macmanes

interleave-reads.py file.1.fq.gz file.2.fq.gz \
| normalize-by-median.py --max-memory-usage 8e10 -C 30 -o -  - \
| trim-low-abund.py -M 8e10 -o 2pass.fq --cutoff 2 --gzip -

arundurvasula

#!/bin/python
#xkcd SFS plots
# usage: ms 20 10000 -t 50 -r 10 1000  > neutral_ms.txt; python XKCD_sfs_plots.py neutral_ms.txt

from matplotlib import pyplot as plt
import numpy as np
from itertools import groupby
from sys import argv

ms_file = open(argv[1])

dwinter

#Finding the number of sequence records by taxonomic group

Ricardo wants to know how to find the number of sequence records associated with sub-groups within a given taxon . This example grew a bit too big to make into a comment, so here it is in gist form.

So, let's find out how many DNA sequences are present in genbank for each

stephenturner

# Generate dataset with 5,000,000 rows, and some random numbers from normal,
# uniform, and cauchy distributions. Write out to file (warning, ~330MB)
n <- 5000000
d <- data.frame(a=1:n, b=rnorm(n), c=runif(n), d=rcauchy(n))
write.table(d, file="test.txt")

# Import the regular way with read.table
system.time(in1 <- read.table("test.txt"))

## Crikey!

wrathematics

library(Rcpp)

body <- "
SEXP foo(const int len, Rcpp::NumericVector pr)
{
  Rcpp::IntegerVector ret(len);
  RNGScope();
  
  for (int i=0; i<len; i++)
  {

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)

ysaotome

#!/bin/zsh
# pyenv install for CentOS 6.5 x86_64 

yum install -y  gcc gcc-c++ make git patch openssl-devel zlib-devel readline-devel sqlite-devel bzip2-devel

git clone git://github.com/yyuu/pyenv.git ~/.pyenv

export PATH="$HOME/.pyenv/bin:$PATH"
eval "$(pyenv init -)"

rchikhi

#!/usr/bin/env python
doc = """
Quickly estimates insert sizes of read datasets, given some sequence(s) they can be mapped to.
Author: Rayan Chikhi         

short usage: <reference> <*.fastq> 

example: 
         estimate-insert-sizes contigs.fa readsA_1.fq readsA_2.fq readsB_1.fq readsB_2.fq

hadley

Notes:

• I've tried to break up in to separate pieces, but it's not always possible: e.g. knowledge of data structures and subsetting are tidy intertwined.

• Level of Bloom's taxonomy listed in square brackets, e.g. http://bit.ly/15gqPEx. Few categories currently assess components higher in the taxonomy.

Programming R curriculum

Data structures

arq5x

HISTCONTROL="erasedups"
export HISTCONTROL