brentp

{
 "metadata": {
  "name": "pandas"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {

brentp

"""
C-alpha test for rare variants. Copied from AssotesteR
Only reports the permutation p-value, not the asymptotic

This also wraps all of the functions in R's AssotesteR using
rpy2. Any function available in AssotesteR, e.g. CALPHA is 
availailable here has r_calpha().
The args are always

casecon: a list of 0's, 1's indicating case/control status

brentp

library(survey)

args = commandArgs(TRUE)
fclin = args[1]
fmeth = args[2]

clin = read.table(fclin, header=T, sep="\t")
clin$Barcode = as.character(clin$Unique.ID)
clin$strata = as.factor(clin$strata)

brentp

from bein import *
from bein.util import *
import os

M = MiniLIMS("data.db")


"""

GATK=/home/brentp/src/gatk/GenomeAnalysisTK-2.0-38-g45f7b0d/

brentp

#!/mnt/storage4/bin/python-2.6.6/bin/python
from toolshed import nopen
import sys

fh = nopen("|showq -r")
header = fh.next().strip().split()

job_name = len(sys.argv) > 1 and sys.argv[1] or None

d = {}

brentp

import itertools
from collections import Counter

def euler_52():
    for i in itertools.count(1):
        nums = [str(i * j) for j in range(1, 7)]
        s = frozenset(nums[0])
        sall = set()
        sall.update(*nums)
        if sall == s:

brentp

UPSTREAM=400
INSTREAM=100
ORG=hg18

mysql --user genome --host genome-mysql.cse.ucsc.edu  -NAD $ORG -e \
    "select chrom, txStart, txEnd, X.geneSymbol, strand from knownGene as K, kgXref as X WHERE txStart != txEnd AND X.kgID = K.name" \
    | awk -v ups=$UPSTREAM -v ins=$INSTREAM 'BEGIN{OFS=FS="\t"}
           $5 == "-" { print $1,$3-ins,$3+ups,$4 } 
           $5 == "+" { print $1,$2-ins,$2+ups,$4 }' \
    | sort -k1,1 -k2,2n \

brentp

from docopt import docopt
import sys

class command(object):
    registry = {}
    short_docs = []
    def __init__(self, doc = None):
        self.short_docs.append(doc)

    def __call__(self, fn):

brentp

"""
qvality must be on the $PATH.
run on a file with pvalues in column 4:

    $ python qvality.py --column 4 input.bed > output.bed

output file will have extra columns for PEP (posterior error prob)
and q-value.

if input.bed has a header, it is retained.

brentp

xs = read.table('mod4.txt', sep="\t", header=T)
y = read.table('y4.txt', sep="\t", header=T)
colnames(y) = "Survival"

df = cbind(y, xs)
print(colnames(df))

print(drop1(lm(Survival ~ SexMale + AgeChild + class_crewTRUE, data=df), test="F"))