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-rw-r--r--wqflask/maintenance/convert_dryad_to_bimbam.py70
-rw-r--r--wqflask/maintenance/gen_select_dataset.py2
-rw-r--r--wqflask/maintenance/quantile_normalize.py4
-rw-r--r--wqflask/wqflask/static/new/javascript/dataset_menu_structure.json34
-rw-r--r--wqflask/wqflask/user_manager.py10
5 files changed, 116 insertions, 4 deletions
diff --git a/wqflask/maintenance/convert_dryad_to_bimbam.py b/wqflask/maintenance/convert_dryad_to_bimbam.py
new file mode 100644
index 00000000..e833b395
--- /dev/null
+++ b/wqflask/maintenance/convert_dryad_to_bimbam.py
@@ -0,0 +1,70 @@
+#!/usr/bin/python
+
+"""
+Convert data dryad files to a BIMBAM _geno and _snps file
+
+
+"""
+
+from __future__ import print_function, division, absolute_import
+import sys
+sys.path.append("..")
+
+
+def read_dryad_file(filename):
+ exclude_count = 0
+ marker_list = []
+ sample_dict = {}
+ sample_list = []
+ geno_rows = []
+ with open(filename, 'r') as the_file:
+ for i, line in enumerate(the_file):
+ if i > 0:
+ if line.split(" ")[1] == "no":
+ sample_name = line.split(" ")[0]
+ sample_list.append(sample_name)
+ sample_dict[sample_name] = line.split(" ")[2:]
+ else:
+ exclude_count += 1
+ else:
+ marker_list = line.split(" ")[2:]
+
+ for i, marker in enumerate(marker_list):
+ this_row = []
+ this_row.append(marker)
+ this_row.append("X")
+ this_row.append("Y")
+ for sample in sample_list:
+ this_row.append(sample_dict[sample][i])
+ geno_rows.append(this_row)
+
+ print(exclude_count)
+
+ return geno_rows
+
+ #for i, marker in enumerate(marker_list):
+ # this_row = []
+ # this_row.append(marker)
+ # this_row.append("X")
+ # this_row.append("Y")
+ # with open(filename, 'r') as the_file:
+ # for j, line in enumerate(the_file):
+ # if j > 0:
+ # this_row.append(line.split(" ")[i+2])
+ # print("row: " + str(i))
+ # geno_rows.append(this_row)
+ #
+ #return geno_rows
+
+def write_bimbam_files(geno_rows):
+ with open('/home/zas1024/cfw_data/CFW_geno.txt', 'w') as geno_fh:
+ for row in geno_rows:
+ geno_fh.write(", ".join(row) + "\n")
+
+def convert_dryad_to_bimbam(filename):
+ geno_file_rows = read_dryad_file(filename)
+ write_bimbam_files(geno_file_rows)
+
+if __name__=="__main__":
+ input_filename = "/home/zas1024/cfw_data/" + sys.argv[1] + ".txt"
+ convert_dryad_to_bimbam(input_filename) \ No newline at end of file
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index 2825c6ea..18b2dac9 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -63,7 +63,7 @@ from pprint import pformat as pf
#conn = Engine.connect()
-def parse_db_uri(db_uri):
+def parse_db_uri():
"""Converts a database URI to the db name, host name, user name, and password"""
parsed_uri = urlparse.urlparse(SQL_URI)
diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py
index c11073fb..41a3aad8 100644
--- a/wqflask/maintenance/quantile_normalize.py
+++ b/wqflask/maintenance/quantile_normalize.py
@@ -59,7 +59,7 @@ def set_data(dataset_name):
orig_file = "/home/zas1024/cfw_data/" + dataset_name + ".txt"
sample_list = []
- with open(orig_file, 'r') as orig_fh, open('quant_norm.csv', 'r') as quant_fh:
+ with open(orig_file, 'r') as orig_fh, open('/home/zas1024/cfw_data/quant_norm.csv', 'r') as quant_fh:
for i, (line1, line2) in enumerate(izip(orig_fh, quant_fh)):
trait_dict = {}
sample_list = []
@@ -118,7 +118,7 @@ if __name__ == '__main__':
#out_filename = sys.argv[1][:-4] + '_quantnorm.txt'
- #success, _ = bulk(es, set_data(sys.argv[1]))
+ success, _ = bulk(es, set_data(sys.argv[1]))
response = es.search(
index = "traits", doc_type = "trait", body = {
diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
index d00b52b8..c605329b 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
+++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
@@ -1966,6 +1966,21 @@
"470",
"EPFLADEL1013",
"EPFL/LISP BXD CD Brown Adipose Affy Mouse Gene 2.0 ST Exon Level (Oct13) RMA"
+ ],
+ [
+ "777",
+ "EL_BXDCDHFDScWAT_0216",
+ "EPFL/LISP BXD CD+HFD Subcutaneous WAT Affy MTA 1.0 Gene Level (Feb16) RMA"
+ ],
+ [
+ "778",
+ "EL_BXDHFDScWAT_0216",
+ "EPFL/LISP BXD HFD Subcutaneous WAT Affy MTA 1.0 Gene Level (Feb16) RMA"
+ ],
+ [
+ "779",
+ "EL_BXDCDScWAT_0216",
+ "EPFL/LISP BXD CD Subcutaneous WAT Affy MTA 1.0 Gene Level (Feb16) RMA **"
]
],
"Adrenal Gland mRNA": [
@@ -3355,6 +3370,15 @@
]
]
},
+ "D2GM": {
+ "Retina mRNA": [
+ [
+ "847",
+ "JAX_D2GM_RSeq_log2Z_0418",
+ "JAX Retina (Apr18) RNA-Seq log2-Z"
+ ]
+ ]
+ },
"EMSR": {},
"HS": {
"Hippocampus mRNA": [
@@ -3955,6 +3979,10 @@
"CXB"
],
[
+ "D2GM",
+ "D2 Glaucoma Model"
+ ],
+ [
"EMSR",
"Ethanol-Medicated Stress Reduction"
],
@@ -5236,6 +5264,12 @@
"Spleen mRNA"
]
],
+ "D2GM": [
+ [
+ "Retina mRNA",
+ "Retina mRNA"
+ ]
+ ],
"EMSR": [],
"HS": [
[
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index d652f2e9..132bae90 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -62,9 +62,17 @@ class AnonUser(object):
self.anon_id, self.cookie = create_signed_cookie()
self.key = "anon_collection:v1:{}".format(self.anon_id)
- @after.after_this_request
+ #ZS: This was originally the commented out function below
+ # For some reason I don't yet understand the commented out code works on production,
+ # but wouldn't set cookies for staging and my branch. The new code (using @app.after_request) seems to work.
+ @app.after_request
def set_cookie(response):
response.set_cookie(self.cookie_name, self.cookie)
+ return response
+
+ #@after.after_this_request
+ #def set_cookie(response):
+ # response.set_cookie(self.cookie_name, self.cookie)
def add_collection(self, new_collection):
collection_dict = dict(name = new_collection.name,