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 curl  -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refFlat.txt.gz" \
 	| gunzip -c \
 	| awk '{n=int($9); split($10,S,/,/);split($11,E,/,/); for(i=1;i<=n;++i) {printf("%s\t%s\t%s\t%s\n",$3,S[i],E[i],$1);} }' \
 	> refFlat.exons.hg19.bed

 bedtools sort -i refFlat.exons.hg19.bed > refFlat.exons.hg19.sorted.bed

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import argparse
import numpy as np
from scipy import ndimage
from scipy.cluster.vq import kmeans
from scipy.misc import imsave


def rgb2hex(r, g, b):
    return '#{:02x}{:02x}{:02x}'.format(r, g, b)

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from IPython.core.magic import (Magics, magics_class, line_magic,
                                cell_magic, line_cell_magic, needs_local_scope)

# The class MUST call this class decorator at creation time
@magics_class
class ProgressMagic(Magics):

    @line_magic
    @needs_local_scope
    def progress(self, line, *args, **kwargs):

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#!/bin/bash

#As an example, get all ".fa.gz" files from a directory

wget -r -np --spider ftp://ftp.ncbi.nlm.nih.gov/genomes/Sus_scrofa/CHR*  2>&1 | grep -Eo "ftp\:.*\.fa\.gz" | uniq

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# requires `tree` package
alias lst='tree -CAL 2 $1'

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alias lst='tree -L 2 $1'

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function csv() { cat "$@" | column -t -s, | less -S; }
function tsv() { cat "$@" | column -t -s"\t" | less -S; }

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shopt -s histappend
export HISTSIZE=100000
export HISTFILESIZE=100000
export HISTCONTROL=ignoredups:erasedups
export PROMPT_COMMAND="history -a;history -c;history -r;$PROMPT_COMMAND"

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# Put in ~/.bash_profile or similar.
# PS1 (prompt)

# Reset
Color_Off="\[\033[0m\]"       # Text Reset
 
# Regular Colors
Black="\[\033[0;30m\]"        # Black
Red="\[\033[0;31m\]"          # Red
Green="\[\033[0;32m\]"        # Green

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