fix errors in tests of example data

Author: AlexTISYoung

setup.py

@@ -56,12 +56,12 @@ def include_dirs(self, dirs):
 
 setup(name='snipar',
       version='0.0.20',
-      description='Library and command line scripts for inferring identity-by-descent (IBD) segments shared between siblings, imputing missing parental genotypes, and for performing family based genome-wide association and polygenic score analyses.',
+      description='Library and command line scripts for inferring identity-by-descent (IBD) segments shared between siblings, imputing missing parental genotypes, performing family based genome-wide association and polygenic score analyses.',
       long_description = long_description,
       long_description_content_type="text/markdown",
       url='https://github.com/alexTISYoung/snipar',
       download_url='https://pypi.org/project/snipar/files',
-      author='Alexander I. Young, Moeen Nehzati',
+      author='Alexander Strudwick Young, Moeen Nehzati, Junming Guan',
       author_email='[email protected]',
       license='MIT',
       include_package_data=True,

snipar/example/example_data/estimate_sim_effects.py

@@ -25,7 +25,7 @@
         breg[i,1] = 1/np.var(b[:,i])
         breg[i,0] = np.cov(b[:,i],ests[:,i])[0,1]*breg[i,1]
         sigma2 = np.var(ests[:,i]-breg[i,0]*b[:,i])
-        breg[i,1] = np.sqrt(sigma2*breg[i,1]/np.float(b.shape[0]))
+        breg[i,1] = np.sqrt(sigma2*breg[i,1]/float(b.shape[0]))
 
     breg[3,0] = np.cov(avg_parental[:,0],(b[:,1]+b[:,2])/2.0)[0,1]/np.var((b[:,1]+b[:,2])/2.0)
     sigma2 = np.var(avg_parental[:,0]-breg[3,0]*(b[:,1]+b[:,2])/2.0)
@@ -40,7 +40,7 @@
     breg[i,1] = 1/np.var(b[:,i])
     breg[i,0] = np.cov(b[:,i],ests[:,i])[0,1]*breg[i,1]
     sigma2 = np.var(ests[:,i]-breg[i,0]*b[:,i])
-    breg[i,1] = np.sqrt(sigma2*breg[i,1]/np.float(b.shape[0]))
+    breg[i,1] = np.sqrt(sigma2*breg[i,1]/float(b.shape[0]))
 
 
 

snipar/tests/test_example.py

@@ -11,10 +11,10 @@ def test_example(self):
         commands2 = [            
             "ibd.py --bed chr_@ --king king.kin0 --agesex agesex.txt --out chr_@ --threads 4 --ld_out",#TODO add option of supressing logging in snipar
             "impute.py --ibd [email protected] --bed chr_@ --king king.kin0 --agesex agesex.txt --out chr_@ --threads 4 -silent_progress",
-            "gwas.py phenotype.txt --bed chr_@ --imp chr_@ --threads 4",
+            "gwas.py phenotype.txt --bed chr_@ --imp chr_@ --threads 4 --out chr_@",
             "python estimate_sim_effects.py chr_1.sumstats.hdf5 phenotype.effects.txt",
             "correlate.py chr_@ effect --ldscores chr_@",
-            "pgs.py direct --bed chr_@ --imp chr_@ --weights direct_weights.txt",
+            "pgs.py direct --bed chr_@ --imp chr_@ --weights direct_weights.txt --A1 nt1 --A2 nt2 --beta_col ldpred_beta --SNP sid",
         ]
         stdout = subprocess.DEVNULL
         if self.log: