num3ric

#!/usr/bin/python -O
import numpy as np
from numpy import array

A, C, G, T = 0, 1, 2, 3
int_to_char = {0:'A', 1:'C', 2:'G', 3:'T'}

#indel = -1
#scoring = array([[1,-1,-1,-1],
                 #[-1,1,-1,-1],

josef-pkt

'''Test of Equivalence and Non-Inferiority

currently only TOST for paired sample
Application for example bioequivalence



Author: Josef Perktold
License: BSD-3

matsen

#!/bin/sh

# Convert all arguments (assumed SVG) to a TIFF acceptable to PLOS
# Requires Inkscape and ImageMagick 6.8 (doesn't work with 6.6.9)

for i in $@; do
  BN=$(basename $i .svg)
  inkscape --without-gui --export-png="$BN.png" --export-dpi 300 $i
  convert -compress LZW -alpha remove $BN.png $BN.tiff
  mogrify -alpha off $BN.tiff

why-not

"""making a dataframe"""
df = pd.DataFrame([[1, 2], [3, 4]], columns=list('AB'))

"""quick way to create an interesting data frame to try things out""" 
df = pd.DataFrame(np.random.randn(5, 4), columns=['a', 'b', 'c', 'd'])

"""convert a dictionary into a DataFrame"""
"""make the keys into columns"""
df = pd.DataFrame(dic, index=[0])

ragingwind

Backend Architectures

Twitter

ror, scala, jetty, erlang, thrift, mongrel, comet server, my-sql, memchached, varnish, kestrel(mq), starling, gizzard, cassandra, hadoop, vertica, munin, nagios, awstats

• Introduce Gizzard of Twitter - 트위터의 새로운 분산 관리 라이브러리 Gizzard를 소개합니다.
• The Architecture Twitter Uses to Deal with 150M Active Users, 300K QPS, a 22 MB/S Firehose, and Send Tweets in Under 5 Seconds
• Scaling Twitter: Making Twitter 10000 Percent Faster

JosefJezek

How to use Pelican on GitHub Pages

Author: Josef Jezek

Install on Ubuntu

Installing Python tools

sudo apt-get install python-setuptools

katychuang

#!/usr/bin/env sh

# first check to see if mongo service is running. you can't delete any files until the service stops so perform a quick check.
launchctl list | grep mongo
  # NOTE: the pipe | symbol means the commands on the right performs on the output from the left
  # grep is a string search utility. `grep mongo` means search for the substring mongo
 
# use the unload command to end the mongo service. this is required to 'unlock' before removing the service.
#    first look for the file to delete
MONGO_SERVICE_FILE=$(ls ~/Library/LaunchAgents/*mongodb*)

bsweger

Useful Pandas Snippets

A personal diary of DataFrame munging over the years.

Data Types and Conversion

Convert Series datatype to numeric (will error if column has non-numeric values)
(h/t @makmanalp)

alimuldal

import numpy as np
from scipy import stats
from itertools import combinations
from statsmodels.stats.multitest import multipletests
from statsmodels.stats.libqsturng import psturng
import warnings


def kw_dunn(groups, to_compare=None, alpha=0.05, method='bonf'):
    """

s-boardman

The [Cufflinks](http://cole-trapnell-lab.github.io/cufflinks/)  Unix package is extremely well regarded for RNA-seq analysis.  Yet it is widely acknowledged that installation is difficult, not least by the [Cufflinks authors themselves](http://cole-trapnell-lab.github.io/cufflinks/getting_started/#installing-a-pre-compiled-binary-release)! Whilst the authors provide precompiled binaries to make the installation process easier [the instructions aren't very explicit](http://cole-trapnell-lab.github.io/cufflinks/getting_started/). Having spent a good hour on Google and StackOverflow I've put together an instruction list for the less experienced Unix user like myself.

Note this guide is for Unix distributions.

1. Download the Cufflinks tar from http://cole-trapnell-lab.github.io/cufflinks/install/
'''shell
wget http://cole-trapnell-lab.github.io/cufflinks/install/
'''
2. Untar the downloaded file
'''shell