jnpaulson

source("http://bioconductor.org/biocLite.R")
biocLite(c("rhdf5","biom"))
library(rhdf5)
library(biom)

# This generates the matrix columns-wise
generate_matrix <- function(x){
	indptr  = x$sample$matrix$indptr+1
	indices = x$sample$matrix$indices+1
	data    = x$sample$matrix$data

8bit-pixies

# R lexer
# based on http://www.jayconrod.com/posts/37/a-simple-interpreter-from-scratch-in-python-part-1

#' Returns list of patterns and token names.
#' This saves typing.
#' 
#' @param pattern a regex pattern
#' @param tag the resulting token tag
tk <- function(pattern, token) {
  return(list(pattern=paste0("^", pattern), tag=token))

davfre

SAM and BAM filtering one-liners

@author: David Fredman, david.fredmanAAAAAA@gmail.com (sans poly-A tail)
@dependencies: http://sourceforge.net/projects/bamtools/ and http://samtools.sourceforge.net/

Please extend with additional/faster/better solutions via a pull request!

BWA mapping (using piping for minimal disk I/O)

streaming_fasta_stats.py

#!/usr/bin/env python

# calculate mean and variance of the sequence lengths in a large fasta file

# method taken from:
# http://math.stackexchange.com/questions/20593/calculate-variance-from-a-stream-of-sample-values

# m_k = m_(k-1) + x_k + m_(k-1)
# v_k = v_(k-1) + (x_k -m_(k-1))(x_k - m_k)

spikegrobstein

# Example configuration for mcwrapper: mcwrapper.conf
# this file can live in any of the following places (in order of priority):
#  - the value of MCWRAPPER_CONFIG_PATH env variable
#  - the current working directory as "mcwrapper.conf"
#  - ~/.mcwrapper.conf
#  - /etc/mcwrapper.conf
#
# Configuration is actual Bash. You can use conditionals... not that you would.

. "/root/minecraft/minecraft-docker"

minrk

#!/usr/bin/env python
"""strip outputs from an IPython Notebook

Opens a notebook, strips its output, and writes the outputless version to the original file.

Useful mainly as a git filter or pre-commit hook for users who don't want to track output in VCS.

This does mostly the same thing as the `Clear All Output` command in the notebook UI.

LICENSE: Public Domain

komasaru

#*********************************************
# ボックス＝ミューラー法法による正規乱数生成
#*********************************************
class RndnumBoxMuller
  # 各種定数
  M  = 10            # 平均
  S  = 2.5           # 標準偏差
  N  = 10000         # 発生させる乱数の個数
  PI = 3.1415926535  # 円周率
  SCALE = N / 100.0  # ヒストグラム用スケール

wasade

#!/bin/env python
#cluster_jobs.py
"""
Simple helper script to make pbs jobs and submit to the cluster 

Will only work if run on bmf or hemisphere

Can run from command line or import into python code.

Author: Micah Hamady

obeleh

I was reading the gist @https://gist.github.com/2012250

I found the autovivification functionality of it pretty cool. If only I could have a parent reference...

Obviously this was not going to be a one-line tree. But that wasn't the goal

A simple variant:

from collections import defaultdict

amueller

# (c) 2012 Andreas Mueller amueller@ais.uni-bonn.de
# License: BSD 2-Clause
#
# See my blog for details: http://peekaboo-vision.blogspot.com

import numpy as np

import matplotlib.pyplot as plt
from matplotlib.animation import FuncAnimation