From 809990fca27c0bae3573c0572c384cb6f6f3325d Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 22 May 2015 21:47:48 +0000
Subject: Fixed issue where correlation didn't work for human traits (and
 probably some others)

---
 wqflask/base/mrna_assay_tissue_data.py          |  6 +++---
 wqflask/base/trait.py                           |  2 ++
 wqflask/wqflask/templates/correlation_page.html | 10 +++++++++-
 3 files changed, 14 insertions(+), 4 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py
index 1a05fce7..b2c0448a 100755
--- a/wqflask/base/mrna_assay_tissue_data.py
+++ b/wqflask/base/mrna_assay_tissue_data.py
@@ -51,15 +51,15 @@ class MrnaAssayTissueData(object):
             
             query += ''' Symbol in {} group by Symbol)
                 as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol
-                and t.Mean = x.maxmean;
+                and t.Mean = x.maxmean;http://docs.python.org/2/library/string.html?highlight=lower#string.lower
                     '''.format(in_clause)
 
         results = g.db.execute(query).fetchall()
         
         for result in results:
             symbol = result[0]
-            if symbol in gene_symbols:
-            #gene_symbols.append(symbol)
+            if symbol.lower() in [gene_symbol.lower() for gene_symbol in gene_symbols]:
+                #gene_symbols.append(symbol)
                 symbol = symbol.lower()
                 
                 self.data[symbol].gene_id = result.GeneId
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 8930c917..7f1170a9 100755
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -423,6 +423,8 @@ class GeneralTrait(object):
                             if result:
                                 self.locus_chr = result[0]
                                 self.locus_mb = result[1]
+                            else:
+                                self.locus = self.locus_chr = self.locus_mb = ""
                         else:
                             self.locus = self.locus_chr = self.locus_mb = ""
                     else:
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 169371be..74919c88 100755
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -85,8 +85,16 @@
                         <td>{{ trait.description }} <br><br> <b>Aliases</b>: {{ trait.alias }}</td>
                         <td>Chr{{ trait.chr }}: {{'%0.6f'|format(trait.mb) if trait.mb != None }}</td>
                         <td>{{'%0.3f'|format(trait.mean)}}</td>
+                        {% if trait.lrs == "" or trait.lrs == 0.000 %}
+                        <td>--</td>
+                        {% else %}
                         <td>{{'%0.3f'|format(trait.lrs)}}</td>
-                        <td>Chr{{ trait.locus_chr }}: {{'%0.3f'|format(trait.locus_mb) }}</td>
+                        {% endif %}
+                        {% if trait.locus_mb == "" %}
+                        <td>--</td>
+                        {% else %}
+                        <td>Chr{{ trait.locus_chr if trait.locus_chr != None }}: {{'%0.3f'|format(trait.locus_mb)}}</td>
+                        {% endif %}
                         <td><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{'%0.3f'|format(trait.sample_r)}}</a></td>
                         <td>{{ trait.num_overlap }}</td>
                         <td>{{'%0.3e'|format(trait.sample_p)}}</td>
-- 
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