PLINK should not run correctly and graph using GN1 image

Updated dataset menu structure json

Increased the width for the label and text field for inputting MAF for PLINK and GEMMA

5 files changed, 117 insertions, 103 deletions

diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 5377201b..a6fa5274 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -87,7 +87,7 @@ class MarkerRegression(object):
  
         self.dataset.group.get_markers()
         if self.mapping_method == "gemma":
-            self.score_type = "LRS"
+            self.score_type = "LOD"
             included_markers, p_values = gemma_mapping.run_gemma(self.dataset, self.samples, self.vals)
             self.dataset.group.get_specified_markers(markers = included_markers)
             self.dataset.group.markers.add_pvalues(p_values)
@@ -492,7 +492,7 @@ class MarkerRegression(object):
         
         self.gen_pheno_txt_file_plink(pheno_filename = plink_output_filename)
         
-        plink_command = PLINK_COMMAND + ' --noweb --ped %s/%s.ped --no-fid --no-parents --no-sex --no-pheno --map %s/%s.map --pheno %s%s.txt --pheno-name %s --maf %s --missing-phenotype -9999 --out %s%s --assoc ' % (PLINK_PATH, self.dataset.group.name, PLINK_PATH, self.dataset.group.name, webqtlConfig.TMPDIR, plink_output_filename, self.this_trait.name, self.maf, webqtlConfig.TMPDIR, plink_output_filename)
+        plink_command = PLINK_COMMAND + ' --noweb --bed %s/%s.bed --bim %s/%s.bim --fam %s/%s.fam --no-fid --no-parents --no-sex --no-pheno --pheno %s%s.txt --pheno-name %s --maf %s --missing-phenotype -9999 --out %s%s --assoc ' % (PLINK_PATH, self.dataset.group.name, PLINK_PATH, self.dataset.group.name, PLINK_PATH, self.dataset.group.name, webqtlConfig.TMPDIR, plink_output_filename, self.this_trait.name, self.maf, webqtlConfig.TMPDIR, plink_output_filename)
         print("plink_command:", plink_command)        
 
         os.system(plink_command)
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index aa6f9562..d6c48a12 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -161,7 +161,6 @@ class ShowTrait(object):
         def check_plink_gemma():
             if (os.path.isfile(PLINK_PATH+"/"+self.dataset.group.name+".bed") and
                 os.path.isfile(PLINK_PATH+"/"+self.dataset.group.name+".map")):
-
                 return True
             else:
                 return False
diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
index 2154541c..2b16383f 100755
--- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
+++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
@@ -117,14 +117,14 @@
                   "Barley1 Leaf MAS 5.0 SCRI (Dec06)"
                ],
                [
-                  "126",
-                  "B30_K_1206_Rn",
-                  "Barley1 Leaf gcRMAn SCRI (Dec06)"
-               ],
-               [
                   "125",
                   "B30_K_1206_R",
                   "Barley1 Leaf gcRMA SCRI (Dec06)"
+               ],
+               [
+                  "126",
+                  "B30_K_1206_Rn",
+                  "Barley1 Leaf gcRMAn SCRI (Dec06)"
                ]
             ],
             "Phenotypes": [
@@ -1340,14 +1340,14 @@
                   "GSE9588 Human Liver Normal (Mar11) Both Sexes"
                ],
                [
-                  "383",
-                  "HLCM_0311",
-                  "GSE9588 Human Liver Normal (Mar11) Males"
-               ],
-               [
                   "384",
                   "HLCF_0311",
                   "GSE9588 Human Liver Normal (Mar11) Females"
+               ],
+               [
+                  "383",
+                  "HLCM_0311",
+                  "GSE9588 Human Liver Normal (Mar11) Males"
                ]
             ],
             "Phenotypes": [
@@ -1510,14 +1510,14 @@
                   "NCI Mammary LMT miRNA v2 (Apr09) RMA"
                ],
                [
-                  "37",
-                  "MA_M_0704_R",
-                  "NCI Mammary mRNA M430 (July04) RMA"
-               ],
-               [
                   "36",
                   "MA_M_0704_M",
                   "NCI Mammary mRNA M430 (July04) MAS5"
+               ],
+               [
+                  "37",
+                  "MA_M_0704_R",
+                  "NCI Mammary mRNA M430 (July04) RMA"
                ]
             ]
          },
@@ -1575,14 +1575,14 @@
             ],
             "Liver mRNA": [
                [
-                  "39",
-                  "LVF2_M_0704_R",
-                  "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) RMA"
-               ],
-               [
                   "38",
                   "LVF2_M_0704_M",
                   "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) MAS5"
+               ],
+               [
+                  "39",
+                  "LVF2_M_0704_R",
+                  "(B6 x BTBR)F2-ob/ob Liver mRNA M430 (Jul04) RMA"
                ]
             ],
             "Phenotypes": [
@@ -1596,11 +1596,6 @@
          "B6D2F2": {
             "Brain mRNA": [
                [
-                  "76",
-                  "BRF2_M_0805_M",
-                  "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) MAS5"
-               ],
-               [
                   "78",
                   "BRF2_M_0805_P",
                   "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) PDNN"
@@ -1611,19 +1606,24 @@
                   "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) RMA"
                ],
                [
+                  "76",
+                  "BRF2_M_0805_M",
+                  "OHSU/VA B6D2F2 Brain mRNA M430 (Aug05) MAS5"
+               ],
+               [
                   "33",
                   "BRF2_M_0304_P",
                   "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) PDNN"
                ],
                [
-                  "32",
-                  "BRF2_M_0304_R",
-                  "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) RMA"
-               ],
-               [
                   "31",
                   "BRF2_M_0304_M",
                   "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) MAS5"
+               ],
+               [
+                  "32",
+                  "BRF2_M_0304_R",
+                  "OHSU/VA B6D2F2 Brain mRNA M430A (Mar04) RMA"
                ]
             ],
             "Genotypes": [
@@ -1685,11 +1685,6 @@
             ],
             "Striatum mRNA": [
                [
-                  "84",
-                  "SA_M2_0905_R",
-                  "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA"
-               ],
-               [
                   "83",
                   "SA_M2_0905_M",
                   "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) MAS5"
@@ -1698,22 +1693,27 @@
                   "85",
                   "SA_M2_0905_P",
                   "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) PDNN"
+               ],
+               [
+                  "84",
+                  "SA_M2_0905_R",
+                  "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA"
                ]
             ]
          },
          "BHF2": {
             "Adipose mRNA": [
                [
-                  "196",
-                  "UCLA_BHF2_ADIPOSE_MALE",
-                  "UCLA BHF2 Adipose Male mlratio"
-               ],
-               [
                   "197",
                   "UCLA_BHF2_ADIPOSE_FEMALE",
                   "UCLA BHF2 Adipose Female mlratio"
                ],
                [
+                  "196",
+                  "UCLA_BHF2_ADIPOSE_MALE",
+                  "UCLA BHF2 Adipose Male mlratio"
+               ],
+               [
                   "165",
                   "UCLA_BHF2_ADIPOSE_0605",
                   "UCLA BHF2 Adipose (June05) mlratio"
@@ -1721,16 +1721,16 @@
             ],
             "Brain mRNA": [
                [
-                  "198",
-                  "UCLA_BHF2_BRAIN_MALE",
-                  "UCLA BHF2 Brain Male mlratio"
-               ],
-               [
                   "199",
                   "UCLA_BHF2_BRAIN_FEMALE",
                   "UCLA BHF2 Brain Female mlratio"
                ],
                [
+                  "198",
+                  "UCLA_BHF2_BRAIN_MALE",
+                  "UCLA BHF2 Brain Male mlratio"
+               ],
+               [
                   "166",
                   "UCLA_BHF2_BRAIN_0605",
                   "UCLA BHF2 Brain (June05) mlratio"
@@ -1745,16 +1745,16 @@
             ],
             "Liver mRNA": [
                [
-                  "200",
-                  "UCLA_BHF2_LIVER_MALE",
-                  "UCLA BHF2 Liver Male mlratio"
-               ],
-               [
                   "201",
                   "UCLA_BHF2_LIVER_FEMALE",
                   "UCLA BHF2 Liver Female mlratio"
                ],
                [
+                  "200",
+                  "UCLA_BHF2_LIVER_MALE",
+                  "UCLA BHF2 Liver Male mlratio"
+               ],
+               [
                   "167",
                   "UCLA_BHF2_LIVER_0605",
                   "UCLA BHF2 Liver (June05) mlratio"
@@ -1946,6 +1946,11 @@
                   "UTHSC Brain mRNA U74Av2 (Nov05) PDNN"
                ],
                [
+                  "81",
+                  "BR_U_0805_P",
+                  "UTHSC Brain mRNA U74Av2 (Aug05) PDNN"
+               ],
+               [
                   "80",
                   "BR_U_0805_M",
                   "UTHSC Brain mRNA U74Av2 (Aug05) MAS5"
@@ -1956,11 +1961,6 @@
                   "UTHSC Brain mRNA U74Av2 (Aug05) RMA"
                ],
                [
-                  "81",
-                  "BR_U_0805_P",
-                  "UTHSC Brain mRNA U74Av2 (Aug05) PDNN"
-               ],
-               [
                   "42",
                   "CB_M_0204_P",
                   "INIA Brain mRNA M430 (Feb04) PDNN"
@@ -2027,11 +2027,6 @@
                   "Eye M430v2 WT Gpnmb (Sep08) RMA"
                ],
                [
-                  "278",
-                  "Eye_M2_0908_R_MT",
-                  "Eye M430v2 Mutant Tyrp1 (Sep08) RMA"
-               ],
-               [
                   "382",
                   "Eye_M2_0908_WTWT",
                   "Eye M430v2 WT WT (Sep08) RMA"
@@ -2042,6 +2037,11 @@
                   "Eye M430v2 WT Tyrp1 (Sep08) RMA"
                ],
                [
+                  "278",
+                  "Eye_M2_0908_R_MT",
+                  "Eye M430v2 Mutant Tyrp1 (Sep08) RMA"
+               ],
+               [
                   "400",
                   "DBA2J-ONH-1212",
                   "Howell et al. 2011, DBA/2J Glaucoma Optic Nerve Head M430 2.0 (Dec12) RMA"
@@ -2164,6 +2164,21 @@
                   "UMUTAffy Hippocampus Exon (Feb09) RMA"
                ],
                [
+                  "780",
+                  "UTHSC_ILM_BXD_hipp_NOEb_0216",
+                  "UTHSC BXD Hippocampus ILM v6.1 NOE Balanced (Feb16) RankInv"
+               ],
+               [
+                  "781",
+                  "UTHSC_ILM_BXD_hipp_RSEb_0216",
+                  "UTHSC BXD Hippocampus ILM v6.1 RSE Balanced (Feb16) RankInv"
+               ],
+               [
+                  "782",
+                  "UTHSC_ILM_BXD_hipp_RSSb_0216",
+                  "UTHSC BXD Hippocampus ILM v6.1 RSS Balanced (Feb16) RankInv"
+               ],
+               [
                   "291",
                   "UT_ILM_BXD_hipp_5T_1112",
                   "UTHSC Hippocampus Illumina v6.1 All Combined (Nov12) RankInv"
@@ -2283,14 +2298,14 @@
                   "Mouse Kidney M430v2 Sex Balanced (Aug06) PDNN"
                ],
                [
-                  "116",
-                  "MA_M2_0706_P",
-                  "Mouse Kidney M430v2 (Jul06) PDNN"
-               ],
-               [
                   "115",
                   "MA_M2_0706_R",
                   "Mouse Kidney M430v2 (Jul06) RMA"
+               ],
+               [
+                  "116",
+                  "MA_M2_0706_P",
+                  "Mouse Kidney M430v2 (Jul06) PDNN"
                ]
             ],
             "Liver Metabolome": [
@@ -2452,16 +2467,16 @@
             ],
             "Neocortex mRNA": [
                [
-                  "375",
-                  "DevNeocortex_ILM6.2P14RInv_1111",
-                  "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov11) RankInv"
-               ],
-               [
                   "374",
                   "DevNeocortex_ILM6.2P3RInv_1111",
                   "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov11) RankInv"
                ],
                [
+                  "375",
+                  "DevNeocortex_ILM6.2P14RInv_1111",
+                  "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov11) RankInv"
+               ],
+               [
                   "284",
                   "HQFNeoc_1210v2_RankInv",
                   "HQF BXD Neocortex ILM6v1.1 (Dec10v2) RankInv"
@@ -2477,14 +2492,14 @@
                   "HQF BXD Neocortex ILM6v1.1 (Feb08) RankInv"
                ],
                [
-                  "274",
-                  "DevNeocortex_ILM6.2P3RInv_1110",
-                  "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv"
-               ],
-               [
                   "275",
                   "DevNeocortex_ILM6.2P14RInv_1110",
                   "BIDMC/UTHSC Dev Neocortex P14 ILMv6.2 (Nov10) RankInv"
+               ],
+               [
+                  "274",
+                  "DevNeocortex_ILM6.2P3RInv_1110",
+                  "BIDMC/UTHSC Dev Neocortex P3 ILMv6.2 (Nov10) RankInv"
                ]
             ],
             "Nucleus Accumbens mRNA": [
@@ -2853,14 +2868,14 @@
             ],
             "Hippocampus mRNA": [
                [
-                  "100",
-                  "HC_M2CB_1205_R",
-                  "Hippocampus Consortium M430v2 CXB (Dec05) RMA"
-               ],
-               [
                   "99",
                   "HC_M2CB_1205_P",
                   "Hippocampus Consortium M430v2 CXB (Dec05) PDNN"
+               ],
+               [
+                  "100",
+                  "HC_M2CB_1205_R",
+                  "Hippocampus Consortium M430v2 CXB (Dec05) RMA"
                ]
             ],
             "Phenotypes": [
@@ -2927,16 +2942,6 @@
             ],
             "Hippocampus mRNA": [
                [
-                  "219",
-                  "Illum_LXS_Hipp_NON_1008",
-                  "Hippocampus Illumina NON (Oct08) RankInv beta"
-               ],
-               [
-                  "212",
-                  "Illum_LXS_Hipp_RSE_1008",
-                  "Hippocampus Illumina RSE (Oct08) RankInv beta"
-               ],
-               [
                   "214",
                   "Illum_LXS_Hipp_NOE_1008",
                   "Hippocampus Illumina NOE (Oct08) RankInv beta"
@@ -2952,6 +2957,16 @@
                   "Hippocampus Illumina NOS (Oct08) RankInv beta"
                ],
                [
+                  "219",
+                  "Illum_LXS_Hipp_NON_1008",
+                  "Hippocampus Illumina NON (Oct08) RankInv beta"
+               ],
+               [
+                  "212",
+                  "Illum_LXS_Hipp_RSE_1008",
+                  "Hippocampus Illumina RSE (Oct08) RankInv beta"
+               ],
+               [
                   "143",
                   "Illum_LXS_Hipp_loess0807",
                   "Hippocampus Illumina (Aug07) LOESS"
@@ -3042,14 +3057,14 @@
             ],
             "Hippocampus mRNA": [
                [
-                  "273",
-                  "UMUTAffyExon_0209_RMA_MDP",
-                  "UMUTAffy Hippocampus Exon (Feb09) RMA MDP"
-               ],
-               [
                   "272",
                   "HC_M2_0606_MDP",
                   "Hippocampus Consortium M430v2 (Jun06) RMA MDP"
+               ],
+               [
+                  "273",
+                  "UMUTAffyExon_0209_RMA_MDP",
+                  "UMUTAffy Hippocampus Exon (Feb09) RMA MDP"
                ]
             ],
             "Liver mRNA": [
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index c23cb010..6252f6f4 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -256,8 +256,8 @@
                 <div class="tab-pane" id="plink">
                     <div style="padding: 20px" class="form-horizontal">
                         <div class="mapping_method_fields form-group">
-                            <label for="maf_plink" class="col-xs-2 control-label">Minor allele threshold</label>
-                            <div style="margin-left: 20px;" class="col-xs-2 controls">
+                            <label for="maf_plink" class="col-xs-3 control-label">Minor allele threshold</label>
+                            <div style="margin-left: 20px;" class="col-xs-3 controls">
                                 <input name="maf_plink" value="0.01" type="text" class="form-control">
                             </div>
                         </div>
@@ -276,8 +276,8 @@
                 <div class="tab-pane" id="gemma">
                     <div style="padding: 20px" class="form-horizontal">
                         <div class="mapping_method_fields form-group">
-                            <label for="maf_gemma" class="col-xs-2 control-label">Minor allele threshold</label>
-                            <div style="margin-left: 20px;" class="col-xs-2 controls">
+                            <label for="maf_gemma" class="col-xs-3 control-label">Minor allele threshold</label>
+                            <div style="margin-left: 20px;" class="col-xs-3 controls">
                                 <input name="maf_gemma" value="0.01" type="text" class="form-control">
                             </div>
                         </div>
diff --git a/wqflask/wqflask/wgcna/wgcna_analysis.py b/wqflask/wqflask/wgcna/wgcna_analysis.py
index f23b1417..9e9f41bc 100644
--- a/wqflask/wqflask/wgcna/wgcna_analysis.py
+++ b/wqflask/wqflask/wgcna/wgcna_analysis.py
@@ -86,8 +86,8 @@ class WGCNA(object):
             trait = t[0]                  # R uses vectors every single element is a vector
             for s in uStrainsR:
                 strain = s[0]             # R uses vectors every single element is a vector
-                rM.rx[strain, trait] = self.input[trait].get(strain)  # Update the matrix location
                 #DEBUG: print(trait, strain, " in python: ", self.input[trait].get(strain), "in R:", rM.rx(strain,trait)[0])
+                rM.rx[strain, trait] = self.input[trait].get(strain)  # Update the matrix location
                 sys.stdout.flush()
 
         self.results = {}