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-rwxr-xr-xwqflask/wqflask/marker_regression/marker_regression.py4
-rwxr-xr-xwqflask/wqflask/show_trait/show_trait.py1
-rwxr-xr-xwqflask/wqflask/static/new/javascript/dataset_menu_structure.json205
-rwxr-xr-xwqflask/wqflask/templates/show_trait_mapping_tools.html8
-rw-r--r--wqflask/wqflask/wgcna/wgcna_analysis.py2
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 = {}
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-26 04:18:20 +0000