Fixed issue where covariates weren't being passed when zooming in or remapping

Added loading paage for zooming/remapping

Added temporary option for checking mapping scale in .geno files

6 files changed, 64 insertions, 22 deletions

diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index a7e11738..2a53b60e 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -166,6 +166,7 @@ class DisplayMappingResults(object):
         #Needing for form submission when doing single chr mapping or remapping after changing options
         self.samples = start_vars['samples']
         self.vals = start_vars['vals']
+        self.transform = start_vars['transform']
         self.mapping_method = start_vars['mapping_method']
         self.mapping_results_path = start_vars['mapping_results_path']
         if self.mapping_method == "rqtl_geno":
@@ -233,6 +234,8 @@ class DisplayMappingResults(object):
             self.covariates = start_vars['covariates']
         if 'maf' in start_vars.keys():
             self.maf = start_vars['maf']
+        else:
+            self.maf = ""
         if 'output_files' in start_vars.keys():
             self.output_files = start_vars['output_files']
         if 'use_loco' in start_vars.keys() and self.mapping_method == "gemma":
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index aae8e602..e1aa290b 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -36,7 +36,10 @@ def run_rqtl_geno(vals, samples, dataset, method, model, permCheck, num_perm, pe
     generate_cross_from_geno(dataset)
     GENOtoCSVR                 = ro.r["GENOtoCSVR"]            # Map the local GENOtoCSVR function
     crossfilelocation = TMPDIR + crossname + ".cross"
-    genofilelocation  = locate(dataset.group.genofile, "genotype")
+    if dataset.group.genofile:
+        genofilelocation  = locate(dataset.group.genofile, "genotype")
+    else:
+        genofilelocation = locate(dataset.group.name + ".geno", "genotype")
     cross_object = GENOtoCSVR(genofilelocation, crossfilelocation)      # TODO: Add the SEX if that is available
 
     if manhattan_plot:
@@ -91,9 +94,11 @@ def run_rqtl_geno(vals, samples, dataset, method, model, permCheck, num_perm, pe
                     perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", n_perm = num_perm, model=model, method=method)
 
             perm_output, suggestive, significant = process_rqtl_perm_results(num_perm, perm_data_frame)          # Functions that sets the thresholds for the webinterface
-            return perm_output, suggestive, significant, process_rqtl_results(result_data_frame, dataset.group.species)
+            the_scale = check_mapping_scale(genofilelocation)
+            return perm_output, suggestive, significant, process_rqtl_results(result_data_frame, dataset.group.species), the_scale
         else:
-            return process_rqtl_results(result_data_frame, dataset.group.species)
+            the_scale = check_mapping_scale(genofilelocation)
+            return process_rqtl_results(result_data_frame, dataset.group.species), the_scale
 
 def generate_cross_from_rdata(dataset):
     rdata_location  = locate(dataset.group.name + ".RData", "genotype/rdata")
@@ -286,4 +291,20 @@ def process_rqtl_results(result, species_name):        # TODO: how to make this
         marker['lod_score'] = output[i][2]
         qtl_results.append(marker)
 
-    return qtl_results
\ No newline at end of file
+    return qtl_results
+
+def check_mapping_scale(genofile_location):
+    scale = "physic"
+    with open(genofile_location, "r") as geno_fh:
+        for line in geno_fh:
+            if line[0] == "@" or line[0] == "#":
+
+                if "@scale" in line:
+                    scale = line.split(":")[1].strip()
+                    break
+                else:
+                    continue
+            else:
+                break
+
+    return scale
\ No newline at end of file
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index e191902c..589be702 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -150,6 +150,10 @@ class RunMapping(object):
         self.suggestive = ""
         self.significant = ""
         self.pair_scan = False # Initializing this since it is checked in views to determine which template to use
+        if 'transform' in start_vars:
+            self.transform = start_vars['transform']
+        else:
+            self.transform = ""
         self.score_type = "LRS" #ZS: LRS or LOD
         self.mapping_scale = "physic"
         self.num_perm = 0
@@ -241,7 +245,6 @@ class RunMapping(object):
 
                     perm_strata = get_perm_strata(self.this_trait, primary_samples, self.categorical_vars, self.samples)
             self.score_type = "LOD"
-            #self.mapping_scale = "morgan"
             self.control_marker = start_vars['control_marker']
             self.do_control = start_vars['do_control']
             if 'mapmethod_rqtl_geno' in start_vars:
@@ -252,9 +255,9 @@ class RunMapping(object):
             #if start_vars['pair_scan'] == "true":
             #    self.pair_scan = True
             if self.permCheck and self.num_perm > 0:
-                self.perm_output, self.suggestive, self.significant, results = rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates)
+                self.perm_output, self.suggestive, self.significant, results, self.mapping_scale = rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates)
             else:
-                results = rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates)
+                results, self.mapping_scale = rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates)
         elif self.mapping_method == "reaper":
             if "startMb" in start_vars: #ZS: Check if first time page loaded, so it can default to ON
                 if "additiveCheck" in start_vars:
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index ba0ebef9..7e05be18 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -36,7 +36,7 @@
         <input type="hidden" name="value:{{ sample }}" value="{{ vals[loop.index - 1] }}">
         {% endfor %}
         <input type="hidden" name="num_vals" value="{{ n_samples }}">
-        <input type="hidden" name="maf">
+        <input type="hidden" name="maf" value="{{ maf }}">
         <input type="hidden" name="use_loco" value="{{ use_loco }}">
         <input type="hidden" name="selected_chr" value="{{ selectedChr }}">
         <input type="hidden" name="manhattan_plot" value="{{ manhattan_plot }}">
@@ -45,10 +45,14 @@
         <input type="hidden" name="num_bootstrap" value="{{ nboot }}">
         <input type="hidden" name="do_control" value="{{ doControl }}">
         <input type="hidden" name="control_marker" value="{{ controlLocus }}">
-        <input type="hidden" name="covariates" values="{{ covariates }}">
+        <input type="hidden" name="covariates" value="{{ covariates }}">
         <input type="hidden" name="mapmethod_rqtl_geno" value="{{ mapmethod_rqtl_geno }}">
         <input type="hidden" name="mapmodel_rqtl_geno" value="{{ mapmodel_rqtl_geno }}">
         <input type="hidden" name="pair_scan" value="{{ pair_scan }}">
+        <input type="hidden" name="transform" value="{{ transform }}">
+        <input type="hidden" name="tool_used" value="Mapping">
+        <input type="hidden" name="wanted_inputs" value="">
+        <input type="hidden" name="form_url" value="/run_mapping">
         
         <div class="container">
           <div class="col-xs-5">
@@ -422,11 +426,19 @@
 
         });
 
+        var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale',
+                            'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars', 'num_bootstrap', 'bootCheck', 'bootstrap_results',
+                            'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'control_marker', 'control_marker_db', 'do_control', 'genofile', 
+                            'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck', 
+                            'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'reaper_version', 'primary_samples', 'num_vals']
+
+        $('input[name=wanted_inputs]').val(mapping_input_list.join(","));
+
         chrView = function(this_chr, chr_mb_list) {
             $('input[name=selected_chr]').val(this_chr)
             $('input[name=chr_mb_list]').val(chr_mb_list)
 
-            $('#marker_regression_form').attr('action', '/run_mapping');
+            $('#marker_regression_form').attr('action', '/loading');
             return $('#marker_regression_form').submit();
         };
 
@@ -436,13 +448,13 @@
             $('input[name=endMb]').val(end_mb)
             //$('input[name=mb_range]').val(start_mb + "," + end_mb)
 
-            $('#marker_regression_form').attr('action', '/run_mapping');
+            $('#marker_regression_form').attr('action', '/loading');
             return $('#marker_regression_form').submit();
         };
 
         remap = function() { 
             $('input[name=selected_chr]').val($('select[name=chromosomes]').val());
-            $('#marker_regression_form').attr('action', '/run_mapping');
+            $('#marker_regression_form').attr('action', '/loading');
             return $('#marker_regression_form').submit(); 
         };
 
diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py
index 40d9925c..edd272c2 100644
--- a/wqflask/wqflask/user_login.py
+++ b/wqflask/wqflask/user_login.py
@@ -42,9 +42,6 @@ def basic_info():
                 user_agent = request.headers.get('User-Agent'))
 
 def encode_password(pass_gen_fields, unencrypted_password):
-    logger.debug("THE TYPE:", type(pass_gen_fields))
-    logger.debug("pass_gen_fields:", pass_gen_fields)
-    logger.debug("hashfunc:", pass_gen_fields['hashfunc'])
     hashfunc = getattr(hashlib, pass_gen_fields['hashfunc'])
 
     salt = base64.b64decode(pass_gen_fields['salt'])
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 76857650..e351a2d4 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -583,18 +583,23 @@ def loading_page():
             if key in wanted or key.startswith(('value:')):
                 start_vars[key] = value
 
-        if 'primary_samples' in start_vars:
-            samples = start_vars['primary_samples'].split(",")
-            for sample in samples:
-                value = start_vars.get('value:' + sample)
-                if value != "x":
-                    num_vals += 1
+        if 'num_vals' in start_vars:
+            num_vals = int(start_vars['num_vals'])
+        else:
+            if 'primary_samples' in start_vars:
+                samples = start_vars['primary_samples'].split(",")
+                for sample in samples:
+                    value = start_vars.get('value:' + sample)
+                    if value != "x":
+                        num_vals += 1
 
         start_vars['num_vals'] = num_vals
+        start_vars['wanted_inputs'] = initial_start_vars['wanted_inputs']
 
         start_vars_container['start_vars'] = start_vars
     else:
         start_vars_container['start_vars'] = initial_start_vars
+
     rendered_template = render_template("loading.html", **start_vars_container)
 
     return rendered_template
@@ -658,7 +663,8 @@ def mapping_results_page():
         'mapmodel_rqtl_geno',
         'temp_trait',
         'reaper_version',
-        'num_vals'
+        'num_vals',
+        'transform'
     )
     start_vars = {}
     for key, value in initial_start_vars.iteritems():