.py b/wqflask/base/species.py
index 85f076ca..9d4cac4c 100644
--- a/wqflask/base/species.py
+++ b/wqflask/base/species.py
@@ -6,14 +6,17 @@ from flask import Flask, g
 
 #from MySQLdb import escape_string as escape
 
+from utility import Bunch
+
 from pprint import pformat as pf
 
 class TheSpecies(object):
     def __init__(self, dataset):
         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()
+        self.chromosomes = Chromosomes(self.dataset)
+        self.genome_mb_length = self.chromosomes.get_genome_mb_length()
+        
         
     #@property
     #def chromosomes(self):
@@ -27,10 +30,22 @@ class TheSpecies(object):
     #            
     #    return chromosomes
 
+class IndChromosome(object):
+    def __init__(self, length):
+        self.length = length
+        
+    @property
+    def mb_length(self):
+        """Chromosome length in megabases"""
+        return self.length / 1000000
+    
+    def set_cm_length(self, genofile_chr):
+        self.cm_length = genofile_chr[-1].cM - genofile_chr[0].cM
 
 
 class Chromosomes(object):
-    def __init__(self, group_name):
+    def __init__(self, dataset):
+        self.dataset = dataset
         self.chromosomes = collections.OrderedDict()
 
         results = g.db.execute("""
@@ -40,27 +55,63 @@ class Chromosomes(object):
                         Chr_Length.SpeciesId = InbredSet.SpeciesId AND
                         InbredSet.Name = %s
                 Order by OrderId
-                """, group_name).fetchall()
+                """, self.dataset.group.name).fetchall()
         print("bike:", results)
 
         for item in results:
-            self.chromosomes[item.Name] = item.Length
+            self.chromosomes[item.Name] = IndChromosome(item.Length)
+        
+        self.set_mb_graph_interval()
+        self.get_cm_length_list()
+
+
+    def set_mb_graph_interval(self):
+        """Empirical megabase interval"""
+        
+        #if self.chromosomes:
+        assert self.chromosomes, "Have to add some code back in apparently to set it to 1"
+        self.mb_graph_interval = self.get_genome_mb_length()/(len(self.chromosomes)*12)
+        #else:
+            #self.mb_graph_interval = 1
 
-        print("self.chromosomes:", self.chromosomes)
 
+    def get_genome_mb_length(self):
+        """Gets the sum of each chromosome's length in megabases"""
 
-    def get_mb_length(self):
-        """Gets the chromosome length in megabases"""
+        return sum([ind_chromosome.mb_length for ind_chromosome in self.chromosomes.values()])
 
-        mb_lengths = chr_length/1000000.0 for name, chr_length in self.chromosomes
 
-        return mb_lengths
+    def get_genome_cm_length(self):
+        """Gets the sum of each chromosome's length in centimorgans"""
 
-    def get_genome_length(self):
-        """Gets the sum of each chromosome's length"""
+        return sum([ind_chromosome.cm_length for ind_chromosome in self.chromosomes.values()])
 
-        genome_length = 0
-        for name, value in self.chromosomes.items():
-            genome_length += value
+    def get_cm_length_list(self):
+        """Chromosome length in centimorgans
+        
+        Calculates the length in centimorgans by subtracting the centimorgan position
+        of the last marker in a chromosome by the position of the first marker
+        
+        """
+        
+        self.dataset.group.read_genotype_file()
+        
+        self.cm_length_list = []
+        
+        for chromosome in self.dataset.group.genotype:
+            self.cm_length_list.append(chromosome[-1].cM - chromosome[0].cM)
+            
+        print("self.cm_length_list:", pf(self.cm_length_list))
+        
+        assert len(self.cm_length_list) == len(self.chromosomes), "Uh-oh lengths should be equal!"
+        for counter, chromosome in enumerate(self.chromosomes.values()):
+            chromosome.cm_length = self.cm_length_list[counter]
+            #self.chromosomes[counter].cm_length = item
+            
+        for key, value in self.chromosomes.items():
+            print("bread - %s: %s" % (key, pf(vars(value))))
+        
 
-        return genome_length
\ No newline at end of file
+# Testing                
+#if __name__ == '__main__':    
+#    foo = dict(bar=dict(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 0aad4e54..73f1246f 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -256,54 +256,58 @@ class MarkerRegression(object):
             #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.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.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')
+            #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.')
-
-            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)
+            #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)
 
-            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)))
+            #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)))
 
             # end: common part with human data
-
+            
+            self.js_data = dict(
+                qtl_results = self.pure_qtl_results,
+                #lrs_array = vars(self.lrs_array),
+            )
 
 
 
@@ -467,7 +471,12 @@ class MarkerRegression(object):
             filtered_results = self.qtl_results
         else:
             suggestive_results = []
+            self.pure_qtl_results = []
             for result in self.qtl_results:
+                self.pure_qtl_results.append(dict(locus=dict(cM=result.locus.cM,
+                                                             chromosome=result.locus.chr),
+                                                  lrs=result.lrs,
+                                                  additive=result.additive))
                 if result.lrs > self.lrs_thresholds.suggestive:
                     suggestive_results.append(result)
             filtered_results = suggestive_results 
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index f6c0dfb0..fc628d77 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -151,10 +151,10 @@ def show_trait_page():
 def marker_regression_page():
     template_vars = marker_regression.MarkerRegression(request.form)
     #print("js_data before dump:", template_vars.js_data)
-    #template_vars.js_data = json.dumps(template_vars.js_data,
-    #                                   default=json_default_handler,
-    #                                   indent="   ")
-    #print("js_data after dump:", template_vars.js_data)
+    template_vars.js_data = json.dumps(template_vars.js_data,
+                                       default=json_default_handler,
+                                       indent="   ")
+    print("[dub] js_data after dump:", template_vars.js_data)
     print("marker_regression template_vars:", pf(template_vars.__dict__))
     return render_template("marker_regression.html", **template_vars.__dict__)
 
@@ -190,6 +190,9 @@ def json_default_handler(obj):
     # Handle custom objects
     if hasattr(obj, '__dict__'):
         return obj.__dict__
+    #elif type(obj) == "Dataset":
+    #     print("Not going to serialize Dataset")
+    #    return None
     else:
         raise TypeError, 'Object of type %s with value of %s is not JSON serializable' % (
             type(obj), repr(obj))