Mercurial > repos > iuc > medaka_consensus

diff convert_VCF_info_fields.py @ 11:0413e62b757a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"
author iuc
date Thu, 22 Apr 2021 20:24:25 +0000
parents eb1f4ba66dc6
children fa11aa8103b2
line wrap: on
line diff
--- a/convert_VCF_info_fields.py	Mon Mar 29 20:06:22 2021 +0000
+++ b/convert_VCF_info_fields.py	Thu Apr 22 20:24:25 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])