Mercurial > repos > iuc > medaka_variant

comparison convert_VCF_info_fields.py @ 10:8ee6b81b7de9 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 20:23:20 +0000
parents 849aebec0dd9
children b7da0d412e48
comparison
equal deleted inserted replaced
9:dbef8b38161e 10:8ee6b81b7de9
9 9
10 import sys 10 import sys
11 from collections import OrderedDict 11 from collections import OrderedDict
12 from math import log10 12 from math import log10
13 13
14 from scipy.stats import fisher_exact 14 import scipy
15 import scipy.stats
15 16
16 17
17 def pval_to_phredqual(pval): 18 def pval_to_phredqual(pval):
18 try: 19 try:
19 ret = round(-10 * log10(pval)) 20 ret = round(-10 * log10(pval))
67 dpspf += sr_list[i] 68 dpspf += sr_list[i]
68 dpspr += sr_list[i + 1] 69 dpspr += sr_list[i + 1]
69 for j, i in enumerate(range(2, len(sr_list), 2)): 70 for j, i in enumerate(range(2, len(sr_list), 2)):
70 dp4 = (sr_list[ref_fwd], sr_list[ref_rev], sr_list[i], sr_list[i + 1]) 71 dp4 = (sr_list[ref_fwd], sr_list[ref_rev], sr_list[i], sr_list[i + 1])
71 dp2x2 = [[dp4[0], dp4[1]], [dp4[2], dp4[3]]] 72 dp2x2 = [[dp4[0], dp4[1]], [dp4[2], dp4[3]]]
72 _, p_val = fisher_exact(dp2x2) 73 _, p_val = scipy.stats.fisher_exact(dp2x2)
73 sb = pval_to_phredqual(p_val) 74 sb = pval_to_phredqual(p_val)
74 75
75 as_ = (sc_list[ref_fwd], sc_list[ref_rev], sc_list[i], sc_list[i + 1]) 76 as_ = (sc_list[ref_fwd], sc_list[ref_rev], sc_list[i], sc_list[i + 1])
76 77
77 info = [] 78 info = []