Mercurial > repos > iuc > medaka_variant

comparison convert_VCF_info_fields.py @ 7:28c13c42de01 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit ed5a3aadbecc0decf9a797447f3ac7700683ea9a"
author iuc
date Mon, 22 Feb 2021 19:59:00 +0000
parents aabb4e1c0b7b
children edf6d4003fad
comparison
equal deleted inserted replaced
6:aabb4e1c0b7b 7:28c13c42de01
13 13
14 from scipy.stats import fisher_exact 14 from scipy.stats import fisher_exact
15 15
16 16
17 def pval_to_phredqual(pval): 17 def pval_to_phredqual(pval):
18 return round(-10 * log10(pval)) 18 try:
19 ret = round(-10 * log10(pval))
20 except ValueError:
21 ret = 2147483647 # transform pval of 0.0 to max signed 32 bit int
22 return ret
19 23
20 24
21 def parseInfoField(info): 25 def parseInfoField(info):
22 info_fields = info.split(';') 26 info_fields = info.split(';')
23 info_dict = OrderedDict() 27 info_dict = OrderedDict()
31 in_vcf = open(in_vcf_filepath, 'r') 35 in_vcf = open(in_vcf_filepath, 'r')
32 out_vcf = open(out_vcf_filepath, 'w') 36 out_vcf = open(out_vcf_filepath, 'w')
33 to_skip = set(['SC', 'SR']) 37 to_skip = set(['SC', 'SR'])
34 for i, line in enumerate(in_vcf): 38 for i, line in enumerate(in_vcf):
35 if i == 1: 39 if i == 1:
36 out_vcf.write("##convert_VCF_info_fields=0.1\n") 40 out_vcf.write("##convert_VCF_info_fields=0.2\n")
37 if line[0:2] == "##": 41 if line[0:2] == "##":
38 if line[0:11] == "##INFO=<ID=": 42 if line[0:11] == "##INFO=<ID=":
39 id_ = line[11:].split(',')[0] 43 id_ = line[11:].split(',')[0]
40 if id_ in to_skip: 44 if id_ in to_skip:
41 continue 45 continue