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authorZachary Sloan2013-07-18 17:39:10 -0500
committerZachary Sloan2013-07-18 17:39:10 -0500
commit0fcadee805a6d4a2007e57a69ab130eb9b1c1a3c (patch)
treec5c981b472d6d4754ad67cdb7e3682641fa6f35e /wqflask
parent89c4dc078c6371e4bc56bf8708fc7dca6c49b350 (diff)
downloadgenenetwork2-0fcadee805a6d4a2007e57a69ab130eb9b1c1a3c.tar.gz
Added Amelie's rat data genotypes
Got human mapping mostly working Fixed dataset dropdown menus
Diffstat (limited to 'wqflask')
-rwxr-xr-xwqflask/base/trait.py3
-rwxr-xr-xwqflask/base/webqtlConfig.py4
-rw-r--r--wqflask/maintenance/gen_select_dataset.py15
-rw-r--r--wqflask/wqflask/correlation/show_corr_results.py2
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/lmm.py4
-rw-r--r--wqflask/wqflask/static/new/javascript/dataset_menu_structure.json248
6 files changed, 131 insertions, 145 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 6648047c..a1e6b0d3 100755
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -319,10 +319,9 @@ class GeneralTrait(object):
#XZ: assign SQL query result to trait attributes.
for i, field in enumerate(self.dataset.display_fields):
- print(" mike: {} -> {} - {}".format(field, type(trait_info[i]), trait_info[i]))
+ #print(" mike: {} -> {} - {}".format(field, type(trait_info[i]), trait_info[i]))
holder = trait_info[i]
if isinstance(trait_info[i], basestring):
- print("is basestring")
holder = unicode(trait_info[i], "utf8")
setattr(self, field, holder)
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index 716986db..d4511212 100755
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -53,8 +53,8 @@ GNROOT = "/home/zas1024/gene/" # Will remove this and dependent items later
SECUREDIR = GNROOT + 'secure/'
COMMON_LIB = GNROOT + 'support/admin'
HTMLPATH = GNROOT + 'web/'
-PYLMM_PATH = '/home/zas1024/'
-SNP_PATH = '/mnt/xvdf1/snps/'
+PYLMM_PATH = '/home/zas1024/plink/'
+SNP_PATH = '/home/zas1024/snps/'
IMGDIR = HTMLPATH +'image/'
IMAGESPATH = HTMLPATH + 'images/'
UPLOADPATH = IMAGESPATH + 'upload/'
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index d653fd2d..8cb94f20 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -47,6 +47,15 @@ import urlparse
from pprint import pformat as pf
+#Engine = sa.create_engine(our_settings.SQLALCHEMY_DATABASE_URI)
+
+# build MySql database connection
+
+#conn = Engine.connect()
+
+
+
+
def parse_db_uri(db_uri):
"""Converts a database URI to the db name, host name, user name, and password"""
@@ -106,7 +115,7 @@ def build_types(species, group):
(all types except phenotype/genotype are tissues)
"""
- Cursor.execute("""select distinct Tissue.Name, concat(Tissue.Name, ' mRNA')
+ Cursor.execute("""select distinct Tissue.Name, Tissue.Name
from ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue, Species
where Species.Name = %s and Species.Id = InbredSet.SpeciesId and
InbredSet.Name = %s and
@@ -161,13 +170,9 @@ def build_datasets(species, group, type_name):
def main():
"""Generates and outputs (as json file) the data for the main dropdown menus on the home page"""
-<<<<<<< HEAD
parse_db_uri(our_settings.DB_URI)
-=======
-
->>>>>>> 1a3a456eb7635337a966913f2e2e75c8a89bb92e
species = get_species()
groups = get_groups(species)
types = get_types(groups)
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 422fa8af..07d70897 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -140,8 +140,6 @@ class CorrelationResults(object):
this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values(
this_trait_vals, target_vals)
- print("num_overlap:", num_overlap)
-
if self.corr_method == 'pearson':
sample_r, sample_p = scipy.stats.pearsonr(this_trait_vals, target_vals)
else:
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index 5bfc3a01..38a49f12 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -138,8 +138,8 @@ def run_human(pheno_vector,
#print("***** Added to {} queue *****".format(key))
for snp, this_id in plink_input:
#with Bench("part before association"):
- if count > 2000:
- break
+ #if count > 2000:
+ # break
count += 1
percent_complete = (float(count) / total_snps) * 100
diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
index a4de53bd..49c44fbd 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
+++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
@@ -798,10 +798,6 @@
"OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA"
],
[
- "SA_M2_0905_R",
- "OHSU/VA B6D2F2 Striatum M430v2 (Sep05) RMA"
- ],
- [
"SA_M2_0905_M",
"OHSU/VA B6D2F2 Striatum M430v2 (Sep05) MAS5"
],
@@ -1052,10 +1048,6 @@
],
"Cerebellum mRNA": [
[
- "CB_M_1004_M",
- "SJUT Cerebellum mRNA M430 (Oct04) MAS5"
- ],
- [
"CB_M_1004_R",
"SJUT Cerebellum mRNA M430 (Oct04) RMA"
],
@@ -1064,6 +1056,10 @@
"SJUT Cerebellum mRNA M430 (Oct04) PDNN"
],
[
+ "CB_M_1004_M",
+ "SJUT Cerebellum mRNA M430 (Oct04) MAS5"
+ ],
+ [
"CB_M_1003_M",
"SJUT Cerebellum mRNA M430 (Oct03) MAS5"
],
@@ -1552,10 +1548,6 @@
],
"Prefrontal Cortex mRNA": [
[
- "VCUEtOH_1206_R",
- "VCU BXD PFC EtOH M430 2.0 (Dec06) RMA"
- ],
- [
"VCUSal_1206_R",
"VCU BXD PFC Sal M430 2.0 (Dec06) RMA"
],
@@ -1730,10 +1722,6 @@
"VCU BXD VTA EtOH M430 2.0 (Jun09) RMA **"
],
[
- "VCUEtOH_0609_R",
- "VCU BXD VTA EtOH M430 2.0 (Jun09) RMA **"
- ],
- [
"VCUSal_0609_R",
"VCU BXD VTA Sal M430 2.0 (Jun09) RMA **"
],
@@ -2018,10 +2006,6 @@
"VCU LXS PFC EtOH M430A 2.0 (Aug06) RMA **"
],
[
- "VCUEtOH_0806_R",
- "VCU LXS PFC EtOH M430A 2.0 (Aug06) RMA **"
- ],
- [
"VCUSal_0806_R",
"VCU LXS PFC Sal M430A 2.0 (Aug06) RMA"
],
@@ -2572,7 +2556,7 @@
],
[
"Leaf mRNA",
- "Leaf mRNA mRNA"
+ "Leaf mRNA"
]
],
"SXM": [
@@ -2586,11 +2570,11 @@
],
[
"Embryo mRNA",
- "Embryo mRNA mRNA"
+ "Embryo mRNA"
],
[
"Leaf mRNA",
- "Leaf mRNA mRNA"
+ "Leaf mRNA"
]
]
},
@@ -2606,7 +2590,7 @@
],
[
"Whole Body mRNA",
- "Whole Body mRNA mRNA"
+ "Whole Body mRNA"
]
],
"Oregon-R_x_2b3": [
@@ -2620,7 +2604,7 @@
],
[
"Whole Body mRNA",
- "Whole Body mRNA mRNA"
+ "Whole Body mRNA"
]
]
},
@@ -2636,7 +2620,7 @@
],
[
"Brain mRNA",
- "Brain mRNA mRNA"
+ "Brain mRNA"
]
],
"AD-cases-controls-Myers": [
@@ -2650,7 +2634,7 @@
],
[
"Brain mRNA",
- "Brain mRNA mRNA"
+ "Brain mRNA"
]
],
"CANDLE": [
@@ -2664,11 +2648,11 @@
],
[
"Methylation",
- "Methylation mRNA"
+ "Methylation"
],
[
"Newborn Cord Blood mRNA",
- "Newborn Cord Blood mRNA mRNA"
+ "Newborn Cord Blood mRNA"
]
],
"CEPH-2004": [
@@ -2682,7 +2666,7 @@
],
[
"Lymphoblast B-cell mRNA",
- "Lymphoblast B-cell mRNA mRNA"
+ "Lymphoblast B-cell mRNA"
]
],
"HB": [
@@ -2696,15 +2680,15 @@
],
[
"Cerebellum mRNA",
- "Cerebellum mRNA mRNA"
+ "Cerebellum mRNA"
],
[
"Prefrontal Cortex mRNA",
- "Prefrontal Cortex mRNA mRNA"
+ "Prefrontal Cortex mRNA"
],
[
"Primary Visual Cortex mRNA",
- "Primary Visual Cortex mRNA mRNA"
+ "Primary Visual Cortex mRNA"
]
],
"HLC": [
@@ -2718,7 +2702,7 @@
],
[
"Liver mRNA",
- "Liver mRNA mRNA"
+ "Liver mRNA"
]
],
"HLT": [
@@ -2732,7 +2716,7 @@
],
[
"Lung mRNA",
- "Lung mRNA mRNA"
+ "Lung mRNA"
]
],
"HSB": [
@@ -2746,67 +2730,67 @@
],
[
"Amygdala mRNA",
- "Amygdala mRNA mRNA"
+ "Amygdala mRNA"
],
[
"Cerebellar Cortex mRNA",
- "Cerebellar Cortex mRNA mRNA"
+ "Cerebellar Cortex mRNA"
],
[
"Dorsolateral Prefrontal Cortex mRNA",
- "Dorsolateral Prefrontal Cortex mRNA mRNA"
+ "Dorsolateral Prefrontal Cortex mRNA"
],
[
"Hippocampus mRNA",
- "Hippocampus mRNA mRNA"
+ "Hippocampus mRNA"
],
[
"Inferior Temporal Cortex mRNA",
- "Inferior Temporal Cortex mRNA mRNA"
+ "Inferior Temporal Cortex mRNA"
],
[
"Medial Prefrontal Cortex mRNA",
- "Medial Prefrontal Cortex mRNA mRNA"
+ "Medial Prefrontal Cortex mRNA"
],
[
"Mediodorsal Nucleus of Thalamus mRNA",
- "Mediodorsal Nucleus of Thalamus mRNA mRNA"
+ "Mediodorsal Nucleus of Thalamus mRNA"
],
[
"Orbital Prefrontal Cortex mRNA",
- "Orbital Prefrontal Cortex mRNA mRNA"
+ "Orbital Prefrontal Cortex mRNA"
],
[
"Posterior Inferior Parietal Cortex mRNA",
- "Posterior Inferior Parietal Cortex mRNA mRNA"
+ "Posterior Inferior Parietal Cortex mRNA"
],
[
"Posterior Superior Temporal Cortex mRNA",
- "Posterior Superior Temporal Cortex mRNA mRNA"
+ "Posterior Superior Temporal Cortex mRNA"
],
[
"Primary Auditory (A1) Cortex mRNA",
- "Primary Auditory (A1) Cortex mRNA mRNA"
+ "Primary Auditory (A1) Cortex mRNA"
],
[
"Primary Motor (M1) Cortex mRNA",
- "Primary Motor (M1) Cortex mRNA mRNA"
+ "Primary Motor (M1) Cortex mRNA"
],
[
"Primary Somatosensory (S1) Cortex mRNA",
- "Primary Somatosensory (S1) Cortex mRNA mRNA"
+ "Primary Somatosensory (S1) Cortex mRNA"
],
[
"Primary Visual Cortex mRNA",
- "Primary Visual Cortex mRNA mRNA"
+ "Primary Visual Cortex mRNA"
],
[
"Striatum mRNA",
- "Striatum mRNA mRNA"
+ "Striatum mRNA"
],
[
"Ventrolateral Prefrontal Cortex mRNA",
- "Ventrolateral Prefrontal Cortex mRNA mRNA"
+ "Ventrolateral Prefrontal Cortex mRNA"
]
]
},
@@ -2822,23 +2806,23 @@
],
[
"Amygdala mRNA",
- "Amygdala mRNA mRNA"
+ "Amygdala mRNA"
],
[
"Brain mRNA",
- "Brain mRNA mRNA"
+ "Brain mRNA"
],
[
"Hippocampus mRNA",
- "Hippocampus mRNA mRNA"
+ "Hippocampus mRNA"
],
[
"Nucleus Accumbens mRNA",
- "Nucleus Accumbens mRNA mRNA"
+ "Nucleus Accumbens mRNA"
],
[
"Prefrontal Cortex mRNA",
- "Prefrontal Cortex mRNA mRNA"
+ "Prefrontal Cortex mRNA"
]
]
},
@@ -2854,7 +2838,7 @@
],
[
"Mammary Tumors mRNA",
- "Mammary Tumors mRNA mRNA"
+ "Mammary Tumors mRNA"
]
],
"AXBXA": [
@@ -2868,19 +2852,19 @@
],
[
"Bone Femur mRNA",
- "Bone Femur mRNA mRNA"
+ "Bone Femur mRNA"
],
[
"Eye mRNA",
- "Eye mRNA mRNA"
+ "Eye mRNA"
],
[
"Heart mRNA",
- "Heart mRNA mRNA"
+ "Heart mRNA"
],
[
"Liver mRNA",
- "Liver mRNA mRNA"
+ "Liver mRNA"
]
],
"B6BTBRF2": [
@@ -2894,7 +2878,7 @@
],
[
"Liver mRNA",
- "Liver mRNA mRNA"
+ "Liver mRNA"
]
],
"B6D2F2": [
@@ -2908,7 +2892,7 @@
],
[
"Brain mRNA",
- "Brain mRNA mRNA"
+ "Brain mRNA"
]
],
"B6D2F2-PSU": [
@@ -2922,7 +2906,7 @@
],
[
"Muscle mRNA",
- "Muscle mRNA mRNA"
+ "Muscle mRNA"
]
],
"B6D2RI": [
@@ -2936,7 +2920,7 @@
],
[
"Hippocampus mRNA",
- "Hippocampus mRNA mRNA"
+ "Hippocampus mRNA"
]
],
"BDF2-1999": [
@@ -2950,7 +2934,7 @@
],
[
"Liver mRNA",
- "Liver mRNA mRNA"
+ "Liver mRNA"
]
],
"BDF2-2005": [
@@ -2964,7 +2948,7 @@
],
[
"Striatum mRNA",
- "Striatum mRNA mRNA"
+ "Striatum mRNA"
]
],
"BHF2": [
@@ -2978,19 +2962,19 @@
],
[
"Adipose mRNA",
- "Adipose mRNA mRNA"
+ "Adipose mRNA"
],
[
"Brain mRNA",
- "Brain mRNA mRNA"
+ "Brain mRNA"
],
[
"Liver mRNA",
- "Liver mRNA mRNA"
+ "Liver mRNA"
],
[
"Muscle mRNA",
- "Muscle mRNA mRNA"
+ "Muscle mRNA"
]
],
"BHHBF2": [
@@ -3004,19 +2988,19 @@
],
[
"Adipose mRNA",
- "Adipose mRNA mRNA"
+ "Adipose mRNA"
],
[
"Brain mRNA",
- "Brain mRNA mRNA"
+ "Brain mRNA"
],
[
"Liver mRNA",
- "Liver mRNA mRNA"
+ "Liver mRNA"
],
[
"Muscle mRNA",
- "Muscle mRNA mRNA"
+ "Muscle mRNA"
]
],
"BXD": [
@@ -3030,119 +3014,119 @@
],
[
"Adrenal Gland mRNA",
- "Adrenal Gland mRNA mRNA"
+ "Adrenal Gland mRNA"
],
[
"Amygdala mRNA",
- "Amygdala mRNA mRNA"
+ "Amygdala mRNA"
],
[
"Bone Femur mRNA",
- "Bone Femur mRNA mRNA"
+ "Bone Femur mRNA"
],
[
"Brain mRNA",
- "Brain mRNA mRNA"
+ "Brain mRNA"
],
[
"Cartilage mRNA",
- "Cartilage mRNA mRNA"
+ "Cartilage mRNA"
],
[
"Cerebellum mRNA",
- "Cerebellum mRNA mRNA"
+ "Cerebellum mRNA"
],
[
"Eye mRNA",
- "Eye mRNA mRNA"
+ "Eye mRNA"
],
[
"Hematopoietic Cells mRNA",
- "Hematopoietic Cells mRNA mRNA"
+ "Hematopoietic Cells mRNA"
],
[
"Hippocampus mRNA",
- "Hippocampus mRNA mRNA"
+ "Hippocampus mRNA"
],
[
"Hypothalamus mRNA",
- "Hypothalamus mRNA mRNA"
+ "Hypothalamus mRNA"
],
[
"Kidney mRNA",
- "Kidney mRNA mRNA"
+ "Kidney mRNA"
],
[
"Leucocytes mRNA",
- "Leucocytes mRNA mRNA"
+ "Leucocytes mRNA"
],
[
"Liver mRNA",
- "Liver mRNA mRNA"
+ "Liver mRNA"
],
[
"Liver Proteome",
- "Liver Proteome mRNA"
+ "Liver Proteome"
],
[
"Lung mRNA",
- "Lung mRNA mRNA"
+ "Lung mRNA"
],
[
"Midbrain mRNA",
- "Midbrain mRNA mRNA"
+ "Midbrain mRNA"
],
[
"Muscle mRNA",
- "Muscle mRNA mRNA"
+ "Muscle mRNA"
],
[
"Neocortex mRNA",
- "Neocortex mRNA mRNA"
+ "Neocortex mRNA"
],
[
"Nucleus Accumbens mRNA",
- "Nucleus Accumbens mRNA mRNA"
+ "Nucleus Accumbens mRNA"
],
[
"Pituitary Gland mRNA",
- "Pituitary Gland mRNA mRNA"
+ "Pituitary Gland mRNA"
],
[
"Popliteal Lymph Node mRNA",
- "Popliteal Lymph Node mRNA mRNA"
+ "Popliteal Lymph Node mRNA"
],
[
"Prefrontal Cortex mRNA",
- "Prefrontal Cortex mRNA mRNA"
+ "Prefrontal Cortex mRNA"
],
[
"Retina mRNA",
- "Retina mRNA mRNA"
+ "Retina mRNA"
],
[
"Spleen mRNA",
- "Spleen mRNA mRNA"
+ "Spleen mRNA"
],
[
"Striatum mRNA",
- "Striatum mRNA mRNA"
+ "Striatum mRNA"
],
[
"T Cell (helper) mRNA",
- "T Cell (helper) mRNA mRNA"
+ "T Cell (helper) mRNA"
],
[
"T Cell (regulatory) mRNA",
- "T Cell (regulatory) mRNA mRNA"
+ "T Cell (regulatory) mRNA"
],
[
"Thymus mRNA",
- "Thymus mRNA mRNA"
+ "Thymus mRNA"
],
[
"Ventral Tegmental Area mRNA",
- "Ventral Tegmental Area mRNA mRNA"
+ "Ventral Tegmental Area mRNA"
]
],
"BXH": [
@@ -3156,15 +3140,15 @@
],
[
"Bone Femur mRNA",
- "Bone Femur mRNA mRNA"
+ "Bone Femur mRNA"
],
[
"Cartilage mRNA",
- "Cartilage mRNA mRNA"
+ "Cartilage mRNA"
],
[
"Liver mRNA",
- "Liver mRNA mRNA"
+ "Liver mRNA"
]
],
"C57BL-6JxC57BL-6NJF2": [
@@ -3188,19 +3172,19 @@
],
[
"Adipose mRNA",
- "Adipose mRNA mRNA"
+ "Adipose mRNA"
],
[
"Brain mRNA",
- "Brain mRNA mRNA"
+ "Brain mRNA"
],
[
"Liver mRNA",
- "Liver mRNA mRNA"
+ "Liver mRNA"
],
[
"Muscle mRNA",
- "Muscle mRNA mRNA"
+ "Muscle mRNA"
]
],
"CXB": [
@@ -3214,11 +3198,11 @@
],
[
"Hippocampus mRNA",
- "Hippocampus mRNA mRNA"
+ "Hippocampus mRNA"
],
[
"Spleen mRNA",
- "Spleen mRNA mRNA"
+ "Spleen mRNA"
]
],
"HS": [
@@ -3232,15 +3216,15 @@
],
[
"Hippocampus mRNA",
- "Hippocampus mRNA mRNA"
+ "Hippocampus mRNA"
],
[
"Liver mRNA",
- "Liver mRNA mRNA"
+ "Liver mRNA"
],
[
"Lung mRNA",
- "Lung mRNA mRNA"
+ "Lung mRNA"
]
],
"HS-CC": [
@@ -3254,7 +3238,7 @@
],
[
"Striatum mRNA",
- "Striatum mRNA mRNA"
+ "Striatum mRNA"
]
],
"LXS": [
@@ -3268,11 +3252,11 @@
],
[
"Hippocampus mRNA",
- "Hippocampus mRNA mRNA"
+ "Hippocampus mRNA"
],
[
"Prefrontal Cortex mRNA",
- "Prefrontal Cortex mRNA mRNA"
+ "Prefrontal Cortex mRNA"
]
],
"MDP": [
@@ -3286,19 +3270,19 @@
],
[
"Bone Femur mRNA",
- "Bone Femur mRNA mRNA"
+ "Bone Femur mRNA"
],
[
"Dorsal Root Ganglia mRNA",
- "Dorsal Root Ganglia mRNA mRNA"
+ "Dorsal Root Ganglia mRNA"
],
[
"Hippocampus mRNA",
- "Hippocampus mRNA mRNA"
+ "Hippocampus mRNA"
],
[
"Liver mRNA",
- "Liver mRNA mRNA"
+ "Liver mRNA"
]
],
"NZBXFVB-N2": [
@@ -3312,7 +3296,7 @@
],
[
"Mammary Tumors mRNA",
- "Mammary Tumors mRNA mRNA"
+ "Mammary Tumors mRNA"
]
],
"SOTNOT-OHSU": [
@@ -3336,7 +3320,7 @@
],
[
"Anterior Cingulate Cortex mRNA",
- "Anterior Cingulate Cortex mRNA mRNA"
+ "Anterior Cingulate Cortex mRNA"
]
]
},
@@ -3362,27 +3346,27 @@
],
[
"Adrenal Gland mRNA",
- "Adrenal Gland mRNA mRNA"
+ "Adrenal Gland mRNA"
],
[
"Heart mRNA",
- "Heart mRNA mRNA"
+ "Heart mRNA"
],
[
"Hippocampus mRNA",
- "Hippocampus mRNA mRNA"
+ "Hippocampus mRNA"
],
[
"Kidney mRNA",
- "Kidney mRNA mRNA"
+ "Kidney mRNA"
],
[
"Liver mRNA",
- "Liver mRNA mRNA"
+ "Liver mRNA"
],
[
"Peritoneal Fat mRNA",
- "Peritoneal Fat mRNA mRNA"
+ "Peritoneal Fat mRNA"
]
],
"SRxSHRSPF2": [
@@ -3396,7 +3380,7 @@
],
[
"Eye mRNA",
- "Eye mRNA mRNA"
+ "Eye mRNA"
]
]
},