Remove references to reaper_version and code for running old qtlreaper

5 files changed, 24 insertions, 136 deletions

diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 77d6e2db..6254b9b9 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -357,8 +357,7 @@ class DisplayMappingResults:
         if 'use_loco' in list(start_vars.keys()) and self.mapping_method == "gemma":
             self.use_loco = start_vars['use_loco']
 
-        if 'reaper_version' in list(start_vars.keys()) and self.mapping_method == "reaper":
-            self.reaper_version = start_vars['reaper_version']
+        if self.mapping_method == "reaper":
             if 'output_files' in start_vars:
                 self.output_files = ",".join(
                     [(the_file if the_file is not None else "") for the_file in start_vars['output_files']])
diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
index 4d6715ba..801674e1 100644
--- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
+++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
@@ -178,101 +178,6 @@ def parse_reaper_output(gwa_filename, permu_filename, bootstrap_filename):
     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):
-    genotype = dataset.group.read_genotype_file(use_reaper=True)
-
-    if manhattan_plot != True:
-        genotype = genotype.addinterval()
-
-    trimmed_samples = []
-    trimmed_values = []
-    for i in range(0, len(samples_before)):
-        try:
-            trimmed_values.append(float(trait_vals[i]))
-            trimmed_samples.append(str(samples_before[i]))
-        except:
-            pass
-
-    perm_output = []
-    bootstrap_results = []
-
-    if num_perm < 100:
-        suggestive = 0
-        significant = 0
-    else:
-        perm_output = genotype.permutation(
-            strains=trimmed_samples, trait=trimmed_values, nperm=num_perm)
-        suggestive = perm_output[int(num_perm * 0.37 - 1)]
-        significant = perm_output[int(num_perm * 0.95 - 1)]
-        # highly_significant = perm_output[int(num_perm*0.99-1)] #ZS: Currently not used, but leaving it here just in case
-
-    json_data['suggestive'] = suggestive
-    json_data['significant'] = significant
-
-    if control_marker != "" and do_control == "true":
-        reaper_results = genotype.regression(strains=trimmed_samples,
-                                             trait=trimmed_values,
-                                             control=str(control_marker))
-        if bootCheck:
-            control_geno = []
-            control_geno2 = []
-            _FIND = 0
-            for _chr in genotype:
-                for _locus in _chr:
-                    if _locus.name == control_marker:
-                        control_geno2 = _locus.genotype
-                        _FIND = 1
-                        break
-                if _FIND:
-                    break
-            if control_geno2:
-                _prgy = list(genotype.prgy)
-                for _strain in trimmed_samples:
-                    _idx = _prgy.index(_strain)
-                    control_geno.append(control_geno2[_idx])
-
-            bootstrap_results = genotype.bootstrap(strains=trimmed_samples,
-                                                   trait=trimmed_values,
-                                                   control=control_geno,
-                                                   nboot=num_bootstrap)
-    else:
-        reaper_results = genotype.regression(strains=trimmed_samples,
-                                             trait=trimmed_values)
-
-        if bootCheck:
-            bootstrap_results = genotype.bootstrap(strains=trimmed_samples,
-                                                   trait=trimmed_values,
-                                                   nboot=num_bootstrap)
-
-    json_data['chr'] = []
-    json_data['pos'] = []
-    json_data['lod.hk'] = []
-    json_data['markernames'] = []
-    # if self.additive:
-    #    self.json_data['additive'] = []
-
-    # Need to convert the QTL objects that qtl reaper returns into a json serializable dictionary
-    qtl_results = []
-    for qtl in reaper_results:
-        reaper_locus = qtl.locus
-        # ZS: Convert chr to int
-        converted_chr = reaper_locus.chr
-        if reaper_locus.chr != "X" and reaper_locus.chr != "X/Y":
-            converted_chr = int(reaper_locus.chr)
-        json_data['chr'].append(converted_chr)
-        json_data['pos'].append(reaper_locus.Mb)
-        json_data['lod.hk'].append(qtl.lrs)
-        json_data['markernames'].append(reaper_locus.name)
-        # if self.additive:
-        #    self.json_data['additive'].append(qtl.additive)
-        locus = {"name": reaper_locus.name, "chr": reaper_locus.chr,
-                 "cM": reaper_locus.cM, "Mb": reaper_locus.Mb}
-        qtl = {"lrs_value": qtl.lrs, "chr": converted_chr, "Mb": reaper_locus.Mb,
-               "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
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 1df53fef..290c4a14 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -271,47 +271,32 @@ class RunMapping:
                     self.bootCheck = False
                     self.num_bootstrap = 0
 
-            self.reaper_version = start_vars['reaper_version']
-
             self.control_marker = start_vars['control_marker']
             self.do_control = start_vars['do_control']
             logger.info("Running qtlreaper")
 
-            if self.reaper_version == "new":
-                self.first_run = True
-                self.output_files = None
-                # ZS: check if first run so existing result files can be used if it isn't (for example zooming on a chromosome, etc)
-                if 'first_run' in start_vars:
-                    self.first_run = False
-                    if 'output_files' in start_vars:
-                        self.output_files = start_vars['output_files'].split(
-                            ",")
-
-                results, self.perm_output, self.suggestive, self.significant, self.bootstrap_results, self.output_files = qtlreaper_mapping.run_reaper(self.this_trait,
-                                                                                                                                                       self.dataset,
-                                                                                                                                                       self.samples,
-                                                                                                                                                       self.vals,
-                                                                                                                                                       self.json_data,
-                                                                                                                                                       self.num_perm,
-                                                                                                                                                       self.bootCheck,
-                                                                                                                                                       self.num_bootstrap,
-                                                                                                                                                       self.do_control,
-                                                                                                                                                       self.control_marker,
-                                                                                                                                                       self.manhattan_plot,
-                                                                                                                                                       self.first_run,
-                                                                                                                                                       self.output_files)
-            else:
-                results, self.json_data, self.perm_output, self.suggestive, self.significant, self.bootstrap_results = qtlreaper_mapping.run_original_reaper(self.this_trait,
-                                                                                                                                                             self.dataset,
-                                                                                                                                                             self.samples,
-                                                                                                                                                             self.vals,
-                                                                                                                                                             self.json_data,
-                                                                                                                                                             self.num_perm,
-                                                                                                                                                             self.bootCheck,
-                                                                                                                                                             self.num_bootstrap,
-                                                                                                                                                             self.do_control,
-                                                                                                                                                             self.control_marker,
-                                                                                                                                                             self.manhattan_plot)
+            self.first_run = True
+            self.output_files = None
+            # ZS: check if first run so existing result files can be used if it isn't (for example zooming on a chromosome, etc)
+            if 'first_run' in start_vars:
+                self.first_run = False
+                if 'output_files' in start_vars:
+                    self.output_files = start_vars['output_files'].split(
+                        ",")
+
+            results, self.perm_output, self.suggestive, self.significant, self.bootstrap_results, self.output_files = qtlreaper_mapping.run_reaper(self.this_trait,
+                                                                                                                                                    self.dataset,
+                                                                                                                                                    self.samples,
+                                                                                                                                                    self.vals,
+                                                                                                                                                    self.json_data,
+                                                                                                                                                    self.num_perm,
+                                                                                                                                                    self.bootCheck,
+                                                                                                                                                    self.num_bootstrap,
+                                                                                                                                                    self.do_control,
+                                                                                                                                                    self.control_marker,
+                                                                                                                                                    self.manhattan_plot,
+                                                                                                                                                    self.first_run,
+                                                                                                                                                    self.output_files)
         elif self.mapping_method == "plink":
             self.score_type = "-logP"
             self.manhattan_plot = True
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
index b75d658e..e42fe8c4 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -145,7 +145,7 @@ var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form
                           'sample_vals', 'vals_hash', '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',
                           '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']
+                          'haplotypeAnalystCheck', 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'primary_samples']
 
 $(".rqtl-geno-tab, #rqtl_geno_compute").on("click", (function(_this) {
   return function() {
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 85aa6b17..980b9362 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -1097,7 +1097,6 @@ def mapping_results_page():
         'mapmethod_rqtl_geno',
         'mapmodel_rqtl_geno',
         'temp_trait',
-        'reaper_version',
         'n_samples',
         'transform'
     )