Merge /home/zas1024/gene

Conflicts:
	wqflask/wqflask/views.py

15 files changed, 423 insertions, 63 deletions

diff --git a/misc/notes.txt b/misc/notes.txt
index 91a0e67c..f6a2bb33 100644
--- a/misc/notes.txt
+++ b/misc/notes.txt
@@ -90,6 +90,9 @@ Reload web server:
 Run server:
 python runserver.py
 
+Run sendmail.py
+python send_mail.py
+
 ===========================================
 
 UFW - default firewall confirguation tool for Ubuntu; eases iptables firewall configuration
diff --git a/web/webqtl/intervalMapping/IntervalMappingPage.py b/web/webqtl/intervalMapping/IntervalMappingPage.py
index 4bdf45ab..c3ef1cbd 100755
--- a/web/webqtl/intervalMapping/IntervalMappingPage.py
+++ b/web/webqtl/intervalMapping/IntervalMappingPage.py
@@ -2038,7 +2038,7 @@ class IntervalMappingPage(templatePage):
 					qtlresult = self.genotype.regression(strains = _strains, trait = _vals)
 
 			self.qtlresults.append(qtlresult)
-		
+
 		if not self.multipleInterval:
 			if self.controlLocus and self.selectedChr > -1:
 				self.genotype.chromosome = [self.genotype[self.selectedChr]]
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index beb62bd7..f25e7974 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -168,13 +168,13 @@ class Markers(object):
         
         for marker, p_value in itertools.izip(self.markers, p_values):
             marker['p_value'] = p_value
-            if marker['p_value'] == 0:
-                marker['lod_score'] = 0
-                marker['lrs_value'] = 0
-            else:
-                marker['lod_score'] = -math.log10(marker['p_value'])
-                #Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values
-                marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61
+            if math.isnan(marker['p_value']):
+                print("p_value is:", marker['p_value'])
+            marker['lod_score'] = -math.log10(marker['p_value'])
+            #Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values
+            marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61
+        
+        
 
 
 class HumanMarkers(Markers):
@@ -189,6 +189,8 @@ class HumanMarkers(Markers):
             marker['name'] = splat[1]
             marker['Mb'] = float(splat[3]) / 1000000
             self.markers.append(marker)
+            
+        #print("markers is: ", pf(self.markers))
 
 
     def add_pvalues(self, p_values):
@@ -315,12 +317,12 @@ class DatasetGroup(object):
 
         #determine default genotype object
         if self.incparentsf1 and genotype_1.type != "intercross":
-            genotype = genotype_2
+            self.genotype = genotype_2
         else:
             self.incparentsf1 = 0
-            genotype = genotype_1
+            self.genotype = genotype_1
 
-        self.samplelist = list(genotype.prgy)
+        self.samplelist = list(self.genotype.prgy)
 
 
 #class DataSets(object):
@@ -438,10 +440,12 @@ class DataSet(object):
         
     def get_trait_data(self, sample_list=None):
         if sample_list:
-            self.samplelist = sample_list + self.group.parlist + self.group.f1list
+            self.samplelist = sample_list
         else:
-            self.samplelist = self.group.samplelist + self.group.parlist + self.group.f1list
-        
+            self.samplelist = self.group.samplelist
+            
+        if (self.group.parlist + self.group.f1list) in self.samplelist:
+            self.samplelist += self.group.parlist + self.group.f1list
         
         query = """
             SELECT Strain.Name, Strain.Id FROM Strain, Species
@@ -501,8 +505,8 @@ class DataSet(object):
                         and {}Freeze.Name = '{}'
                         and {}.Id = {}XRef.{}Id
                         order by {}.Id
-                        """.format(*mescape(self.type, self.type, self.type, self.type,
-                                   self.name, dataset_type, self.type, self.type, dataset_type))
+                        """.format(*mescape(self.type, self.type, self.type, self.name, 
+                                    dataset_type, self.type, dataset_type, dataset_type))
             else:
                 query += """
                         WHERE {}XRef.{}FreezeId = {}Freeze.Id
diff --git a/wqflask/maintenance/quick_search_table.py b/wqflask/maintenance/quick_search_table.py
index eef61857..f0075df0 100644
--- a/wqflask/maintenance/quick_search_table.py
+++ b/wqflask/maintenance/quick_search_table.py
@@ -13,8 +13,10 @@ each trait, its dataset, and several columns determined by its trait type (pheno
 
 from __future__ import absolute_import, division, print_function
 
-#import sys
-#sys.path.append("../../..")
+	# We do this here so we can use zach_settings
+# Not to avoid other absoulte_imports
+import sys
+sys.path.append("../../..")
 
 import simplejson as json
 
@@ -504,4 +506,4 @@ def main():
     ProbeSetXRef.run()
 
 if __name__ == "__main__":
-    main()
\ No newline at end of file
+    main()
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index a5c80674..8f23165c 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -178,10 +178,10 @@ class CorrelationResults(object):
                     trait_object.lit_corr = lit_corr_data[trait][1]
                 self.correlation_results.append(trait_object)
             
-            if self.corr_type != "lit":
+            if self.corr_type != "lit" and self.dataset.type == "ProbeSet":
                 self.do_lit_correlation_for_trait_list()
             
-            if self.corr_type != "tissue":
+            if self.corr_type != "tissue" and self.dataset.type == "ProbeSet":
                 self.do_tissue_correlation_for_trait_list()
             
             #print("self.correlation_results: ", pf(self.correlation_results))
diff --git a/wqflask/wqflask/interval_mapping/interval_mapping.py b/wqflask/wqflask/interval_mapping/interval_mapping.py
new file mode 100755
index 00000000..aca99cbe
--- /dev/null
+++ b/wqflask/wqflask/interval_mapping/interval_mapping.py
@@ -0,0 +1,312 @@
+from __future__ import absolute_import, print_function, division
+
+from base.trait import GeneralTrait
+from base import data_set  #import create_dataset
+
+from pprint import pformat as pf
+
+import string
+import sys
+import os
+import collections
+
+import numpy as np
+from scipy import linalg
+import rpy2.robjects
+
+import simplejson as json
+
+#from redis import Redis
+
+
+from base.trait import GeneralTrait
+from base import data_set
+from base import species
+from base import webqtlConfig
+from wqflask.my_pylmm.data import prep_data
+from wqflask.my_pylmm.pyLMM import lmm
+from wqflask.my_pylmm.pyLMM import input
+from utility import helper_functions
+from utility import Plot, Bunch
+from utility import temp_data
+
+from utility.benchmark import Bench
+
+
+class IntervalMapping(object):
+
+    def __init__(self, start_vars, temp_uuid):
+
+        #Currently only getting trait data for one trait, but will need
+        #to change this to accept multiple traits once the collection page is implemented
+        helper_functions.get_species_dataset_trait(self, start_vars)
+
+        tempdata = temp_data.TempData(temp_uuid)
+        
+        self.samples = [] # Want only ones with values
+        self.vals = []
+
+        for sample in self.dataset.group.samplelist:
+            value = start_vars['value:' + sample]
+            self.samples.append(str(sample))
+            self.vals.append(value)
+ 
+        self.set_options(start_vars)
+ 
+        self.gen_qtl_results(tempdata)
+
+        #Get chromosome lengths for drawing the interval map plot
+        chromosome_mb_lengths = {}
+        for key in self.species.chromosomes.chromosomes.keys():
+            chromosome_mb_lengths[key] = self.species.chromosomes.chromosomes[key].mb_length
+        
+        self.js_data = dict(
+            lrs_lod = self.lrs_lod,
+            chromosomes = chromosome_mb_lengths,
+            qtl_results = self.qtl_results,
+        )
+
+    def set_options(self, start_vars):
+        """Sets various options (physical/genetic mapping, # permutations, which chromosome"""
+        
+        self.plot_scale = start_vars['scale']
+        #if self.plotScale == 'physic' and not fd.genotype.Mbmap:
+        #    self.plotScale = 'morgan'
+        self.num_permutations = start_vars['num_permutations']
+        self.do_bootstrap = start_vars['do_bootstrap']
+        self.control_locus = start_vars['control_locus']
+        self.selected_chr = start_vars['selected_chr']
+        self.weighted_regression = start_vars['weighted']
+        self.lrs_lod = start_vars['lrs_lod']
+
+
+    def gen_qtl_results(self, tempdata):
+        """Generates qtl results for plotting interval map"""
+
+        self.dataset.group.get_markers()
+        self.dataset.read_genotype_file()
+
+        samples, values, variances = self.trait.export_informative()
+        if self.control_locus:
+            if self.weighted_regression:
+                self.qtl_results = self.dataset.genotype.regression(strains = samples,
+                                                              trait = values,
+                                                              variance = variances,
+                                                              control = self.control_locus)
+            else:
+                self.qtl_results = self.dataset.genotype.regression(strains = samples,
+                                                              trait = values,
+                                                              control = self.control_locus)
+        else:
+            if self.weighted_regression:
+                self.qtl_results = self.dataset.genotype.regression(strains = samples,
+                                                              trait = values,
+                                                              variance = variances)
+            else:
+                self.qtl_results = self.dataset.genotype.regression(strains = samples,
+                                                              trait = values)
+
+
+        #pheno_vector = np.array([val == "x" and np.nan or float(val) for val in self.vals])
+
+        #if self.dataset.group.species == "human":
+        #    p_values, t_stats = self.gen_human_results(pheno_vector, tempdata)
+        #else:
+        genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers.markers]
+        
+        no_val_samples = self.identify_empty_samples()
+        trimmed_genotype_data = self.trim_genotypes(genotype_data, no_val_samples)
+        
+        genotype_matrix = np.array(trimmed_genotype_data).T
+        
+        #t_stats, p_values = lmm.run(
+        #    pheno_vector,
+        #    genotype_matrix,
+        #    restricted_max_likelihood=True,
+        #    refit=False,
+        #    temp_data=tempdata
+        #)
+        
+        #self.dataset.group.markers.add_pvalues(p_values)
+        
+        #self.qtl_results = self.dataset.group.markers.markers
+
+    def gen_qtl_results_2(self, tempdata):
+        """Generates qtl results for plotting interval map"""
+    
+        self.dataset.group.get_markers()
+        self.dataset.read_genotype_file()
+    
+        pheno_vector = np.array([val == "x" and np.nan or float(val) for val in self.vals])
+    
+        #if self.dataset.group.species == "human":
+        #    p_values, t_stats = self.gen_human_results(pheno_vector, tempdata)
+        #else:
+        genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers.markers]
+        
+        no_val_samples = self.identify_empty_samples()
+        trimmed_genotype_data = self.trim_genotypes(genotype_data, no_val_samples)
+        
+        genotype_matrix = np.array(trimmed_genotype_data).T
+        
+        t_stats, p_values = lmm.run(
+            pheno_vector,
+            genotype_matrix,
+            restricted_max_likelihood=True,
+            refit=False,
+            temp_data=tempdata
+        )
+        
+        self.dataset.group.markers.add_pvalues(p_values)
+        
+        self.qtl_results = self.dataset.group.markers.markers
+
+
+    def identify_empty_samples(self):
+        no_val_samples = []
+        for sample_count, val in enumerate(self.vals):
+            if val == "x":
+                no_val_samples.append(sample_count)
+        return no_val_samples
+        
+        
+    def trim_genotypes(self, genotype_data, no_value_samples):
+        trimmed_genotype_data = []
+        for marker in genotype_data:
+            new_genotypes = []
+            for item_count, genotype in enumerate(marker):
+                if item_count in no_value_samples:
+                    continue
+                try:
+                    genotype = float(genotype)
+                except ValueError:
+                    genotype = np.nan
+                    pass
+                new_genotypes.append(genotype)
+            trimmed_genotype_data.append(new_genotypes)
+        return trimmed_genotype_data
+
+    #def get_qtl_results(self):
+    #    """Gets the LOD (or LRS) score at each marker in order do the qtl mapping"""
+    #
+    #    
+    #    
+    #    #self.genotype = self.genotype.addinterval()
+    #    #resultSlice = []
+    #    #controlGeno = []
+    #    
+    #    #if self.multipleInterval:
+    #    #    self.suggestive = 0
+    #    #    self.significance = 0
+    #    #    if self.selectedChr > -1:
+    #    #        self.genotype.chromosome = [self.genotype[self.selectedChr]]
+    #    #else:
+    #    #single interval mapping
+    #    #try:
+    #    #    self.suggestive = float(fd.formdata.getvalue('permSuggestive'))
+    #    #    self.significance = float(fd.formdata.getvalue('permSignificance'))
+    #    #except:
+    #    #    self.suggestive = None
+    #    #    self.significance = None
+    #    
+    #    #NOT DOING MULTIPLE TRAITS YET, BUT WILL NEED TO LATER
+    #    #_strains, _vals, _vars = self.traitList[0].exportInformative(weightedRegression)
+    #    
+    #    #if webqtlUtil.ListNotNull(_vars):
+    #    #    pass
+    #    #else:
+    #    #    weightedRegression = 0
+    #    #    _strains, _vals, _vars = self.traitList[0].exportInformative()
+    #        
+    #    ##locate genotype of control Locus
+    #    #if self.controlLocus:
+    #    #    controlGeno2 = []
+    #    #    _FIND = 0
+    #    #    for _chr in self.genotype:
+    #    #        for _locus in _chr:
+    #    #            if _locus.name == self.controlLocus:
+    #    #                controlGeno2 = _locus.genotype
+    #    #                _FIND = 1
+    #    #                break
+    #    #        if _FIND:
+    #    #            break
+    #    #    if controlGeno2:
+    #    #        _prgy = list(self.genotype.prgy)
+    #    #        for _strain in _strains:
+    #    #            _idx = _prgy.index(_strain)
+    #    #            controlGeno.append(controlGeno2[_idx])
+    #    #    else:
+    #    #        return "The control marker you selected is not in the genofile."
+    #    #
+    #    #    
+    #    #    if self.significance and self.suggestive:
+    #    #        pass
+    #    #    else:
+    #    #        if self.permChecked:
+    #    #            if weightedRegression:
+    #    #                self.LRSArray = self.genotype.permutation(strains = _strains, trait = _vals, 
+    #    #                    variance = _vars, nperm=fd.nperm)
+    #    #            else:
+    #    #                self.LRSArray = self.genotype.permutation(strains = _strains, trait = _vals, 
+    #    #                    nperm=fd.nperm)
+    #    #            self.suggestive = self.LRSArray[int(fd.nperm*0.37-1)]
+    #    #            self.significance = self.LRSArray[int(fd.nperm*0.95-1)]
+    #    #
+    #    #        else:
+    #    #            self.suggestive = 9.2
+    #    #            self.significance = 16.1
+    #    #
+    #    #    #calculating bootstrap
+    #    #    #from now on, genotype could only contain a single chromosome 
+    #    #    #permutation need to be performed genome wide, this is not the case for bootstrap
+    #    #    
+    #    #    #due to the design of qtlreaper, composite regression need to be performed genome wide
+    #    #    if not self.controlLocus and self.selectedChr > -1:
+    #    #        self.genotype.chromosome = [self.genotype[self.selectedChr]]
+    #    #    elif self.selectedChr > -1: #self.controlLocus and self.selectedChr > -1
+    #    #        lociPerChr = map(len, self.genotype)
+    #    #        resultSlice = reduce(lambda X, Y: X+Y, lociPerChr[:self.selectedChr], 0)
+    #    #        resultSlice = [resultSlice,resultSlice+lociPerChr[self.selectedChr]]
+    #    #    else:
+    #    #        pass
+    #        
+    #    #calculate QTL for each trait
+    #    self.qtl_results = []
+    #
+    #    #for thisTrait in self.traitList:
+    #    _strains, _vals, _vars = thisTrait.exportInformative(weightedRegression)
+    #    if self.controlLocus:
+    #        if weightedRegression:
+    #            qtlresult = self.genotype.regression(strains = _strains, trait = _vals, 
+    #                    variance = _vars, control = self.controlLocus)
+    #        else:
+    #            qtlresult = self.genotype.regression(strains = _strains, trait = _vals,
+    #                control = self.controlLocus)
+    #        if resultSlice:
+    #            qtlresult = qtlresult[resultSlice[0]:resultSlice[1]]
+    #    else:
+    #        if weightedRegression:
+    #            qtlresult = self.genotype.regression(strains = _strains, trait = _vals, 
+    #                    variance = _vars)
+    #        else:
+    #            qtlresult = self.genotype.regression(strains = _strains, trait = _vals)
+    #
+    #    self.qtlresults.append(qtlresult)
+    #    
+    #    if not self.multipleInterval:
+    #        if self.controlLocus and self.selectedChr > -1:
+    #            self.genotype.chromosome = [self.genotype[self.selectedChr]]
+    #            
+    #        if self.bootChecked:
+    #            if controlGeno:
+    #                self.bootResult = self.genotype.bootstrap(strains = _strains, trait = _vals,
+    #                    control = controlGeno, nboot=fd.nboot)
+    #            elif weightedRegression:
+    #                self.bootResult = self.genotype.bootstrap(strains = _strains, trait = _vals, 
+    #                    variance = _vars, nboot=fd.nboot)
+    #            else:
+    #                self.bootResult = self.genotype.bootstrap(strains = _strains, trait = _vals, 
+    #                    nboot=fd.nboot)
+    #        else:
+    #            self.bootResult = []
+
diff --git a/wqflask/wqflask/my_pylmm/data/geno_to_ped.py b/wqflask/wqflask/my_pylmm/data/geno_to_ped.py
new file mode 100644
index 00000000..9091ad9a
--- /dev/null
+++ b/wqflask/wqflask/my_pylmm/data/geno_to_ped.py
@@ -0,0 +1,22 @@
+from __future__ import absolute_import, division, print_function
+
+import csv
+
+class ConvertToPed(object):
+
+    def __init__(self, input_file, output_file):
+        self.input_file = input_file
+        self.output_file = output_file
+        
+    def convert(self):
+    
+        self.haplotype_notation = {
+        '@mat': "1",
+        '@pat': "0",
+        '@het': "0.5",
+        '@unk': "NA"
+        }
+        
+        with open(self.output_file, "w") as self.output_fh:
+            self.process_csv()
+        
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 8efba6a7..a14eeb44 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -29,9 +29,9 @@
 {% macro header(main, second) %}
     <header class="jumbotron subhead" id="overview">
         <div class="container">
-            <h1>Login</h1>
+            <h1>{{ main }}</h1>
             <p class="lead">
-               Gain access to GeneNetwork.
+               {{ second }}
             </p>               
         </div>
     </header>
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 7db8ea49..f3bb5531 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -6,12 +6,8 @@
     <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
 {% endblock %}
 {% block content %}
-
-    <header class="jumbotron subhead" id="overview">
-        <div class="container">
-            <h1>Correlation</h1>
-        </div>
-    </header>
+    
+    {{ header("Correlation", 'Trait: {} Dataset: {}'.format(this_trait.name, dataset.name)) }}
 
     <table id="corr_results" class="table table-hover table-striped table-bordered">
         <thead>
diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html
index 98682e57..d177a7bd 100644
--- a/wqflask/wqflask/templates/index_page.html
+++ b/wqflask/wqflask/templates/index_page.html
@@ -3,8 +3,6 @@
 {% block content %}
 <!-- Start of body -->
 
-
-
     <header class="jumbotron subhead" id="overview">
         <div class="container">
             <h1>GeneNetwork</h1>
diff --git a/wqflask/wqflask/templates/marker_regression.html b/wqflask/wqflask/templates/marker_regression.html
index 9260acab..64d2e9b7 100644
--- a/wqflask/wqflask/templates/marker_regression.html
+++ b/wqflask/wqflask/templates/marker_regression.html
@@ -9,14 +9,8 @@
 {% endblock %}
 {% block content %} <!-- Start of body -->
 
-    <header class="jumbotron subhead" id="overview">
-        <div class="container">
-            <h1>Marker Regression</h1>
-            <p class="lead">
-                {{ this_trait.name }}: {{ this_trait.description_fmt }}
-            </p>
-        </div>
-    </header>
+    {{ header("Marker Regression",
+        '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }}
 
     <div class="container">
         <div>
diff --git a/wqflask/wqflask/templates/quick_search.html b/wqflask/wqflask/templates/quick_search.html
index b0e38708..2f268c5a 100644
--- a/wqflask/wqflask/templates/quick_search.html
+++ b/wqflask/wqflask/templates/quick_search.html
@@ -2,14 +2,9 @@
 {% block title %}QuickSearch Results{% endblock %}
 {% block content %}
 <!-- Start of body -->
-    <header class="jumbotron subhead" id="overview">
-        <div class="container">
-            <h1>QuickSearch Results</h1>
-            <p class="lead">
-                GeneNetwork found {{ numify(results|count, "record", "records") }}.
-            </p>
-        </div>
-    </header>
+
+    {{ header("QuickSearch Results",
+        'GeneNetwork found {}.'.format(numify(results|count, "record", "records"))) }}
 
     <div class="container">
         <div class="page-header">
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 11f68bba..1fe7cce9 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -2,14 +2,8 @@
 {% block title %}Search Results{% endblock %}
 {% block content %}
 <!-- Start of body -->
-    <header class="jumbotron subhead" id="overview">
-        <div class="container">
-            <h1>Search Results</h1>
-            <p class="lead">
-                GeneNetwork found {{ numify(results|count, "record", "records") }}.
-            </p>
-        </div>
-    </header>
+    {{ header("Search Results",
+        'GeneNetwork found {}.'.format(numify(results|count, "record", "records"))) }}
 
     <div class="container">
         <div class="page-header">
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 799245c3..e3c84de7 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -7,14 +7,9 @@
 {% endblock %}
 {% block content %} <!-- Start of body -->
 
-    <header class="jumbotron subhead" id="overview">
-        <div class="container">
-            <h1>{{ this_trait.symbol}}</h1>
-            <p class="lead">
-                {{ this_trait.name }}: {{ this_trait.description_fmt }}
-            </p>
-        </div>
-    </header>
+    {{ header("{}".format(this_trait.symbol),
+        '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }}
+
 
     <form method="post" action="/corr_compute" name="trait_page" id="trait_data_form"
     class="form-horizontal">
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 98b6039f..e6b99649 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -32,6 +32,7 @@ from base.data_set import create_datasets_list
 from wqflask.show_trait import show_trait
 from wqflask.show_trait import export_trait_data
 from wqflask.marker_regression import marker_regression
+from wqflask.interval_mapping import interval_mapping
 from wqflask.correlation import show_corr_results
 from utility import temp_data
 
@@ -246,6 +247,50 @@ def marker_regression_page():
 
     return rendered_template
 
+@app.route("/interval_mapping", methods=('POST',))
+def interval_mapping_page():
+    initial_start_vars = request.form
+    temp_uuid = initial_start_vars['temp_uuid']
+    wanted = (
+        'trait_id',
+        'dataset',
+        'suggestive'
+    )
+
+    start_vars = {}
+    for key, value in initial_start_vars.iteritems():
+        if key in wanted or key.startswith(('value:')):
+            start_vars[key] = value
+
+    version = "v1"
+    key = "interval_mapping:{}:".format(version) + json.dumps(start_vars, sort_keys=True)
+    print("key is:", pf(key))
+    with Bench("Loading cache"):
+        result = Redis.get(key)
+
+    if result:
+        print("Cache hit!!!")
+        with Bench("Loading results"):
+            result = pickle.loads(result)
+    else:
+        print("Cache miss!!!")
+        template_vars = interval_mapping.IntervalMapping(start_vars, temp_uuid)
+
+        template_vars.js_data = json.dumps(template_vars.js_data,
+                                           default=json_default_handler,
+                                           indent="   ")
+
+        result = template_vars.__dict__
+        
+        #causeerror
+        Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL))
+        Redis.expire(key, 60*60)
+
+    with Bench("Rendering template"):
+        rendered_template = render_template("interval_mapping.html", **result)
+
+    return rendered_template
+
 @app.route("/corr_compute", methods=('POST',))
 def corr_compute_page():
     print("In corr_compute, request.form is:", pf(request.form))