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#!/usr/bin/python

import array
import gzip
import struct
import numpy as np
import multiprocessing as mp


class BinaryGenoWriter(object):

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1. Download and install the CUDA toolkit.
    - http://developer.nvidia.com/cuda-downloads
    - For Mac, http://developer.download.nvidia.com/compute/cuda/4_2/rel/toolkit/cudatoolkit_4.2.9_macos.pkg

2. Download and install the CUDA drivers for you system.
    - http://developer.nvidia.com/cuda-downloads
    - For Mac, http://developer.download.nvidia.com/compute/cuda/4_2/rel/drivers/devdriver_4.2.10_macos.dmg

3. Download and install the cudapp library
http://code.google.com/p/cudpp/

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echo "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmGm12878HMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmH1hescHMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmHepg2HMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmHmecHMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmHsmmHMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmHuvecHMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmK562HMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmNhekHMM.bed.gz
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/wgEncodeBroadHmmNhlfHMM.bed.gz" \
> chromhmm-files.txt

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This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.

It was created by graph-tool configure 2.2.14, which was
generated by GNU Autoconf 2.68.  Invocation command line was

  $ ./configure --disable-debug --disable-dependency-tracking --prefix=/usr/local/Cellar/graph-tool/2.2.14

## --------- ##
## Platform. ##

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# alias the raw data files
ln -s C0PYJACXX_s7_0_GSL48index_10_SL16067.fastq.gz 0h-IP-nbn.fq.gz
ln -s C0PYJACXX_s7_0_GSL48index_11_SL16068.fastq.gz 3Gy-IP-nbn.fq.gz
ln -s C0PYJACXX_s7_0_GSL48index_12_SL16069.fastq.gz PpoI-IP-nbn.fq.gz
ln -s C0PYJACXX_s7_0_GSL48index_7_SL16064.fastq.gz 0h-Input.fq.gz
ln -s C0PYJACXX_s7_0_GSL48index_8_SL16065.fastq.gz 3Gy-Input.fq.gz
ln -s C0PYJACXX_s7_0_GSL48index_9_SL16066.fastq.gz PpoI-Input.fq.gz

# build a list of sample stubs
SAMPLES="0h-Input 0h-IP-nbn 3Gy-Input 3Gy-IP-nbn PpoI-Input PpoI-IP-nbn"

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# 1. Get the ENCODE segmentations from EBI.
# consensus
wget http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/awgHub/byDataType/segmentations/jan2011/gm12878.combined.bb
wget http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/awgHub/byDataType/segmentations/jan2011/h1hesc.combined.bb
wget http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/awgHub/byDataType/segmentations/jan2011/helas3.combined.bb
wget http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/awgHub/byDataType/segmentations/jan2011/hepg2.combined.bb
wget http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/awgHub/byDataType/segmentations/jan2011/huvec.combined.bb
wget http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/awgHub/byDataType/segmentations/jan2011/k562.combined.bb

# Segway (ahem; https://twitter.com/michaelhoffman/status/246679147164880897)

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$ make clean
cd lib && make clean
rm -f *.o zlib-1.2.3/*.o zlib-1.2.3/libz.1.2.3.dylib
cd python && rm -fr build khmer/*.so

$ make all
cd lib && make
cd zlib-1.2.3; ./configure --shared; make; rm minigzip.o; rm example.o
Checking for gcc...
Checking for shared library support...

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HISTCONTROL="erasedups"
export HISTCONTROL

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{
    "pile": {
        "chrom": "chr1"
        "start": 102033445
        "end":   102033446
        "ref":   "G"
        "total_ref_alleles": 45
        "total_alt_alleles": 15
        "total_fwd_a": 7
        "total_rev_a": 8

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Genome arithmetic for data exploration

The goal of today's practical session is to get your hands dirty with bedtools. We will be studying ChiP-seq data from three different cell types. Each cell type was assayed for H3K27ac. Our research goal is to understand and explore the similarities and differences between the ChIP peaks observed in the 3 different cell types.