Changed GEMMA mapping to use -lmm 2 (Likelihood ratio test) as a parameter instead of -lmm 1 (Wald test)

Added script to convert .geno files to JSON to maintenance folder (geno_to_json.py)

4 files changed, 214 insertions, 12 deletions

diff --git a/wqflask/maintenance/geno_to_json.py b/wqflask/maintenance/geno_to_json.py
new file mode 100644
index 00000000..789a1691
--- /dev/null
+++ b/wqflask/maintenance/geno_to_json.py
@@ -0,0 +1,195 @@
+#!/usr/bin/python
+
+"""
+Convert .geno files to json
+
+This file goes through all of the genofiles in the genofile directory (.geno)
+and converts them to json files that are used when running the marker regression
+code
+
+"""
+
+from __future__ import print_function, division, absolute_import
+import sys
+sys.path.append("..")
+import os
+import glob
+import traceback
+import gzip
+
+#import numpy as np
+#from pyLMM import lmm
+
+import simplejson as json
+
+from pprint import pformat as pf
+
+class EmptyConfigurations(Exception): pass
+
+        
+
+class Marker(object):
+    def __init__(self):
+        self.name = None
+        self.chr = None
+        self.cM = None
+        self.Mb = None
+        self.genotypes = []
+
+class ConvertGenoFile(object):
+
+    def __init__(self, input_file, output_file):
+        
+        self.input_file = input_file
+        self.output_file = output_file
+        
+        self.mb_exists = False
+        self.cm_exists = False
+        self.markers = []
+        
+        self.latest_row_pos = None
+        self.latest_col_pos = None
+        
+        self.latest_row_value = None
+        self.latest_col_value = None
+        
+    def convert(self):
+
+        self.haplotype_notation = {
+            '@mat': "1",
+            '@pat': "0",
+            '@het': "0.5",
+            '@unk': "NA"
+            }
+        
+        self.configurations = {}
+        #self.skipped_cols = 3
+        
+        #if self.input_file.endswith(".geno.gz"):
+        #    print("self.input_file: ", self.input_file)
+        #    self.input_fh = gzip.open(self.input_file)
+        #else:
+        self.input_fh = open(self.input_file)
+        
+        with open(self.output_file, "w") as self.output_fh:
+            #if self.file_type == "geno":
+            self.process_csv()
+            #elif self.file_type == "snps":
+            #    self.process_snps_file()
+
+
+    def process_csv(self):
+        for row_count, row in enumerate(self.process_rows()):
+            row_items = row.split("\t")
+
+            this_marker = Marker()
+            this_marker.name = row_items[1]
+            this_marker.chr = row_items[0]
+            if self.cm_exists and self.mb_exists:
+                this_marker.cM = row_items[2]
+                this_marker.Mb = row_items[3]
+                genotypes = row_items[4:]
+            elif self.cm_exists:
+                this_marker.cM = row_items[2]
+                genotypes = row_items[3:]
+            elif self.mb_exists:
+                this_marker.Mb = row_items[2]
+                genotypes = row_items[3:]
+            else:
+                genotypes = row_items[2:]
+            for item_count, genotype in enumerate(genotypes):
+                if genotype.upper() in self.configurations:
+                    this_marker.genotypes.append(self.configurations[genotype.upper()])
+                else:
+                    this_marker.genotypes.append("NA")
+                
+            #print("this_marker is:", pf(this_marker.__dict__))   
+            #if this_marker.chr == "14":
+            self.markers.append(this_marker.__dict__)
+
+        with open(self.output_file, 'w') as fh:
+            json.dump(self.markers, fh, indent="   ", sort_keys=True)
+                
+                # print('configurations:', str(configurations))
+                #self.latest_col_pos = item_count + self.skipped_cols
+                #self.latest_col_value = item
+                
+                #if item_count != 0:
+                #    self.output_fh.write(" ")
+                #self.output_fh.write(self.configurations[item.upper()])
+                    
+            #self.output_fh.write("\n")
+
+
+    def process_rows(self):
+        for self.latest_row_pos, row in enumerate(self.input_fh):
+            #if self.input_file.endswith(".geno.gz"):
+            #    print("row: ", row)
+            self.latest_row_value = row
+            # Take care of headers
+            if not row.strip():
+                continue
+            if row.startswith('#'):
+                continue
+            if row.startswith('Chr'):
+                if 'Mb' in row.split():
+                    self.mb_exists = True
+                if 'cM' in row.split():
+                    self.cm_exists = True
+                continue
+            if row.startswith('@'):
+                key, _separater, value = row.partition(':')
+                key = key.strip()
+                value = value.strip()
+                if key in self.haplotype_notation:
+                    self.configurations[value] = self.haplotype_notation[key]
+                continue
+            if not len(self.configurations):
+                raise EmptyConfigurations
+            yield row
+
+    @classmethod
+    def process_all(cls, old_directory, new_directory):
+        os.chdir(old_directory)
+        for input_file in glob.glob("*"):
+            if not input_file.endswith(('geno', '.geno.gz')):
+                continue
+            group_name = ".".join(input_file.split('.')[:-1])
+            output_file = os.path.join(new_directory, group_name + ".json")
+            print("%s -> %s" % (
+                os.path.join(old_directory, input_file), output_file))
+            convertob = ConvertGenoFile(input_file, output_file)
+            try:
+                convertob.convert()
+            except EmptyConfigurations as why:
+                print("  No config info? Continuing...")
+                #excepted = True
+                continue
+            except Exception as why:
+
+                print("  Exception:", why)
+                print(traceback.print_exc())
+                print("    Found in row %s at tabular column %s" % (convertob.latest_row_pos,
+                                                                convertob.latest_col_pos))
+                print("    Column is:", convertob.latest_col_value)
+                print("    Row is:", convertob.latest_row_value)
+                break
+            
+    #def process_snps_file(cls, snps_file, new_directory):
+    #    output_file = os.path.join(new_directory, "mouse_families.json")
+    #    print("%s -> %s" % (snps_file, output_file))
+    #    convertob = ConvertGenoFile(input_file, output_file)
+        
+
+
+if __name__=="__main__":
+    Old_Geno_Directory = """/home/zas1024/genotype_files/genotype/"""
+    New_Geno_Directory = """/home/zas1024/genotype_files/genotype/json/"""
+    #Input_File = """/home/zas1024/gene/genotype_files/genotypes/BXD.geno"""
+    #Output_File = """/home/zas1024/gene/wqflask/wqflask/pylmm/data/bxd.snps"""
+    #convertob = ConvertGenoFile("/home/zas1024/gene/genotype_files/genotypes/SRxSHRSPF2.geno", "/home/zas1024/gene/genotype_files/new_genotypes/SRxSHRSPF2.json")
+    #convertob.convert()
+    ConvertGenoFile.process_all(Old_Geno_Directory, New_Geno_Directory)
+    #ConvertGenoFiles(Geno_Directory)
+    
+    #process_csv(Input_File, Output_File)
\ No newline at end of file
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 157e4f33..0e31e73e 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -33,7 +33,7 @@ def run_gemma(this_dataset, samples, vals, covariates, method, use_loco):
         gen_covariates_file(this_dataset, covariates)
 
     if method == "gemma_plink":
-        gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/%s.cXX.txt -lmm 1 -maf 0.1' % (flat_files('mapping'),
+        gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/%s.cXX.txt -lmm 2 -maf 0.1' % (flat_files('mapping'),
                                                                                         this_dataset.group.name,
                                                                                         flat_files('mapping'),
                                                                                         this_dataset.group.name)
@@ -43,7 +43,7 @@ def run_gemma(this_dataset, samples, vals, covariates, method, use_loco):
                                                                                    webqtlConfig.GENERATED_IMAGE_DIR,
                                                                                    this_dataset.group.name)
         else:
-            #gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/%s.sXX.txt -lmm 1 -maf 0.1 -o %s_output' % (flat_files('mapping'),
+            #gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/%s.sXX.txt -lmm 2 -maf 0.1 -o %s_output' % (flat_files('mapping'),
             gemma_command += ' -outdir %s -o %s_output' % (webqtlConfig.GENERATED_IMAGE_DIR,
                                                            this_dataset.group.name)
     else:
@@ -69,20 +69,20 @@ def run_gemma(this_dataset, samples, vals, covariates, method, use_loco):
 
             gwa_output_filename = this_dataset.group.name + "_GWA_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
             if covariates != "":
-                gemma_command += ' -c %s/%s_covariates.txt -a %s/%s_snps.txt -lmm 1 -maf 0.1 -debug > %s/gn2/%s.json' % (flat_files('mapping'),
+                gemma_command += ' -c %s/%s_covariates.txt -a %s/%s_snps.txt -lmm 2 -maf 0.1 -debug > %s/gn2/%s.json' % (flat_files('mapping'),
                                                                                                                                          this_dataset.group.name,
                                                                                                                                          flat_files('genotype/bimbam'),
                                                                                                                                          genofile_name,
                                                                                                                                          TEMPDIR,
                                                                                                                                          gwa_output_filename)
             else:
-                gemma_command += ' -a %s/%s_snps.txt -lmm 1 -maf 0.1 -debug > %s/gn2/%s.json' % (flat_files('genotype/bimbam'),
+                gemma_command += ' -a %s/%s_snps.txt -lmm 2 -maf 0.1 -debug > %s/gn2/%s.json' % (flat_files('genotype/bimbam'),
                                                                                                                  genofile_name,
                                                                                                                  TEMPDIR,
                                                                                                                  gwa_output_filename)
 
         else:
-            gemma_command = GEMMA_COMMAND + ' -g %s/%s_geno.txt -p %s/%s_pheno.txt -a %s/%s_snps.txt -k %s/%s.cXX.txt -lmm 1 -maf 0.1' % (flat_files('genotype/bimbam'),
+            gemma_command = GEMMA_COMMAND + ' -g %s/%s_geno.txt -p %s/%s_pheno.txt -a %s/%s_snps.txt -k %s/%s.cXX.txt -lmm 2 -maf 0.1' % (flat_files('genotype/bimbam'),
                                                                                             genofile_name,
                                                                                             flat_files('genotype/bimbam'),
                                                                                             genofile_name,
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index da713325..8e9c5b4c 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -1062,10 +1062,6 @@ class MarkerRegression(object):
 
                 #draw gray blocks for 3' and 5' UTR blocks
                 if cdsStart and cdsEnd:
-                    logger.debug("txStart:", txStart)
-                    logger.debug("cdsStart:", cdsStart)
-                    logger.debug("txEnd:", txEnd)
-                    logger.debug("cdsEnd:", cdsEnd)
                     utrStartPix = (txStart-startMb)*plotXScale + xLeftOffset
                     utrEndPix = (cdsStart-startMb)*plotXScale + xLeftOffset
                     if (utrStartPix < xLeftOffset):
@@ -1721,8 +1717,8 @@ class MarkerRegression(object):
         for i, qtlresult in enumerate(self.qtlresults):
             m = 0
             thisLRSColor = self.colorCollection[0]
-
             if qtlresult['chr'] != previous_chr and self.selectedChr == -1:
+
                 if self.manhattan_plot != True:
                     canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
 
@@ -1760,7 +1756,6 @@ class MarkerRegression(object):
                 AdditiveCoordXY = []
                 previous_chr = qtlresult['chr']
                 previous_chr_as_int += 1
-
                 newStartPosX = (self.ChrLengthDistList[previous_chr_as_int - 1]+self.GraphInterval)*plotXScale
                 if newStartPosX != oldStartPosX:
                     startPosX += newStartPosX
@@ -1773,7 +1768,6 @@ class MarkerRegression(object):
                 this_chr = str(self.ChrList[self.selectedChr][1]+1)
             if self.selectedChr == -1 or str(qtlresult['chr']) == this_chr:
                 Xc = startPosX + (qtlresult['Mb']-startMb)*plotXScale
-
                 # updated by NL 06-18-2011:
                 # fix the over limit LRS graph issue since genotype trait may give infinite LRS;
                 # for any lrs is over than 460(LRS max in this system), it will be reset to 460
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 0ecf1eb9..d40a7bd6 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -343,6 +343,19 @@
                             </div>
                         </div>
                         <div class="mapping_method_fields form-group">
+                            <label style="text-align: right;" class="col-xs-3 control-label">Use LOCO</label>
+                            <div style="margin-left:20px;" class="col-xs-6 controls">
+                                <label class="radio-inline">
+                                    <input type="radio" name="use_loco" value="True" checked="">
+                                    Yes
+                                </label>
+                                <label class="radio-inline">
+                                    <input type="radio" name="use_loco" value="False">
+                                    No
+                               </label>
+                            </div>
+                        </div>
+                        <div class="mapping_method_fields form-group">
                             <label style="text-align: right;" class="col-xs-3 control-label">Covariates</label>
                             <div style="margin-left:20px;" class="col-xs-7">
                               {% if g.user_session.user_ob and (g.user_session.user_ob.display_num_collections() == "") %}