roryk

import numpy
import scipy.stats as stats

def outlier_resistant(coverage):
  median = float(numpy.median(coverage))
  deviations = [abs(x - median) for x in coverage]
  # median absolute deviation estimator of the standard deviation
  mad = 1.4826 * float(numpy.median(deviations))
  return int(median), int(mad)

roryk

[ 51%] Performing build step for 'libsparsehash'
cd /tmp/sailfish20150920-18016-i304l8/sailfish-0.7.4/external/sparsehash-sparsehash-2.0.2 && /Applications/Xcode.app/Contents/Developer/usr/bin/make
[ -d src/sparsehash/internal ] || mkdir -p src/sparsehash/internal
echo "/*" > src/sparsehash/internal/_sparsehash_config
echo " * NOTE: This file is for internal use only." >> src/sparsehash/internal/_sparsehash_config
echo " *       Do not use these #defines in your own program!" >> src/sparsehash/internal/_sparsehash_config
echo " */" >> src/sparsehash/internal/_sparsehash_config
awk '{prevline=currline; currline=$0;} \
	        /^#/ {in_second_file = 1;} \
	        !in_second_file {if (currline !~ /^ *$/) {inc[currline]=0}}; \

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

#!/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