Merge pull request #206 from dvitale199/sexcheck

Sexcheck

Author: dvitale199

.gitignore

@@ -9,4 +9,5 @@ requirements.txt
 .DS_Store
 dist/*
 the_real_genotools.egg-info/*
-geno_tools.egg-info/*
+geno_tools.egg-info/*
+.venv/

genotools/qc.py

@@ -165,8 +165,8 @@ def run_sex_prune(self, check_sex=[0.25,0.75]):
         bfiles_to_pfiles(pfile_path=geno_path)
 
         # check sex 2 methods
-        plink_cmd1 = f"{plink_exec} --bfile {geno_path} --check-sex 0.25 0.75 --maf 0.05 --out {sex_tmp1}"
-        plink_cmd2 = f"{plink_exec} --bfile {geno_path} --chr 23 --from-bp 2781479 --to-bp 155701383 --maf 0.05 --geno 0.05 --hwe 1E-5 --check-sex  0.25 0.75 --out {sex_tmp2}"
+        plink_cmd1 = f"{plink_exec} --bfile {geno_path} --check-sex {check_sex[0]} {check_sex[1]} --maf 0.05 --out {sex_tmp1}"
+        plink_cmd2 = f"{plink_exec} --bfile {geno_path} --chr 23 --from-bp 2781479 --to-bp 155701383 --maf 0.05 --geno 0.05 --hwe 1E-5 --check-sex {check_sex[0]} {check_sex[1]} --out {sex_tmp2}"
 
         cmds = [plink_cmd1, plink_cmd2]
         for cmd in cmds:

setup.py

@@ -18,7 +18,7 @@
 
 setup(
     name='the_real_genotools', 
-    version='1.3.4', 
+    version='1.3.5', 
     packages=find_packages(),
     author='Dan Vitale',
     author_email='[email protected]',