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from math import sqrt


def jeffreys_interval(af, n_samples, alpha=0.05):
    # https://en.wikipedia.org/wiki/Binomial_proportion_confidence_interval
    """
    >>> jeffreys_interval(0.2, 5) #doctest: +ELLIPSIS
    (0.02251..., 0.6286...)
    >>> jeffreys_interval(0.2, 10) #doctest: +ELLIPSIS
    (0.0440..., 0.5027...)

brentp

from __future__ import print_function
from pyfaidx import Fasta
from cyvcf2 import VCF
import string
import re
import sys

try:  # 2.x
    maketrans = string.maketrans
except AttributeError:  # 3.x

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import csv
import re
import sys
import os.path
import string

sex_replace = {'m': 1, 'male': 1, 'female': 2, 'f': 2}
phenotype_replace = {'affected': 2, 'unaffected': 1}

if False:

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with-bcolz	time (seconds)	bcolz-time	md5sum	num_lines	filter
True	2.8	0.62	5281fecb8571cc7c8e832e5682e865bb	16778	(gt_phred_ll_homalt).(*).(==0).(all)
False	155.2	NA	5281fecb8571cc7c8e832e5682e865bb	16778	(gt_phred_ll_homalt).(*).(==0).(all)
True	3.1	0.74	b2b75c9a56e128410a0e19708f096e2f	16750	((gt_phred_ll_homalt).().(==0).(all)) and (gt_types).().(==HOM_ALT).(all)
False	212.8	NA	b2b75c9a56e128410a0e19708f096e2f	16750	((gt_phred_ll_homalt).().(==0).(all)) and (gt_types).().(==HOM_ALT).(all)
True	1.4	0.42	c4885f35d03bed862d1e9d0ece71bc7c	2367	(gt_depths.{dad} > 20 and gt_depths.{mom} > 20 and gt_depths.{kid} > 20) and (gt_types.{dad} == HOM_REF and gt_types.{mom} == HOM_REF and gt_types.{kid} != HOM_REF)
False	203.0	NA	c4885f35d03bed862d1e9d0ece71bc7c	2367	(gt_depths.{dad} > 20 and gt_depths.{mom} > 20 and gt_depths.{kid} > 20) and (gt_types.{dad} == HO

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$ gemini de_novo --columns "chrom, start, end, ref, alt" test.de_novo.db --min-kindreds 1 --gt-pl-max 1000 | cols

chrom  start      end        ref  alt  gene    variant_id    family_id  family_members                                                     family_genotypes  affected_samples  family_count
chr10  48003991   48003992   C    T    ASAH2C  variant_id:2  2          2_dad(dad;unaffected),2_mom(mom;unaffected),2_kid(child;affected)  C/C,C/C,C/T       2_kid             2
chr10  48004991   48004992   C    T    ASAH2C  variant_id:3  3          3_dad(dad;unaffected),3_mom(mom;unaffected),3_kid(child;affected)  C/C,C/C,C/T       3_kid             2
chr10  135336655  135336656  G    A    SPRN    variant_id:4  2          2_dad(dad;unaffected),2_mom(mom;unaffected),2_kid(child;affected)  G/G,G/G,G/A       2_kid             2
chr10  135336655  135336656  G    A    SPRN    variant_id:4  1          1_dad(dad;unaffected),1_mom(mom;unaffected),1_kid(child;affected)  G/G,G/G,G/A       1_kid             2
chr10  135

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from bx.bbi import bigwig_file
from bx.bbi import bigbed_file
print bigwig_file
import time
from hashlib import md5

prefix = '/data/gemini/data/hg19_fitcons_fc-i6-0_V1-01'


print "before bw: 8.6 seconds"

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"""
This will standardize input file genotype fields to have AD=REF,ALT1,ALT2 ... (a
la GTK).

For platypus:  --depth NR --alt-depth NV
    varscan:   --ref-depth RD --alt-depth AD
    samtools:  --ref-depth DP4 (untested)

"""
import argparse

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set -eo pipefail

REF=human_g1k_v37_decoy.fasta
VCF=Mills_and_1000G_gold_standard.indels.b37.vcf.gz
VCF=/usr/local/src/gemini/test/test.mult-alts.fb.vep.vcf.gz

java -Xmx4G -jar /usr/local/src/gatk/GenomeAnalysisTK.jar -T LeftAlignAndTrimVariants --splitMultiallelics --trimAlleles \
    -R $REF \
    --variant $VCF -o gatk.norm.vcf

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"""
Generate sorted random numbers.
method from: http://repository.cmu.edu/cgi/viewcontent.cgi?article=3483&context=compsci

Has same interface as random module except it takes N as the first argument
for the number of numbers to generate.
"""
from random import random as rand, seed

def random(N):

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package main

import (
	"bufio"
	"compress/gzip"
	"container/heap"
	"fmt"
	"io"
	"os"
	"strconv"