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authorzsloan2012-05-23 14:34:27 -0500
committerzsloan2012-05-23 14:34:27 -0500
commit511b0bc7875e24574da60d549a9b37d4deba56b3 (patch)
treec9a48dc3258c33571655dfa082e13722c1db588c /web
parentff26666747535f4c2641d695ffb5182822a71458 (diff)
downloadgenenetwork2-511b0bc7875e24574da60d549a9b37d4deba56b3.tar.gz
Update web/webqtl/correlation/CorrelationPage.py
Diffstat (limited to 'web')
-rwxr-xr-xweb/webqtl/correlation/CorrelationPage.py27
1 files changed, 1 insertions, 26 deletions
diff --git a/web/webqtl/correlation/CorrelationPage.py b/web/webqtl/correlation/CorrelationPage.py
index 42059117..ce8b8165 100755
--- a/web/webqtl/correlation/CorrelationPage.py
+++ b/web/webqtl/correlation/CorrelationPage.py
@@ -1,4 +1,4 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+## Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
#
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU Affero General Public License
@@ -54,9 +54,6 @@ import logging
logging.basicConfig(filename="/tmp/gn_log", level=logging.INFO)
_log = logging.getLogger("correlation")
-debug_file = open("/home/zas1024/gn/web/corr_debug.txt","w")
-debug_file2 = open("/home/zas1024/gn/web/corr_debug2.txt","w")
-
METHOD_SAMPLE_PEARSON = "1"
METHOD_SAMPLE_RANK = "2"
METHOD_LIT = "3"
@@ -222,38 +219,16 @@ def get_species(fd, cursor):
def sortTraitCorrelations(traits, method="1"):
- for trait in traits:
- if trait.lit_corr != None and float(trait.lit_corr) > 0.6:
- debug_file.write(str(trait.lit_corr) + "\n")
if method in TISSUE_METHODS:
- #traits.sort(key=lambda trait: trait.tissue_corr != None and abs(float(trait.tissue_corr)) or 0)
traits.sort(key=lambda trait: trait.tissue_corr != None and abs(trait.tissue_corr), reverse=True)
elif method == METHOD_LIT:
- #traits.sort(key=lambda trait: trait.lit_corr != None and abs(float(trait.lit_corr)) or 0)
traits.sort(key=lambda trait: trait.lit_corr != None and abs(trait.lit_corr), reverse=True)
else:
- #traits.sort(key=lambda trait: trait.correlation != None and abs(float(trait.correlation)) or 0)
traits.sort(key=lambda trait: trait.correlation != None and abs(trait.correlation), reverse=True)
- for trait in traits:
- if trait.lit_corr != None and float(trait.lit_corr) > 0.6:
- debug_file2.write(str(trait.lit_corr) + "\n")
-
return traits
-
-def cmpTraitCorr(A,B):
- try:
- if abs(A.correlation) < abs(B.correlation):
- return 1
- elif abs(A.correlation) == abs(B.correlation):
- return 0
- else:
- return -1
- except:
- return 0
-
def auth_user_for_db(db, cursor, target_db_name, privilege, username):
"""Authorize a user for access to a database if that database is
confidential. A db (identified by a record in ProbeSetFreeze) contains a