Mercurial > repos > iuc > medaka_consensus

comparison 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
comparison
equal deleted inserted replaced
10:db25ec99c3ea 11:0413e62b757a
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 = []