Mercurial > repos > iuc > medaka_variant_pipeline

diff convert_VCF_info_fields.py @ 10:7623e5888be9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
author: iuc
date: Thu, 22 Apr 2021 20:24:49 +0000
parents: 1040a307be0c
children: 597407d61386
--- a/convert_VCF_info_fields.py	Mon Mar 29 20:06:01 2021 +0000
+++ b/convert_VCF_info_fields.py	Thu Apr 22 20:24:49 2021 +0000
@@ -11,7 +11,8 @@
 from collections import OrderedDict
 from math import log10
 
-from scipy.stats import fisher_exact
+import scipy
+import scipy.stats
 
 
 def pval_to_phredqual(pval):
@@ -69,7 +70,7 @@
                 for j, i in enumerate(range(2, len(sr_list), 2)):
                     dp4 = (sr_list[ref_fwd], sr_list[ref_rev], sr_list[i], sr_list[i + 1])
                     dp2x2 = [[dp4[0], dp4[1]], [dp4[2], dp4[3]]]
-                    _, p_val = fisher_exact(dp2x2)
+                    _, p_val = scipy.stats.fisher_exact(dp2x2)
                     sb = pval_to_phredqual(p_val)
 
                     as_ = (sc_list[ref_fwd], sc_list[ref_rev], sc_list[i], sc_list[i + 1])