roryk

class Foo(object):

    def __init__(self):
        self.history = {"var1": [], "var2": [], "var3": [], "var4": []}

    def update(self, to_update):
        for k, v in self.history.iteritems():
            if k == to_update:
                v.append(1)
            else:

roryk

import tempfile
import gffutils
import os
from argparse import ArgumentParser

def get_gtf_db(gtf, in_memory=False):
    """
    create a gffutils DB
    """
    db_file = gtf + ".db"

roryk

<style TYPE="text/css">
code.has-jax {font: inherit; font-size: 100%; background: inherit; border: inherit;}
</style>
<script type="text/x-mathjax-config">
MathJax.Hub.Config({
    tex2jax: {
        inlineMath: [['$','$'], ['\\(','\\)']],
        skipTags: ['script', 'noscript', 'style', 'textarea', 'pre'] // removed 'code' entry
    }
});

roryk

# to add latex equations to a Rmd file, enclose the equations using the $ $ syntax
# and run knit_equation on the Rmd file instead of knit
knit_equation = function(rmd, md) {
  require('knitr')
  require('RCurl')
  gist_url = 'https://gist.github.com/roryk/4476421/raw/d08080c206b5663e0451a5ef6c56635a0c6f0f17/gistfile1'
  #gist_url = 'https://gist.github.com/raw/4476421/d08080c206b5663e0451a5ef6c56635a0c6f0f17/gistfile1'
  tmp = tempfile()
  knit(rmd, tmp)
  f = file(md, "w")

roryk

#!/bin/bash
set -e

# Figure out where this script is located.
SELFSCRIPT="`readlink -f \"$0\"`"
SELFDIR="`dirname \"$SELFSCRIPT\"`"
SELFDIR="`cd \"$SELFDIR\" && pwd`"

# Temporarily set PATH and LD_LIBRARY_PATH
export PATH=$SELFDIR/bin:$PATH

roryk

import os
import subprocess
from argparse import ArgumentParser

def find_parallel_environment(queue):
    """Find an SGE/OGE parallel environment for running multicore jobs in specified queue.
    """
    base_queue = os.path.splitext(queue)[0]
    queue = base_queue + ".q"

roryk

Tom Knight and the Lisp Machine

A novice was trying to fix a broken Lisp machine by turning the power off and on.

Knight, seeing what the student was doing, spoke sternly: “You cannot fix a machine by just power-cycling it with no understanding of what is going wrong.”

Knight turned the machine off and on.

The machine worked.

roryk

#!/bin/bash
TMPDIR=download
START=1161
END=1438
mkdir -p ${TMPDIR}
parallel -j 4 wget -P download https://theweekinchess.com/zips/twic{}g.zip ::: $(seq ${START} ${END})
unzip -d ${TMPDIR} ${TMPDIR}/'*.zip'
cat ${TMPDIR}/*.pgn > twic_pgn_${START}_${END}.pgn
zip twic_pgn_${START}_${END}.zip twic_pgn_${START}_${END}.pgn
rm twic_pgn_${START}_${END}.pgn