l-modolo

#!/bin/sh
# compute reads length distribution from a fastq file
awk 'NR%4 == 2 {lengths[length($0)]++} END {for (l in lengths) {print l, lengths[l]}}'  file.fastq

even4void

(add-to-list 'auto-mode-alist '("\\.md\\'" . markdown-mode))
(add-to-list 'auto-mode-alist '("\\.Rmd\\'" . markdown-mode))
(add-to-list 'auto-mode-alist '("\\.rmd\\'" . markdown-mode))
(add-hook 'markdown-mode-hook 'turn-on-outline-minor-mode)

(defun rmarkdown-new-chunk (name)
  "Insert a new R chunk."
  (interactive "sChunk name: ")
  (insert "\n```{r " name "}\n")
  (save-excursion

mmstick

#!/bin/bash
cd /tmp

if ! which lynx > /dev/null; then sudo apt-get install lynx -y; fi

if [ "$(getconf LONG_BIT)" == "64" ]; then arch=amd64; else arch=i386; fi

function download() {
   wget $(lynx -dump -listonly -dont-wrap-pre $kernelURL | grep "$1" | grep "$2" | grep "$arch" | cut -d ' ' -f 4)
}

randomphrase

#define BOOST_TEST_MODULE subcommand options
#include <boost/test/unit_test.hpp>
#include <boost/program_options.hpp>
#include <boost/variant/variant.hpp>
#include <boost/variant/get.hpp>

struct GenericOptions {
    bool debug_;
};

cmaureir

Source: https://confluence.rcs.griffith.edu.au/display/v20zCluster/Sun+Grid+Engine+SGE+state+letter+symbol+codes+meanings

Category	State	SGE Letter Code
Pending	pending	qw
Pending	pending, user hold	qw
Pending	pending, system hold	hqw
Pending	pending, user and system hold	hqw
Pending	pending, user hold, re-queue	hRwq
Pending	pending, system hold, re-queue	hRwq

lmullen

SLIDES := $(patsubst %.md,%.md.slides.pdf,$(wildcard *.md))
HANDOUTS := $(patsubst %.md,%.md.handout.pdf,$(wildcard *.md))

all : $(SLIDES) $(HANDOUTS)

%.md.slides.pdf : %.md
	pandoc $^ -t beamer --slide-level 2 -o $@

%.md.handout.pdf : %.md
	pandoc $^ -t beamer --slide-level 2 -V handout -o $@ 

randyzwitch

import pandas as pd
from matplotlib import pyplot as plt
import matplotlib as mpl
import seaborn as sns
%matplotlib inline

#Read in data & create total column
stacked_bar_data = pd.read_csv("C:\stacked_bar.csv")
stacked_bar_data["total"] = stacked_bar_data.Series1 + stacked_bar_data.Series2

armish

# This function sorts the matrix for better visualization of mutual exclusivity across genes
memoSort <- function(M) {
	geneOrder <- sort(rowSums(M), decreasing=TRUE, index.return=TRUE)$ix;
	scoreCol <- function(x) {
		score <- 0;
		for(i in 1:length(x)) {
			if(x[i]) {
				score <- score + 2^(length(x)-i);
			}
		}

danielecook

#
# This script calculates the depth of coverage and breadth of coverage for a given bam. 
# Outputs a dictionary containing the contig/chromosome names and the depth and breadth of coverage for each
# and for the entire genome.
#
# If you optionally specify the name of the mitochondrial chromosome (e.g. mtDNA, chrM, chrMT)
# The script will also generate breadth and depth of coverage for the nuclear genome AND the ratio
# of mtDNA:nuclearDNA; which can act as a proxy in some cases for mitochondrial count within an individual.
# 
# Author: Daniel E. Cook

amroamroamro

Python version of the MATLAB code in this Stack Overflow post: https://stackoverflow.com/a/18648210/97160

The example shows how to determine the best-fit plane/surface (1st or higher order polynomial) over a set of three-dimensional points.

Implemented in Python + NumPy + SciPy + matplotlib.