comparison convert_VCF_info_fields.py @ 10:9fb055604648 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"

9:43815fa60f3a

import sys
from collections import OrderedDict
from math import log10

from scipy.stats import fisher_exact


def pval_to_phredqual(pval):
    try:
        ret = round(-10 * log10(pval))

                    dpspf += sr_list[i]
                    dpspr += sr_list[i + 1]
                for j, i in enumerate(range(2, len(sr_list), 2)):
                    dp4 = (sr_list[ref_fwd], sr_list[ref_rev], sr_list[i], sr_list[i + 1])
                    dp2x2 = [[dp4[0], dp4[1]], [dp4[2], dp4[3]]]
                    _, p_val = fisher_exact(dp2x2)
                    sb = pval_to_phredqual(p_val)

                    as_ = (sc_list[ref_fwd], sc_list[ref_rev], sc_list[i], sc_list[i + 1])

                    info = []

10:9fb055604648

import sys
from collections import OrderedDict
from math import log10

import scipy
import scipy.stats


def pval_to_phredqual(pval):
    try:
        ret = round(-10 * log10(pval))

                    dpspf += sr_list[i]
                    dpspr += sr_list[i + 1]
                for j, i in enumerate(range(2, len(sr_list), 2)):
                    dp4 = (sr_list[ref_fwd], sr_list[ref_rev], sr_list[i], sr_list[i + 1])
                    dp2x2 = [[dp4[0], dp4[1]], [dp4[2], dp4[3]]]
                    _, p_val = scipy.stats.fisher_exact(dp2x2)
                    sb = pval_to_phredqual(p_val)

                    as_ = (sc_list[ref_fwd], sc_list[ref_rev], sc_list[i], sc_list[i + 1])

                    info = []