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authorLei Yan2014-07-18 17:47:36 +0000
committerLei Yan2014-07-18 17:47:36 +0000
commitc424db452c243c6f0f64ee58d2d7baeb147dd3c8 (patch)
tree5c65cdafd8315e7cedb45c8002a1112d8cc1c477 /wqflask/utility
parentee0769c22472ea9dc1addd3886afd62d54ff2c00 (diff)
parent8c45fcf1e9228108034fab96bc7e7eaa7740f06c (diff)
downloadgenenetwork2-c424db452c243c6f0f64ee58d2d7baeb147dd3c8.tar.gz
Merge /home/zas1024/gene
Conflicts: wqflask/base/data_set.py
Diffstat (limited to 'wqflask/utility')
-rwxr-xr-xwqflask/utility/helper_functions.py15
-rwxr-xr-xwqflask/utility/webqtlUtil.py64
2 files changed, 79 insertions, 0 deletions
diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py
index 44f5321e..ca3e2350 100755
--- a/wqflask/utility/helper_functions.py
+++ b/wqflask/utility/helper_functions.py
@@ -19,3 +19,18 @@ def get_species_dataset_trait(self, start_vars):
#if read_genotype:
#self.dataset.group.read_genotype_file()
#self.genotype = self.dataset.group.genotype
+
+
+def get_trait_db_obs(self, trait_db_list):
+
+ self.trait_list = []
+ for i, trait_db in enumerate(trait_db_list):
+ if i == (len(trait_db_list) - 1):
+ break
+ trait_name, dataset_name = trait_db.split(":")
+ #print("dataset_name:", dataset_name)
+ dataset_ob = data_set.create_dataset(dataset_name)
+ trait_ob = GeneralTrait(dataset=dataset_ob,
+ name=trait_name,
+ cellid=None)
+ self.trait_list.append((trait_ob, dataset_ob)) \ No newline at end of file
diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py
index 99451e33..4d7981d9 100755
--- a/wqflask/utility/webqtlUtil.py
+++ b/wqflask/utility/webqtlUtil.py
@@ -89,6 +89,70 @@ PROGRESSBAR = HT.Image('/images/waitAnima2.gif', alt='checkblue',align="middle",
# Accessory Functions
#########################################
+def inverseCumul(p):
+ #Coefficients in rational approximations.
+ a = [-3.969683028665376e+01,2.209460984245205e+02,-2.759285104469687e+02,1.383577518672690e+02,-3.066479806614716e+01,2.506628277459239e+00]
+
+ b = [-5.447609879822406e+01,1.615858368580409e+02,-1.556989798598866e+02,6.680131188771972e+01,-1.328068155288572e+01]
+
+ c = [-7.784894002430293e-03,-3.223964580411365e-01,-2.400758277161838e+00,-2.549732539343734e+00,4.374664141464968e+00,2.938163982698783e+00]
+
+ d = [7.784695709041462e-03,3.224671290700398e-01,2.445134137142996e+00,3.754408661907416e+00]
+
+ #Define break-points.
+
+ p_low = 0.02425
+ p_high = 1 - p_low
+
+ #Rational approximation for lower region.
+
+ if p > 0 and p < p_low:
+ q = sqrt(-2*log(p))
+ x = (((((c[0]*q+c[1])*q+c[2])*q+c[3])*q+c[4])*q+c[5]) / ((((d[0]*q+d[1])*q+d[2])*q+d[3])*q+1)
+
+
+ #Rational approximation for central region.
+
+ elif p>= p_low and p <= p_high:
+ q = p - 0.5
+ r = q*q
+ x = (((((a[0]*r+a[1])*r+a[2])*r+a[3])*r+a[4])*r+a[5])*q /(((((b[0]*r+b[1])*r+b[2])*r+b[3])*r+b[4])*r+1)
+
+ #Rational approximation for upper region.
+
+ elif p>p_high and p < 1:
+ q = sqrt(-2*log(1-p))
+ x = -(((((c[0]*q+c[1])*q+c[2])*q+c[3])*q+c[4])*q+c[5]) /((((d[0]*q+d[1])*q+d[2])*q+d[3])*q+1)
+
+ else:
+ return None
+
+ if p>0 and p < 1:
+ e = 0.5 * erfcc(-x/sqrt(2)) - p
+ u = e * sqrt(2*pi) * exp(x*x/2)
+ x = x - u/(1 + x*u/2)
+ return x
+ else:
+ return None
+
+def erfcc(x):
+ z=abs(x)
+ t=1.0/(1.0+0.5*z)
+ ans=t*exp(-z*z-1.26551223+t*(1.00002368+t*(0.37409196+t*(0.09678418+t*(-0.18628806+t*(0.27886807+t*(-1.13520398+t*(1.48851587+t*(-0.82215223+t*0.17087277)))))))))
+ if x>=0.0:
+ return ans
+ else:
+ return 2.0-ans
+
+def U(n):
+ x=pow(0.5,1.0/n)
+ m=[1-x]
+ for i in range(2,n):
+ a=(i-0.3175)/(n+0.365)
+ m.append(a)
+ m.append(x)
+ return m
+
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