comparison convert_VCF_info_fields.py @ 7:28c13c42de01 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit ed5a3aadbecc0decf9a797447f3ac7700683ea9a"

6:aabb4e1c0b7b

from scipy.stats import fisher_exact


def pval_to_phredqual(pval):
    return round(-10 * log10(pval))


def parseInfoField(info):
    info_fields = info.split(';')
    info_dict = OrderedDict()

    in_vcf = open(in_vcf_filepath, 'r')
    out_vcf = open(out_vcf_filepath, 'w')
    to_skip = set(['SC', 'SR'])
    for i, line in enumerate(in_vcf):
        if i == 1:
            out_vcf.write("##convert_VCF_info_fields=0.1\n")
        if line[0:2] == "##":
            if line[0:11] == "##INFO=<ID=":
                id_ = line[11:].split(',')[0]
                if id_ in to_skip:
                    continue

7:28c13c42de01

from scipy.stats import fisher_exact


def pval_to_phredqual(pval):
    try:
        ret = round(-10 * log10(pval))
    except ValueError:
        ret = 2147483647  # transform pval of 0.0 to max signed 32 bit int
    return ret


def parseInfoField(info):
    info_fields = info.split(';')
    info_dict = OrderedDict()

    in_vcf = open(in_vcf_filepath, 'r')
    out_vcf = open(out_vcf_filepath, 'w')
    to_skip = set(['SC', 'SR'])
    for i, line in enumerate(in_vcf):
        if i == 1:
            out_vcf.write("##convert_VCF_info_fields=0.2\n")
        if line[0:2] == "##":
            if line[0:11] == "##INFO=<ID=":
                id_ = line[11:].split(',')[0]
                if id_ in to_skip:
                    continue