mikeyk

#! /usr/bin/env python

import redis
import random
import pylibmc
import sys

r = redis.Redis(host = 'localhost', port = 6389)
mc = pylibmc.Client(['localhost:11222'])

ogrisel

Line #      Hits         Time  Per Hit   % Time  Line Contents
==============================================================
   627                                           def expected_mutual_information(contingency, n_samples):
   628                                               """Calculate the expected mutual information for two labelings."""
   629        25           82      3.3      0.0      R, C = contingency.shape
   630        25           53      2.1      0.0      N = n_samples
   631        25         1059     42.4      0.0      a = np.sum(contingency, axis=1, dtype='int')
   632        25          932     37.3      0.0      b = np.sum(contingency, axis=0, dtype='int')
   633        25           58      2.3      0.0      emi = 0
   634      1839         4005      2.2      0.0      for i in range(R):

brentp

# NOTE the /Modules/

./configure --prefix=/vol1/home/brentp/installed/ \
     --with-python-config-dir=/vol1/home/brentp/src/python/Python-2.7.2/Modules/ \
     --enable-pythoninterp=yes --with-features=huge 

brentp

ORG=hg19
USER=brentp

# from: http://nsaunders.wordpress.com/2011/05/18/how-to-create-a-partial-ucsc-genome-mysql-database/

# create database
mysql -u $USER  -e "CREATE DATABASE $ORG";
mkdir -p ucsc-data/$ORG
cd ucsc-data/$ORG
for table in knownGene refGene ensGene kgXref chromInfo cpgIslandExt cytoBand

brentp

"""
    %prog [options] files
"""
import optparse
import sys
import gzip
from itertools import izip


def nopen(f, mode="rb"):

aurora

function clone(object)
    local dict = {}
    
    local function clone(object)
        if (type(object) ~= "table") then
            return object
        elseif (dict[object]) then
            return dict[object]
        end

brentp

sudo apt-get install libtool
git clone git://dnaa.git.sourceforge.net/gitroot/dnaa/dnaa dnaa-git
cd dnaa-git
# bfast required. see above gist
cp -r ../bfast-git ./bfast
# samtools require. see above gist.
cp -r ../samtools-svn/ ./samtools

sh autogen.sh && ./configure && make && sudo make install