Changed a lot about how mapping scale is read and gave the option to change mapping scale when both scales are available

7 files changed, 177 insertions, 48 deletions

diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 2a53b60e..f70bc555 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -265,14 +265,12 @@ class DisplayMappingResults(object):
         else:
             self.colorCollection = [self.LRS_COLOR]
 
+        self.dataset.group.genofile = self.genofile_string.split(":")[0]
         if self.mapping_method == "reaper" and self.manhattan_plot != True:
             self.genotype = self.dataset.group.read_genotype_file(use_reaper=True)
         else:
             self.genotype = self.dataset.group.read_genotype_file()
 
-        #if self.mapping_method == "rqtl_geno" and self.genotype.filler == True:
-        #    self.genotype = self.genotype.read_rdata_output(self.qtlresults)
-
         #Darwing Options
         try:
            if self.selectedChr > -1:
@@ -1761,9 +1759,9 @@ class DisplayMappingResults(object):
                 break
 
         if all_int:
-            max_lrs_width = canvas.stringWidth("%d" % LRS_LOD_Max, font=LRSScaleFont) + 30
+            max_lrs_width = canvas.stringWidth("%d" % LRS_LOD_Max, font=LRSScaleFont) + 40
         else:
-            max_lrs_width = canvas.stringWidth("%2.1f" % LRS_LOD_Max, font=LRSScaleFont) + 20
+            max_lrs_width = canvas.stringWidth("%2.1f" % LRS_LOD_Max, font=LRSScaleFont) + 30
 
         #draw the "LRS" or "LOD" string to the left of the axis
         canvas.drawString(self.LRS_LOD, xLeftOffset - max_lrs_width - 15*(zoom-1), \
@@ -1899,13 +1897,16 @@ class DisplayMappingResults(object):
                 this_chr = str(self.ChrList[self.selectedChr][1]+1)
 
             if self.selectedChr == -1 or str(qtlresult['chr']) == this_chr:
-                if self.plotScale != "physic" and self.genotype.filler == True:
-                    if self.selectedChr != -1:
-                        start_cm = self.genotype[self.selectedChr - 1][0].cM
-                        Xc = startPosX + (qtlresult['Mb'] - start_cm)*plotXScale
-                    else:
-                        start_cm = self.genotype[previous_chr_as_int][0].cM
-                        Xc = startPosX + ((qtlresult['Mb']-start_cm-startMb)*plotXScale)*(((qtlresult['Mb']-start_cm-startMb)*plotXScale)/((qtlresult['Mb']-start_cm-startMb+self.GraphInterval)*plotXScale))
+                if self.plotScale != "physic" and self.mapping_method == "reaper" and not self.manhattan_plot:
+                    Xc = startPosX + (qtlresult['cM']-startMb)*plotXScale
+                    if hasattr(self.genotype, "filler"):
+                        if self.genotype.filler:
+                            if self.selectedChr != -1:
+                                start_cm = self.genotype[self.selectedChr - 1][0].cM
+                                Xc = startPosX + (qtlresult['Mb'] - start_cm)*plotXScale
+                            else:
+                                start_cm = self.genotype[previous_chr_as_int][0].cM
+                                Xc = startPosX + ((qtlresult['Mb']-start_cm-startMb)*plotXScale)*(((qtlresult['Mb']-start_cm-startMb)*plotXScale)/((qtlresult['Mb']-start_cm-startMb+self.GraphInterval)*plotXScale))
                 else:
                     Xc = startPosX + (qtlresult['Mb']-startMb)*plotXScale
 
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index c1a56787..8c294460 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -11,7 +11,7 @@ from utility.tools import locate, TEMPDIR
 import utility.logger
 logger = utility.logger.getLogger(__name__ )
 
-def run_rqtl_geno(vals, samples, dataset, method, model, permCheck, num_perm, perm_strata_list, do_control, control_marker, manhattan_plot, pair_scan, cofactors):
+def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permCheck, num_perm, perm_strata_list, do_control, control_marker, manhattan_plot, pair_scan, cofactors):
     ## Get pointers to some common R functions
     r_library     = ro.r["library"]                 # Map the library function
     r_c           = ro.r["c"]                       # Map the c function
@@ -33,7 +33,13 @@ def run_rqtl_geno(vals, samples, dataset, method, model, permCheck, num_perm, pe
     #    genofilelocation  = locate(crossname + ".RData", "genotype/rdata")
     #    cross_object = read_cross_from_rdata(genofilelocation)  # Map the local GENOtoCSVR function
     #except:
-    generate_cross_from_geno(dataset)
+
+    if mapping_scale == "morgan":
+        scale_units = "cM"
+    else:
+        scale_units = "Mb"
+
+    generate_cross_from_geno(dataset, scale_units)
     GENOtoCSVR                 = ro.r["GENOtoCSVR"]            # Map the local GENOtoCSVR function
     crossfilelocation = TMPDIR + crossname + ".cross"
     if dataset.group.genofile:
@@ -47,6 +53,8 @@ def run_rqtl_geno(vals, samples, dataset, method, model, permCheck, num_perm, pe
     else:
         cross_object = calc_genoprob(cross_object, step=1, stepwidth="max")
 
+    logger.debug("VAL LEN:", len(vals))
+
     pheno_string = sanitize_rqtl_phenotype(vals)
 
     cross_object = add_phenotype(cross_object, pheno_string, "the_pheno")                 # Add the phenotype
@@ -94,11 +102,9 @@ 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
-            the_scale = check_mapping_scale(genofilelocation)
-            return perm_output, suggestive, significant, process_rqtl_results(result_data_frame, dataset.group.species), the_scale
+            return perm_output, suggestive, significant, process_rqtl_results(result_data_frame, dataset.group.species)
         else:
-            the_scale = check_mapping_scale(genofilelocation)
-            return process_rqtl_results(result_data_frame, dataset.group.species), the_scale
+            return process_rqtl_results(result_data_frame, dataset.group.species)
 
 def generate_cross_from_rdata(dataset):
     rdata_location  = locate(dataset.group.name + ".RData", "genotype/rdata")
@@ -110,7 +116,7 @@ def generate_cross_from_rdata(dataset):
        }
     """ % (rdata_location))
 
-def generate_cross_from_geno(dataset):        # TODO: Need to figure out why some genofiles have the wrong format and don't convert properly
+def generate_cross_from_geno(dataset, scale_units):        # TODO: Need to figure out why some genofiles have the wrong format and don't convert properly
 
     ro.r("""
        trim <- function( x ) { gsub("(^[[:space:]]+|[[:space:]]+$)", "", x) }
@@ -127,21 +133,23 @@ def generate_cross_from_geno(dataset):        # TODO: Need to figure out why som
          type <- getGenoCode(header, 'type')
          if(type == '4-way'){
             genocodes <- c('1','2','3','4')
+            genodata <- read.csv(genotypes, sep='\t', skip=toskip, header=TRUE, na.strings=getGenoCode(header,'unk'), colClasses='character', comment.char = '#', crosstype="4way")
          } else {
             genocodes <- c(getGenoCode(header, 'mat'), getGenoCode(header, 'het'), getGenoCode(header, 'pat'))             # Get the genotype codes
+            genodata <- read.csv(genotypes, sep='\t', skip=toskip, header=TRUE, na.strings=getGenoCode(header,'unk'), colClasses='character', comment.char = '#')
          }
-         genodata <- read.csv(genotypes, sep='\t', skip=toskip, header=TRUE, na.strings=getGenoCode(header,'unk'), colClasses='character', comment.char = '#')
          cat('Genodata:', toskip, " ", dim(genodata), genocodes, '\n')
          if(is.null(phenotype)) phenotype <- runif((ncol(genodata)-4))                                                     # If there isn't a phenotype, generate a random one
          if(is.null(sex)) sex <- rep('m', (ncol(genodata)-4))                                                              # If there isn't a sex phenotype, treat all as males
          outCSVR <- rbind(c('Pheno', '', '', phenotype),                                                                   # Phenotype
                           c('sex', '', '', sex),                                                                           # Sex phenotype for the mice
-                          cbind(genodata[,c('Locus','Chr', 'cM')], genodata[, 5:ncol(genodata)]))                          # Genotypes
+                          cbind(genodata[,c('Locus','Chr', '%s')], genodata[, 5:ncol(genodata)]))                    # Genotypes
          write.table(outCSVR, file = out, row.names=FALSE, col.names=FALSE,quote=FALSE, sep=',')                           # Save it to a file
          require(qtl)
          if(type == '4-way'){
            cat('Loading in as 4-WAY\n')
-           cross = read.cross(file=out, 'csvr', genotypes=genocodes, crosstype="4way", convertXdata=FALSE)                 # Load the created cross file using R/qtl read.cross
+           cross = read.cross(file=out, 'csvr', genotypes=genocodes)
+           #cross = read.cross(file=out, 'csvr', genotypes=genocodes, crosstype="4way", convertXdata=FALSE)                 # Load the created cross file using R/qtl read.cross
          }else{
            cat('Loading in as normal\n')
            cross = read.cross(file=out, 'csvr', genotypes=genocodes)                                                       # Load the created cross file using R/qtl read.cross
@@ -152,7 +160,7 @@ def generate_cross_from_geno(dataset):        # TODO: Need to figure out why som
          }
          return(cross)
       }
-    """ % (dataset.group.genofile))
+    """ % (dataset.group.genofile, scale_units))
 
 def add_perm_strata(cross, perm_strata):
     col_string = 'c("the_strata")'
@@ -300,20 +308,4 @@ 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
-
-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
+    return qtl_results
\ 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 589be702..7449d8ce 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -156,6 +156,8 @@ class RunMapping(object):
             self.transform = ""
         self.score_type = "LRS" #ZS: LRS or LOD
         self.mapping_scale = "physic"
+        if "mapping_scale" in start_vars:
+            self.mapping_scale = start_vars['mapping_scale']
         self.num_perm = 0
         self.perm_output = []
         self.bootstrap_results = []
@@ -255,9 +257,9 @@ 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, 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)
+                self.perm_output, self.suggestive, self.significant, results= rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.mapping_scale, 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, 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)
+                results = rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.mapping_scale, 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:
@@ -429,7 +431,7 @@ class RunMapping(object):
               with Bench("Trimming Markers for Table"):
                   self.trimmed_markers = trim_markers_for_table(results)
 
-              chr_lengths = get_chr_lengths(self.mapping_scale, self.dataset, self.qtl_results)
+              chr_lengths = get_chr_lengths(self.mapping_scale, self.mapping_method, self.dataset, self.qtl_results)
 
               #ZS: For zooming into genome browser, need to pass chromosome name instead of number
               if self.dataset.group.species == "mouse":
@@ -643,7 +645,7 @@ def geno_db_exists(this_dataset):
     except:
         return "False"
 
-def get_chr_lengths(mapping_scale, dataset, qtl_results):
+def get_chr_lengths(mapping_scale, mapping_method, dataset, qtl_results):
     chr_lengths = []
     if mapping_scale == "physic":
         for i, the_chr in enumerate(dataset.species.chromosomes.chromosomes):
@@ -666,8 +668,12 @@ def get_chr_lengths(mapping_scale, dataset, qtl_results):
                 this_chr = chr_as_num
                 highest_pos = 0
             else:
-                if float(result['Mb']) > highest_pos:
-                    highest_pos = float(result['Mb'])
+                if mapping_method == "reaper":
+                    if float(result['cM']) > highest_pos:
+                        highest_pos = float(result['cM'])
+                else:
+                    if float(result['Mb']) > highest_pos:
+                        highest_pos = float(result['Mb'])
 
     return chr_lengths
 
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 8883e627..40e344b8 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -22,6 +22,7 @@ from base import webqtlConfig
 from base import webqtlCaseData
 from wqflask.show_trait.SampleList import SampleList
 from utility import webqtlUtil, Plot, Bunch, helper_functions
+from utility.tools import locate_ignore_error
 from base.trait import GeneralTrait
 from base import data_set
 from db import webqtlDatabaseFunction
@@ -170,6 +171,17 @@ class ShowTrait(object):
 
         self.genofiles = self.dataset.group.get_genofiles()
 
+        if "QTLReaper" or "R/qtl" in dataset.group.mapping_names: #ZS: No need to grab scales from .geno file unless it's using a mapping method that reads .geno files
+            if self.genofiles:
+                self.scales_in_geno = get_genotype_scales(self.genofiles)
+            else:
+                self.scales_in_geno = get_genotype_scales(self.dataset.group + ".geno")
+
+            if len(self.scales_in_geno) < 2:
+                hddn['mapping_scale'] = self.scales_in_geno[self.scales_in_geno.keys()[0]][0]
+        else:
+            self.scales_in_geno = {}
+
         self.has_num_cases = has_num_cases(self.this_trait)
 
         self.stats_table_width, self.trait_table_width = get_table_widths(self.sample_groups, self.has_num_cases)
@@ -239,6 +251,7 @@ class ShowTrait(object):
                 #hddn['control_marker'] = self.nearest_marker1+","+self.nearest_marker2
         hddn['do_control'] = False
         hddn['maf'] = 0.05
+        hddn['mapping_scale'] = "physic"
         hddn['compare_traits'] = []
         hddn['export_data'] = ""
         hddn['export_format'] = "excel"
@@ -251,6 +264,7 @@ class ShowTrait(object):
                        short_description = short_description,
                        unit_type = trait_units,
                        dataset_type = self.dataset.type,
+                       scales_in_geno = self.scales_in_geno,
                        data_scale = self.dataset.data_scale,
                        sample_group_types = self.sample_group_types,
                        sample_lists = sample_lists,
@@ -597,4 +611,77 @@ def get_categorical_variables(this_trait, sample_list):
             if num_distinct < 10:
                 categorical_var_list.append(sample_list.attributes[attribute].name)
 
-    return categorical_var_list
\ No newline at end of file
+    return categorical_var_list
+
+def get_genotype_scales(genofiles):
+    geno_scales = {}
+    if type(genofiles) is list:
+        for the_file in genofiles:
+            file_location = the_file['location']
+            geno_scales[file_location] = get_scales_from_genofile(file_location)
+    else:
+        geno_scales[genofiles] = get_scales_from_genofile(genofiles)
+
+    return geno_scales
+
+def get_scales_from_genofile(file_location):
+    geno_path = locate_ignore_error(file_location, 'genotype')
+
+    if not geno_path: #ZS: This is just to allow the code to run when
+        return [["physic", "Mb"]]
+    cm_and_mb_cols_exist = True
+    cm_column = None
+    mb_column = None
+    with open(geno_path, "r") as geno_fh:
+        for i, line in enumerate(geno_fh):
+            if line[0] == "#" or line[0] == "@":
+                if "@scale" in line: #ZS: If the scale is made explicit in the metadata, use that
+                    scale = line.split(":")[1].strip()
+                    if scale == "morgan":
+                        return [["morgan", "cM"]]
+                    else:
+                        return [["physic", "Mb"]]
+                else:
+                    continue
+            if line[:3] == "Chr":
+                first_marker_line = i + 1
+                if line.split("\t")[2].strip() == "cM":
+                    cm_column = 2
+                elif line.split("\t")[3].strip() == "cM":
+                    cm_column = 3
+                if line.split("\t")[2].strip() == "Mb":
+                    mb_column = 2
+                elif line.split("\t")[3].strip() == "Mb":
+                    mb_column = 3
+                break
+
+        #ZS: This attempts to check whether the cM and Mb columns are 'real', since some .geno files have one column be a copy of the other column, or have one column that is all 0s
+        cm_all_zero = True
+        mb_all_zero = True
+        cm_mb_all_equal = True
+        for i, line in enumerate(geno_fh):
+            if first_marker_line <= i < first_marker_line + 10: #ZS: I'm assuming there won't be more than 10 markers where the position is listed as 0
+                if cm_column:
+                    cm_val = line.split("\t")[cm_column].strip()
+                    if cm_val != "0":
+                        cm_all_zero = False
+                if mb_column:
+                    mb_val = line.split("\t")[mb_column].strip()
+                    if mb_val != "0":
+                        mb_all_zero = False
+                if cm_column and mb_column:
+                    if cm_val != mb_val:
+                        cm_mb_all_equal = False
+            else:
+                if i > first_marker_line + 10:
+                    break
+
+    #ZS: This assumes that both won't be all zero, since if that's the case mapping shouldn't be an option to begin with
+    if mb_all_zero:
+        return [["morgan", "cM"]]
+    elif cm_mb_all_equal:
+        return [["physic", "Mb"]]
+    elif cm_and_mb_cols_exist:
+        return [["physic", "Mb"], ["morgan", "cM"]]
+    else:
+        return [["physic", "Mb"]]
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 478ed87e..7176a0da 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -165,6 +165,7 @@
         url = "/loading";
         $('input[name=method]').val("rqtl_geno");
         $('input[name=selected_chr]').val($('#chr_rqtl_geno').val());
+        $('input[name=mapping_scale]').val($('#scale_rqtl_geno').val());
         $('input[name=genofile]').val($('#genofile_rqtl_geno').val());
         $('input[name=num_perm]').val($('input[name=num_perm_rqtl_geno]').val());
         $('input[name=categorical_vars]').val(js_data.categorical_vars)
@@ -210,6 +211,7 @@
         url = "/loading";
         $('input[name=method]').val("reaper");
         $('input[name=selected_chr]').val($('#chr_reaper').val());
+        $('input[name=mapping_scale]').val($('#scale_reaper').val());
         $('input[name=genofile]').val($('#genofile_reaper').val());
         $('input[name=num_perm]').val($('input[name=num_perm_reaper]').val());
         $('input[name=control_marker]').val($('input[name=control_reaper]').val());
@@ -289,4 +291,21 @@
     return toggle_enable_disable("#suggestive_lrs");
   });
 
+  $('#genofile_rqtl_geno').change(function() {
+    geno_location = $(this).children("option:selected").val().split(":")[0]
+    $('#scale_rqtl_geno').empty()
+    the_scales = js_data.scales_in_geno[geno_location]
+    for (var i = 0; i < the_scales.length; i++){
+      $('#scale_rqtl_geno').append($("<option></option>").attr("value", the_scales[i][0]).text(the_scales[i][1]));
+    }
+  });
+  $('#genofile_reaper').change(function() {
+    geno_location = $(this).children("option:selected").val().split(":")[0]
+    $('#scale_reaper').empty()
+    the_scales = js_data.scales_in_geno[geno_location]
+    for (var i = 0; i < the_scales.length; i++){
+      $('#scale_reaper').append($("<option></option>").attr("value", the_scales[i][0]).text(the_scales[i][1]));
+    }
+  });
+
 }).call(this);
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 7e05be18..94ac0350 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -274,7 +274,11 @@
                 {% endif %}
                 <td align="right">{{marker.chr}}</td>
                 {% if plotScale != "physic" %}
+                {% if 'cM' in marker %}
+                <td align="right">{{ '%0.3f' | format(marker.cM|float) }}</td>
+                {% else %}
                 <td align="right">{{ '%0.3f' | format(marker.Mb|float) }}</td>
+                {% endif %}
                 {% else %}
                 <td align="right">{{ '%0.6f' | format(marker.Mb|float) }}</td>
                 {% endif %}
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 777d4a2d..7c897409 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -121,6 +121,16 @@
                         </div>
                         {% if genofiles and genofiles|length>0 %}
                         <div class="mapping_method_fields form-group">
+                            <label for="scale_select" style="text-align: right;" class="col-xs-3 control-label">Map Scale</label>
+                            <div style="margin-left:20px;" class="col-xs-2 controls">
+                                <select id="scale_reaper" class="form-control" style="width: 80px;">
+                                    {% for item in scales_in_geno[genofiles[0]['location']] %}
+                                    <option value="{{ item[0] }}">{{ item[1] }}</option>
+                                    {% endfor %}
+                                </select>
+                            </div>
+                        </div>
+                        <div class="mapping_method_fields form-group">
                             <label style="text-align: right;" for="genofiles" class="col-xs-3 control-label">Genotypes</label>
                             <div style="margin-left:20px;" class="col-xs-4 controls">
                                 <select id="genofile_reaper" class="form-control">
@@ -225,7 +235,17 @@
                                 </select>
                             </div>
                         </div>
-                        {% if genofiles and genofiles|length>0 %}
+                        {% if genofiles and genofiles|length > 0 %}
+                        <div class="mapping_method_fields form-group">
+                            <label for="scale_select" style="text-align: right;" class="col-xs-3 control-label">Map Scale</label>
+                            <div style="margin-left:20px;" class="col-xs-2 controls">
+                                <select id="scale_rqtl_geno" class="form-control" style="width: 80px;">
+                                    {% for item in scales_in_geno[genofiles[0]['location']] %}
+                                    <option value="{{ item[0] }}">{{ item[1] }}</option>
+                                    {% endfor %}
+                                </select>
+                            </div>
+                        </div>
                         <div class="mapping_method_fields form-group">
                             <label style="text-align:right;" for="genofiles" class="col-xs-3 control-label">Genotypes</label>
                             <div style="margin-left:20px;" class="col-xs-4 controls">