necrolyte2

prefix=$HOME
PYTHON_VERSION=2.7.8
tmpdir=$HOME/tmp-python
rm -rf $tmpdir; mkdir -p $tmpdir
pushd $tmpdir && wget --no-check-certificate https://www.python.org/ftp/python/${PYTHON_VERSION}/Python-${PYTHON_VERSION}.tgz -O- | tar xzf - && pushd Python-${PYTHON_VERSION} && ./configure --prefix $prefix && make && make install && popd && popd

necrolyte2

# Install our own python
prefix=$(mktemp -d)
cd $prefix
version=2.7.8
wget --no-check-certificate https://www.python.org/ftp/python/${version}/Python-${version}.tgz -O- | tar xzf -
cd Python-${version}
./configure --prefix $prefix
make
make install
cd ..

necrolyte2

import re
import os
from os.path import *
import sys
import csv
from datetime import datetime
from collections import defaultdict
import itertools

gisaid_file = 'H3N2_GISAID.csv'

necrolyte2

<?xml version="1.0" encoding="UTF-8"?>
<Module>
  <ModulePrefs title="Hello, world!">
    <Require feature="opensocial-0.8"/>
  </ModulePrefs>
  <Content type="html"><![CDATA[
    <script type="text/javascript">
        function init() {
           document.getElementById("handler").innerHTML = "Hello, world.";
        }

necrolyte2

#!/usr/bin/env python

import sys

from Bio import SeqIO

f = sys.argv[1]

seqs = SeqIO.parse(f,'fasta')

necrolyte2

import os

import tempdir

class BaseTester(object):
    def setUp(self):
        ''' Auto enter temporary directory '''
        self.tdir = tempdir.TempDir()
        os.chdir(self.tdir.name)

necrolyte2

#!/usr/bin/env python

import subprocess
import argparse

# Can test with
# python -m doctest dnaplotter.py

def count_ref_bases(reference):
    '''

necrolyte2

#!/bin/bash

# Max amount of idle time in seconds before pm-suspend is invoked
# Default is 1 hour
idlemax=$((60*60))

# Run forever
while [ 1 ]
do
        # Keep checking to see if samba has locked files

necrolyte2

#!/usr/bin/env python

import sys

from Bio import SeqIO
from Bio.SeqIO.QualityIO import PairedFastaQualIterator

import argparse

parser = argparse.ArgumentParser()

necrolyte2

#! /bin/sh

### BEGIN INIT INFO
# Provides:          xbmc
# Required-Start:    $all
# Required-Stop:     $all
# Default-Start:     2 3 4 5
# Default-Stop:      0 1 6
# Short-Description: starts instance of XBMC
# Description:       starts instance of XBMC using start-stop-daemon and xinit