Fixed serious issue that caused output to be wrong for new reaper mapping

Haplotype analyst now works for GEMMA

Increased margin a bit to fix minor issue with buttons getting cut off on certain Safari versions for bar chart

5 files changed, 27 insertions, 11 deletions

diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py
index e8780879..44e2722f 100644
--- a/wqflask/utility/gen_geno_ob.py
+++ b/wqflask/utility/gen_geno_ob.py
@@ -47,20 +47,20 @@ class genotype(object):
                 elif line[0] == "@":
                     label = line.split(":")[0][1:]
                     if label == "name":
-                        self.group = line.split(":")[1]
+                        self.group = line.split(":")[1].strip()
                     elif label == "filler":
-                        if line.split(":")[1] == "yes":
+                        if line.split(":")[1].strip() == "yes":
                             self.filler = True
                     elif label == "type":
-                        self.type = line.split(":")[1]
+                        self.type = line.split(":")[1].strip()
                     elif label == "mat":
-                        self.mat = line.split(":")[1]
+                        self.mat = line.split(":")[1].strip()
                     elif label == "pat":
-                        self.pat = line.split(":")[1]
+                        self.pat = line.split(":")[1].strip()
                     elif label == "het":
-                        self.het = line.split(":")[1]
+                        self.het = line.split(":")[1].strip()
                     elif label == "unk":
-                        self.unk = line.split(":")[1]
+                        self.unk = line.split(":")[1].strip()
                     else:
                         continue
                 elif line[:3] == "Chr":
@@ -133,6 +133,7 @@ class Locus(object):
             start_pos = 4
         else:
             start_pos = 3
+
         for allele in marker_row[start_pos:]:
             if allele in geno_table.keys():
                 self.genotype.append(geno_table[allele])
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index f3755758..a2f9651b 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -1341,7 +1341,7 @@ class DisplayMappingResults(object):
 
         for i, _chr in enumerate(self.genotype):
             if _chr.name == self.ChrList[self.selectedChr][0]:
-                for j, _geno in enumerate(_chr[1]):
+                for j, _geno in enumerate(_chr[1].genotype):
 
                     plotbxd=0
                     for item in smd:
diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
index 50e6bd7e..fe216166 100644
--- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
+++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
@@ -1,4 +1,4 @@
-import os, math, string, random, json
+import os, math, string, random, json, re
 
 from base import webqtlConfig
 from base.trait import GeneralTrait
@@ -105,6 +105,9 @@ def parse_reaper_output(gwa_filename, permu_filename, bootstrap_filename):
                 marker['additive'] = float(line.split("\t")[6])
                 marker_obs.append(marker)
 
+    #ZS: Results have to be reordered because the new reaper returns results sorted alphabetically by chr for some reason, resulting in chr 1 being followed by 10, etc
+    sorted_indices = natural_sort(marker_obs)
+
     permu_vals = []
     if permu_filename:
         with open("{}{}.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, permu_filename)) as permu_file:
@@ -117,6 +120,9 @@ def parse_reaper_output(gwa_filename, permu_filename, bootstrap_filename):
             for line in bootstrap_file:
                 bootstrap_vals.append(int(line))
 
+    marker_obs = [marker_obs[i] for i in sorted_indices]
+    bootstrap_vals = [bootstrap_vals[i] for i in sorted_indices]
+
     return marker_obs, permu_vals, bootstrap_vals
 
 def run_original_reaper(this_trait, dataset, samples_before, trait_vals, json_data, num_perm, bootCheck, num_bootstrap, do_control, control_marker, manhattan_plot):
@@ -210,3 +216,12 @@ def run_original_reaper(this_trait, dataset, samples_before, trait_vals, json_da
                "cM":reaper_locus.cM, "name":reaper_locus.name, "additive":qtl.additive, "dominance":qtl.dominance}
         qtl_results.append(qtl)
     return qtl_results, json_data, perm_output, suggestive, significant, bootstrap_results
+
+def natural_sort(marker_list):
+    """
+    Function to naturally sort numbers + strings, adopted from user Mark Byers here: https://stackoverflow.com/questions/4836710/does-python-have-a-built-in-function-for-string-natural-sort
+    Changed to return indices instead of values, though, since the same reordering needs to be applied to bootstrap results
+    """
+    convert = lambda text: int(text) if text.isdigit() else text.lower()
+    alphanum_key = lambda key: [ convert(c) for c in re.split('([0-9]+)', str(marker_list[key]['chr'])) ]
+    return sorted(range(len(marker_list)), key = alphanum_key)
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 1fc792d8..8422b1d2 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -144,7 +144,7 @@
                     <span style="color:red;">*</span>
                   <br>
                   <input type="checkbox" name="showGenes" class="checkbox" style="display: inline; margin-top: 0px;" {% if geneChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Gene Track </span> <span style="color:red;">*</span><br>
-                  {% if plotScale != "morgan" and mapping_method != "gemma" and mapping_method != "plink" %}
+                  {% if plotScale != "morgan" %}
                   <input type="checkbox" name="haplotypeAnalystCheck" class="checkbox" style="display: inline; margin-top: 0px;" {% if haplotypeAnalystChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Haplotype Analyst </span> <span style="color:red;">*</span><br>
                   {% endif %}
                   <input type="checkbox" name="viewLegend" class="checkbox" style="display: inline; margin-top: 0px;" {% if legendChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Legend </span>
diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html
index 1093e1bb..4653b398 100644
--- a/wqflask/wqflask/templates/show_trait_statistics.html
+++ b/wqflask/wqflask/templates/show_trait_statistics.html
@@ -70,7 +70,7 @@
                             </select>
                         </div>
                         {% endif %}
-                        <div id="update_bar_chart" class="btn-group">
+                        <div id="update_bar_chart" class="btn-group" style="margin-bottom: 5px;">
                             <button type="button" class="btn btn-default sort_by_name" value="name">
                             <i class="icon-resize-horizontal"></i> Sort By Name
                             </button>