Mercurial > repos > iuc > medaka_variant_pipeline

comparison convert_VCF_info_fields.py @ 10:7623e5888be9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"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
comparison
equal deleted inserted replaced
9:336b3def9b2b 10:7623e5888be9
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 = []