Created file gen_group_samplelists that iterates through all genofiles

and builds each groups' samplelist

5 files changed, 206 insertions, 123 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 30221503..cf219fda 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -16,8 +16,6 @@
 # Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
 # at rwilliams@uthsc.edu and xzhou15@uthsc.edu
 #
-#we
-#
 # This module is used by GeneNetwork project (www.genenetwork.org)
 
 from __future__ import absolute_import, print_function, division
@@ -27,6 +25,7 @@ import string
 import collections
 
 import json
+import gzip
 import cPickle as pickle
 import itertools
 
@@ -52,8 +51,6 @@ from pprint import pformat as pf
 DS_NAME_MAP = {}
 
 def create_dataset(dataset_name, dataset_type = None):
-    
-    print("dataset_type:", dataset_type)
     if not dataset_type:
         dataset_type = Dataset_Getter(dataset_name)
         #dataset_type = get_dataset_type_from_json(dataset_name)
@@ -129,7 +126,7 @@ def create_datasets_list():
                 for result in g.db.execute(query).fetchall():
                     #The query at the beginning of this function isn't necessary here, but still would
                     #rather just reuse it
-                    print("type: {}\tname: {}".format(dataset_type, result.Name))
+                    #print("type: {}\tname: {}".format(dataset_type, result.Name))
                     dataset = create_dataset(result.Name, dataset_type)
                     datasets.append(dataset)
             
@@ -261,6 +258,36 @@ class DatasetGroup(object):
         if maternal and paternal:
             self.parlist = [maternal, paternal]
 
+    def get_sample_list(self):
+        genofilename = str(os.path.join(webqtlConfig.GENODIR, self.name + '.geno'))
+        genofile = open(genofilename, "r")
+        for line in genofile:
+            line = line.strip()
+            if line.startswith(("#", "@")):
+                continue
+            headline = line
+            break
+        headers = headline.split("\t")
+        if headers[3] == "Mb":
+            self.samplelist = headers[4:]
+        else:
+            self.samplelist = headers[3:]
+
+        #if genotype_1.type == "group" and self.parlist:
+        #    genotype_2 = genotype_1.add(Mat=self.parlist[0], Pat=self.parlist[1])       #, F1=_f1)
+        #else:
+        #    genotype_2 = genotype_1 
+
+        #determine default genotype object
+        #if self.incparentsf1 and genotype_1.type != "intercross":
+        #    genotype = genotype_2
+        #else:
+        #    self.incparentsf1 = 0
+        #    genotype = genotype_1
+
+        #self.samplelist = list(genotype.prgy)
+    
+
     def read_genotype_file(self):
         '''Read genotype from .geno file instead of database'''
         #if self.group == 'BXD300':
@@ -275,7 +302,18 @@ class DatasetGroup(object):
 
         # reaper barfs on unicode filenames, so here we ensure it's a string
         full_filename = str(os.path.join(webqtlConfig.GENODIR, self.name + '.geno'))
-        genotype_1.read(full_filename)
+        if os.path.isfile(full_filename):
+            print("Reading file: ", full_filename)
+            genotype_1.read(full_filename)
+            print("File read")
+        else:
+            try:
+                full_filename = str(os.path.join(webqtlConfig.TMPDIR, self.name + '.geno'))
+                #print("Reading file")
+                genotype_1.read(full_filename)
+                #print("File read")
+            except IOError:
+                print("File doesn't exist!")
 
         if genotype_1.type == "group" and self.parlist:
             genotype_2 = genotype_1.add(Mat=self.parlist[0], Pat=self.parlist[1])       #, F1=_f1)
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index d4511212..67a9c63f 100755
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -35,7 +35,7 @@ NCBI_LOCUSID = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrie
 UCSC_REFSEQ = "http://genome.cse.ucsc.edu/cgi-bin/hgGene?db=%s&hgg_gene=%s&hgg_chrom=chr%s&hgg_start=%s&hgg_end=%s"
 GENBANK_ID = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide&cmd=search&doptcmdl=DocSum&term=%s"
 OMIM_ID = "http://www.ncbi.nlm.nih.gov/omim/%s"
-UNIGEN_ID = "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=%s&CID=%s"
+UNIGEN_ID = "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=%s&CID=%s";
 HOMOLOGENE_ID = "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=homologene&Cmd=DetailsSearch&Term=%s"
 PUBMEDLINK_URL = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=%s&dopt=Abstract"
 UCSC_POS = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=mammal&org=%s&db=%s&position=chr%s:%s-%s&pix=800&Submit=submit"
@@ -53,12 +53,12 @@ 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/plink/'
-SNP_PATH = '/home/zas1024/snps/' 
+PYLMM_PATH = '/home/zas1024/'
+SNP_PATH = '/mnt/xvdf1/snps/' 
 IMGDIR = HTMLPATH +'image/'
 IMAGESPATH = HTMLPATH + 'images/'
 UPLOADPATH = IMAGESPATH + 'upload/'
-TMPDIR = HTMLPATH + 'tmp/'
+TMPDIR = '/tmp/'
 GENODIR = HTMLPATH + 'genotypes/'
 NEWGENODIR = HTMLPATH + 'new_genotypes/'
 GENO_ARCHIVE_DIR = GENODIR + 'archive/'
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index 8cb94f20..d4e47327 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -115,7 +115,7 @@ def build_types(species, group):
     (all types except phenotype/genotype are tissues)
      
     """
-    Cursor.execute("""select distinct Tissue.Name, Tissue.Name
+    Cursor.execute("""select distinct Tissue.Name, concat(Tissue.Name, ' mRNA')
                        from ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue, Species
                        where Species.Name = %s and Species.Id = InbredSet.SpeciesId and
                        InbredSet.Name = %s and
@@ -192,6 +192,8 @@ def main():
                 datasets=datasets,
                 )
 
+    print("data:", data)
+
     output_file = """../wqflask/static/new/javascript/dataset_menu_structure.json"""
 
     with open(output_file, 'w') as fh:
diff --git a/wqflask/maintenance/get_group_samplelists.py b/wqflask/maintenance/get_group_samplelists.py
new file mode 100644
index 00000000..2434038e
--- /dev/null
+++ b/wqflask/maintenance/get_group_samplelists.py
@@ -0,0 +1,43 @@
+from __future__ import absolute_import, print_function, division
+
+import os
+import glob
+import gzip
+
+from base import webqtlConfig
+
+
+def get_sample_list_dir(geno_dir="/home/zas1024/gene/web/genotypes/"):
+    os.chdir(geno_dir)
+    
+    for group_file in glob.glob("*"):
+        if group_file.lower().endswith(('.geno', '.geno.gz')):
+            #group_name = genofilename.split('.')[0]
+            sample_list = get_sample_list(group_file)
+            print("\n\n{}\n\n".format(sample_list))
+
+
+def get_sample_list(group_file):
+    print(group_file)
+    genofilename = str(os.path.join(webqtlConfig.GENODIR, group_file))
+    if genofilename.lower().endswith('.geno.gz'):
+        genofile = gzip.open(genofilename)
+    else:
+        genofile = open(genofilename)
+    for line in genofile:
+        line = line.strip()
+        if not line:
+            continue
+        if line.startswith(("#", "@")):
+            continue
+        headline = line
+        break
+    headers = headline.split("\t")
+    if headers[3] == "Mb":
+        samplelist = headers[4:]
+    else:
+        samplelist = headers[3:]
+    return samplelist
+
+if __name__ == '__main__':
+    get_sample_list_dir()
diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
index 49c44fbd..4aae20ba 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
+++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
@@ -2556,7 +2556,7 @@
             ],
             [
                "Leaf mRNA",
-               "Leaf mRNA"
+               "Leaf mRNA mRNA"
             ]
          ],
          "SXM": [
@@ -2570,11 +2570,11 @@
             ],
             [
                "Embryo mRNA",
-               "Embryo mRNA"
+               "Embryo mRNA mRNA"
             ],
             [
                "Leaf mRNA",
-               "Leaf mRNA"
+               "Leaf mRNA mRNA"
             ]
          ]
       },
@@ -2590,7 +2590,7 @@
             ],
             [
                "Whole Body mRNA",
-               "Whole Body mRNA"
+               "Whole Body mRNA mRNA"
             ]
          ],
          "Oregon-R_x_2b3": [
@@ -2604,7 +2604,7 @@
             ],
             [
                "Whole Body mRNA",
-               "Whole Body mRNA"
+               "Whole Body mRNA mRNA"
             ]
          ]
       },
@@ -2620,7 +2620,7 @@
             ],
             [
                "Brain mRNA",
-               "Brain mRNA"
+               "Brain mRNA mRNA"
             ]
          ],
          "AD-cases-controls-Myers": [
@@ -2634,7 +2634,7 @@
             ],
             [
                "Brain mRNA",
-               "Brain mRNA"
+               "Brain mRNA mRNA"
             ]
          ],
          "CANDLE": [
@@ -2648,11 +2648,11 @@
             ],
             [
                "Methylation",
-               "Methylation"
+               "Methylation mRNA"
             ],
             [
                "Newborn Cord Blood mRNA",
-               "Newborn Cord Blood mRNA"
+               "Newborn Cord Blood mRNA mRNA"
             ]
          ],
          "CEPH-2004": [
@@ -2666,7 +2666,7 @@
             ],
             [
                "Lymphoblast B-cell mRNA",
-               "Lymphoblast B-cell mRNA"
+               "Lymphoblast B-cell mRNA mRNA"
             ]
          ],
          "HB": [
@@ -2680,15 +2680,15 @@
             ],
             [
                "Cerebellum mRNA",
-               "Cerebellum mRNA"
+               "Cerebellum mRNA mRNA"
             ],
             [
                "Prefrontal Cortex mRNA",
-               "Prefrontal Cortex mRNA"
+               "Prefrontal Cortex mRNA mRNA"
             ],
             [
                "Primary Visual Cortex mRNA",
-               "Primary Visual Cortex mRNA"
+               "Primary Visual Cortex mRNA mRNA"
             ]
          ],
          "HLC": [
@@ -2702,7 +2702,7 @@
             ],
             [
                "Liver mRNA",
-               "Liver mRNA"
+               "Liver mRNA mRNA"
             ]
          ],
          "HLT": [
@@ -2716,7 +2716,7 @@
             ],
             [
                "Lung mRNA",
-               "Lung mRNA"
+               "Lung mRNA mRNA"
             ]
          ],
          "HSB": [
@@ -2730,67 +2730,67 @@
             ],
             [
                "Amygdala mRNA",
-               "Amygdala mRNA"
+               "Amygdala mRNA mRNA"
             ],
             [
                "Cerebellar Cortex mRNA",
-               "Cerebellar Cortex mRNA"
+               "Cerebellar Cortex mRNA mRNA"
             ],
             [
                "Dorsolateral Prefrontal Cortex mRNA",
-               "Dorsolateral Prefrontal Cortex mRNA"
+               "Dorsolateral Prefrontal Cortex mRNA mRNA"
             ],
             [
                "Hippocampus mRNA",
-               "Hippocampus mRNA"
+               "Hippocampus mRNA mRNA"
             ],
             [
                "Inferior Temporal Cortex mRNA",
-               "Inferior Temporal Cortex mRNA"
+               "Inferior Temporal Cortex mRNA mRNA"
             ],
             [
                "Medial Prefrontal Cortex mRNA",
-               "Medial Prefrontal Cortex mRNA"
+               "Medial Prefrontal Cortex mRNA mRNA"
             ],
             [
                "Mediodorsal Nucleus of Thalamus mRNA",
-               "Mediodorsal Nucleus of Thalamus mRNA"
+               "Mediodorsal Nucleus of Thalamus mRNA mRNA"
             ],
             [
                "Orbital Prefrontal Cortex mRNA",
-               "Orbital Prefrontal Cortex mRNA"
+               "Orbital Prefrontal Cortex mRNA mRNA"
             ],
             [
                "Posterior Inferior Parietal Cortex mRNA",
-               "Posterior Inferior Parietal Cortex mRNA"
+               "Posterior Inferior Parietal Cortex mRNA mRNA"
             ],
             [
                "Posterior Superior Temporal Cortex mRNA",
-               "Posterior Superior Temporal Cortex mRNA"
+               "Posterior Superior Temporal Cortex mRNA mRNA"
             ],
             [
                "Primary Auditory (A1) Cortex mRNA",
-               "Primary Auditory (A1) Cortex mRNA"
+               "Primary Auditory (A1) Cortex mRNA mRNA"
             ],
             [
                "Primary Motor (M1) Cortex mRNA",
-               "Primary Motor (M1) Cortex mRNA"
+               "Primary Motor (M1) Cortex mRNA mRNA"
             ],
             [
                "Primary Somatosensory (S1) Cortex mRNA",
-               "Primary Somatosensory (S1) Cortex mRNA"
+               "Primary Somatosensory (S1) Cortex mRNA mRNA"
             ],
             [
                "Primary Visual Cortex mRNA",
-               "Primary Visual Cortex mRNA"
+               "Primary Visual Cortex mRNA mRNA"
             ],
             [
                "Striatum mRNA",
-               "Striatum mRNA"
+               "Striatum mRNA mRNA"
             ],
             [
                "Ventrolateral Prefrontal Cortex mRNA",
-               "Ventrolateral Prefrontal Cortex mRNA"
+               "Ventrolateral Prefrontal Cortex mRNA mRNA"
             ]
          ]
       },
@@ -2806,23 +2806,23 @@
             ],
             [
                "Amygdala mRNA",
-               "Amygdala mRNA"
+               "Amygdala mRNA mRNA"
             ],
             [
                "Brain mRNA",
-               "Brain mRNA"
+               "Brain mRNA mRNA"
             ],
             [
                "Hippocampus mRNA",
-               "Hippocampus mRNA"
+               "Hippocampus mRNA mRNA"
             ],
             [
                "Nucleus Accumbens mRNA",
-               "Nucleus Accumbens mRNA"
+               "Nucleus Accumbens mRNA mRNA"
             ],
             [
                "Prefrontal Cortex mRNA",
-               "Prefrontal Cortex mRNA"
+               "Prefrontal Cortex mRNA mRNA"
             ]
          ]
       },
@@ -2838,7 +2838,7 @@
             ],
             [
                "Mammary Tumors mRNA",
-               "Mammary Tumors mRNA"
+               "Mammary Tumors mRNA mRNA"
             ]
          ],
          "AXBXA": [
@@ -2852,19 +2852,19 @@
             ],
             [
                "Bone Femur mRNA",
-               "Bone Femur mRNA"
+               "Bone Femur mRNA mRNA"
             ],
             [
                "Eye mRNA",
-               "Eye mRNA"
+               "Eye mRNA mRNA"
             ],
             [
                "Heart mRNA",
-               "Heart mRNA"
+               "Heart mRNA mRNA"
             ],
             [
                "Liver mRNA",
-               "Liver mRNA"
+               "Liver mRNA mRNA"
             ]
          ],
          "B6BTBRF2": [
@@ -2878,7 +2878,7 @@
             ],
             [
                "Liver mRNA",
-               "Liver mRNA"
+               "Liver mRNA mRNA"
             ]
          ],
          "B6D2F2": [
@@ -2892,7 +2892,7 @@
             ],
             [
                "Brain mRNA",
-               "Brain mRNA"
+               "Brain mRNA mRNA"
             ]
          ],
          "B6D2F2-PSU": [
@@ -2906,7 +2906,7 @@
             ],
             [
                "Muscle mRNA",
-               "Muscle mRNA"
+               "Muscle mRNA mRNA"
             ]
          ],
          "B6D2RI": [
@@ -2920,7 +2920,7 @@
             ],
             [
                "Hippocampus mRNA",
-               "Hippocampus mRNA"
+               "Hippocampus mRNA mRNA"
             ]
          ],
          "BDF2-1999": [
@@ -2934,7 +2934,7 @@
             ],
             [
                "Liver mRNA",
-               "Liver mRNA"
+               "Liver mRNA mRNA"
             ]
          ],
          "BDF2-2005": [
@@ -2948,7 +2948,7 @@
             ],
             [
                "Striatum mRNA",
-               "Striatum mRNA"
+               "Striatum mRNA mRNA"
             ]
          ],
          "BHF2": [
@@ -2962,19 +2962,19 @@
             ],
             [
                "Adipose mRNA",
-               "Adipose mRNA"
+               "Adipose mRNA mRNA"
             ],
             [
                "Brain mRNA",
-               "Brain mRNA"
+               "Brain mRNA mRNA"
             ],
             [
                "Liver mRNA",
-               "Liver mRNA"
+               "Liver mRNA mRNA"
             ],
             [
                "Muscle mRNA",
-               "Muscle mRNA"
+               "Muscle mRNA mRNA"
             ]
          ],
          "BHHBF2": [
@@ -2988,19 +2988,19 @@
             ],
             [
                "Adipose mRNA",
-               "Adipose mRNA"
+               "Adipose mRNA mRNA"
             ],
             [
                "Brain mRNA",
-               "Brain mRNA"
+               "Brain mRNA mRNA"
             ],
             [
                "Liver mRNA",
-               "Liver mRNA"
+               "Liver mRNA mRNA"
             ],
             [
                "Muscle mRNA",
-               "Muscle mRNA"
+               "Muscle mRNA mRNA"
             ]
          ],
          "BXD": [
@@ -3014,119 +3014,119 @@
             ],
             [
                "Adrenal Gland mRNA",
-               "Adrenal Gland mRNA"
+               "Adrenal Gland mRNA mRNA"
             ],
             [
                "Amygdala mRNA",
-               "Amygdala mRNA"
+               "Amygdala mRNA mRNA"
             ],
             [
                "Bone Femur mRNA",
-               "Bone Femur mRNA"
+               "Bone Femur mRNA mRNA"
             ],
             [
                "Brain mRNA",
-               "Brain mRNA"
+               "Brain mRNA mRNA"
             ],
             [
                "Cartilage mRNA",
-               "Cartilage mRNA"
+               "Cartilage mRNA mRNA"
             ],
             [
                "Cerebellum mRNA",
-               "Cerebellum mRNA"
+               "Cerebellum mRNA mRNA"
             ],
             [
                "Eye mRNA",
-               "Eye mRNA"
+               "Eye mRNA mRNA"
             ],
             [
                "Hematopoietic Cells mRNA",
-               "Hematopoietic Cells mRNA"
+               "Hematopoietic Cells mRNA mRNA"
             ],
             [
                "Hippocampus mRNA",
-               "Hippocampus mRNA"
+               "Hippocampus mRNA mRNA"
             ],
             [
                "Hypothalamus mRNA",
-               "Hypothalamus mRNA"
+               "Hypothalamus mRNA mRNA"
             ],
             [
                "Kidney mRNA",
-               "Kidney mRNA"
+               "Kidney mRNA mRNA"
             ],
             [
                "Leucocytes mRNA",
-               "Leucocytes mRNA"
+               "Leucocytes mRNA mRNA"
             ],
             [
                "Liver mRNA",
-               "Liver mRNA"
+               "Liver mRNA mRNA"
             ],
             [
                "Liver Proteome",
-               "Liver Proteome"
+               "Liver Proteome mRNA"
             ],
             [
                "Lung mRNA",
-               "Lung mRNA"
+               "Lung mRNA mRNA"
             ],
             [
                "Midbrain mRNA",
-               "Midbrain mRNA"
+               "Midbrain mRNA mRNA"
             ],
             [
                "Muscle mRNA",
-               "Muscle mRNA"
+               "Muscle mRNA mRNA"
             ],
             [
                "Neocortex mRNA",
-               "Neocortex mRNA"
+               "Neocortex mRNA mRNA"
             ],
             [
                "Nucleus Accumbens mRNA",
-               "Nucleus Accumbens mRNA"
+               "Nucleus Accumbens mRNA mRNA"
             ],
             [
                "Pituitary Gland mRNA",
-               "Pituitary Gland mRNA"
+               "Pituitary Gland mRNA mRNA"
             ],
             [
                "Popliteal Lymph Node mRNA",
-               "Popliteal Lymph Node mRNA"
+               "Popliteal Lymph Node mRNA mRNA"
             ],
             [
                "Prefrontal Cortex mRNA",
-               "Prefrontal Cortex mRNA"
+               "Prefrontal Cortex mRNA mRNA"
             ],
             [
                "Retina mRNA",
-               "Retina mRNA"
+               "Retina mRNA mRNA"
             ],
             [
                "Spleen mRNA",
-               "Spleen mRNA"
+               "Spleen mRNA mRNA"
             ],
             [
                "Striatum mRNA",
-               "Striatum mRNA"
+               "Striatum mRNA mRNA"
             ],
             [
                "T Cell (helper) mRNA",
-               "T Cell (helper) mRNA"
+               "T Cell (helper) mRNA mRNA"
             ],
             [
                "T Cell (regulatory) mRNA",
-               "T Cell (regulatory) mRNA"
+               "T Cell (regulatory) mRNA mRNA"
             ],
             [
                "Thymus mRNA",
-               "Thymus mRNA"
+               "Thymus mRNA mRNA"
             ],
             [
                "Ventral Tegmental Area mRNA",
-               "Ventral Tegmental Area mRNA"
+               "Ventral Tegmental Area mRNA mRNA"
             ]
          ],
          "BXH": [
@@ -3140,15 +3140,15 @@
             ],
             [
                "Bone Femur mRNA",
-               "Bone Femur mRNA"
+               "Bone Femur mRNA mRNA"
             ],
             [
                "Cartilage mRNA",
-               "Cartilage mRNA"
+               "Cartilage mRNA mRNA"
             ],
             [
                "Liver mRNA",
-               "Liver mRNA"
+               "Liver mRNA mRNA"
             ]
          ],
          "C57BL-6JxC57BL-6NJF2": [
@@ -3172,19 +3172,19 @@
             ],
             [
                "Adipose mRNA",
-               "Adipose mRNA"
+               "Adipose mRNA mRNA"
             ],
             [
                "Brain mRNA",
-               "Brain mRNA"
+               "Brain mRNA mRNA"
             ],
             [
                "Liver mRNA",
-               "Liver mRNA"
+               "Liver mRNA mRNA"
             ],
             [
                "Muscle mRNA",
-               "Muscle mRNA"
+               "Muscle mRNA mRNA"
             ]
          ],
          "CXB": [
@@ -3198,11 +3198,11 @@
             ],
             [
                "Hippocampus mRNA",
-               "Hippocampus mRNA"
+               "Hippocampus mRNA mRNA"
             ],
             [
                "Spleen mRNA",
-               "Spleen mRNA"
+               "Spleen mRNA mRNA"
             ]
          ],
          "HS": [
@@ -3216,15 +3216,15 @@
             ],
             [
                "Hippocampus mRNA",
-               "Hippocampus mRNA"
+               "Hippocampus mRNA mRNA"
             ],
             [
                "Liver mRNA",
-               "Liver mRNA"
+               "Liver mRNA mRNA"
             ],
             [
                "Lung mRNA",
-               "Lung mRNA"
+               "Lung mRNA mRNA"
             ]
          ],
          "HS-CC": [
@@ -3238,7 +3238,7 @@
             ],
             [
                "Striatum mRNA",
-               "Striatum mRNA"
+               "Striatum mRNA mRNA"
             ]
          ],
          "LXS": [
@@ -3252,11 +3252,11 @@
             ],
             [
                "Hippocampus mRNA",
-               "Hippocampus mRNA"
+               "Hippocampus mRNA mRNA"
             ],
             [
                "Prefrontal Cortex mRNA",
-               "Prefrontal Cortex mRNA"
+               "Prefrontal Cortex mRNA mRNA"
             ]
          ],
          "MDP": [
@@ -3270,19 +3270,19 @@
             ],
             [
                "Bone Femur mRNA",
-               "Bone Femur mRNA"
+               "Bone Femur mRNA mRNA"
             ],
             [
                "Dorsal Root Ganglia mRNA",
-               "Dorsal Root Ganglia mRNA"
+               "Dorsal Root Ganglia mRNA mRNA"
             ],
             [
                "Hippocampus mRNA",
-               "Hippocampus mRNA"
+               "Hippocampus mRNA mRNA"
             ],
             [
                "Liver mRNA",
-               "Liver mRNA"
+               "Liver mRNA mRNA"
             ]
          ],
          "NZBXFVB-N2": [
@@ -3296,7 +3296,7 @@
             ],
             [
                "Mammary Tumors mRNA",
-               "Mammary Tumors mRNA"
+               "Mammary Tumors mRNA mRNA"
             ]
          ],
          "SOTNOT-OHSU": [
@@ -3320,7 +3320,7 @@
             ],
             [
                "Anterior Cingulate Cortex mRNA",
-               "Anterior Cingulate Cortex mRNA"
+               "Anterior Cingulate Cortex mRNA mRNA"
             ]
          ]
       },
@@ -3346,27 +3346,27 @@
             ],
             [
                "Adrenal Gland mRNA",
-               "Adrenal Gland mRNA"
+               "Adrenal Gland mRNA mRNA"
             ],
             [
                "Heart mRNA",
-               "Heart mRNA"
+               "Heart mRNA mRNA"
             ],
             [
                "Hippocampus mRNA",
-               "Hippocampus mRNA"
+               "Hippocampus mRNA mRNA"
             ],
             [
                "Kidney mRNA",
-               "Kidney mRNA"
+               "Kidney mRNA mRNA"
             ],
             [
                "Liver mRNA",
-               "Liver mRNA"
+               "Liver mRNA mRNA"
             ],
             [
                "Peritoneal Fat mRNA",
-               "Peritoneal Fat mRNA"
+               "Peritoneal Fat mRNA mRNA"
             ]
          ],
          "SRxSHRSPF2": [
@@ -3380,7 +3380,7 @@
             ],
             [
                "Eye mRNA",
-               "Eye mRNA"
+               "Eye mRNA mRNA"
             ]
          ]
       },