Kevin Murray kdmurray91

## snakemake_3.9.0+dfsg-1_amd64.build
dpkg-checkbuilddeps: error: Unmet build dependencies: python3-pytools
[1;33mW: Unmet build-dependency in source[0m
dpkg-buildpackage: info: source package snakemake
dpkg-buildpackage: info: source version 3.9.0+dfsg-1
dpkg-buildpackage: info: source distribution UNRELEASED
dpkg-buildpackage: info: source changed by Kevin Murray <kdmfoss@gmail.com>
 dpkg-source --before-build snakemake
dpkg-source: info: applying 0001-Use-the-inbuild-sphinx.ext.napoleon.patch
dpkg-source: info: applying 0003-Use-debian-s-mathjax-package.patch
dpkg-source: info: applying 0003-Compat-fix.patch

## update-julia.sh
#!/bin/bash

declare -A urls
urls[0.5]='https://s3.amazonaws.com/julialang/bin/linux/x64/0.5/julia-0.5-latest-linux-x86_64.tar.gz'
urls[nightly]='https://s3.amazonaws.com/julianightlies/bin/linux/x64/julia-latest-linux64.tar.gz'

set -xeuo pipefail
MAINVER=0.5
PREFIX=${PREFIX:-$HOME}

## tara
tara init af2573173e19a6ada1ab4a3486468336e05607e9
Wed Jun 8 15:26:44 2016 +1000

## mpmc_queue.hh
template<typename Data>
class concurrent_queue
{
private:
    std::queue<Data> the_queue;
    mutable std::mutex the_mutex;
    std::condition_variable the_condition_variable;
public:
    void push(Data const& data)
    {

## rundebcitest
#!/bin/bash

if [ $# -lt 1 ]
then
	echo "USAGE: run-debci-test <PKG.changes> [<outdir>]"
	exit 1
fi

if [ $# -eq 2 ]
then

## download-all-debmed-dupstreammeta.sh
for pkg in $(cat allpkgs)
do
	mkdir -p "${pkg}"
	wget -nv -O "${pkg}/upstream_metadata" \
	       	"http://anonscm.debian.org/cgit/debian-med/${pkg}.git/plain/debian/upstream/metadata" \
		|| rm -f "${pkg}/upstream_metadata"
done


## eigencalc.cc
/*
 * ============================================================================
 *
 *       Filename:  eigencalc.cc
 *        License:  GPLv3+
 *         Author:  Kevin Murray, spam@kdmurray.id.au
 *
 * ============================================================================
 */

## tst.py
from __future__ import print_function, division
from frisk.kmerhash import *
import screed
from matplotlib import pyplot as plt
from functools import partial
import multiprocessing as mp
from os import path


def seq_ivom(gen):

## tst.py
from frisk.kmerhash import *
import screed

r = screed.open('/home/kevin/ws/seqs/TAIR10_gen/TAIR10.fasta.gz')
for x in r:
    seq = x.sequence[:100000]
    break

winsz = 3000
ivs = []

## code_challenge_5.py
# given a sequence find kmers of a given length that occur equal to t or more
# times in a given length of window in the sequence

from collections import deque


def kmer_frequency(text, k, window, thresh=3):
    counts = dict()
    kmers = deque()
    for w in range(len(text)-window+1):