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import argparse | |
import sqlite3 | |
import sys | |
import numpy as np | |
import pandas as pd | |
def main(): | |
parser = argparse.ArgumentParser() | |
parser.add_argument("in_csv_0") |
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library("ChIPpeakAnno") | |
library("GenomicRanges") | |
library("org.At.tair.db") | |
library("TxDb.Athaliana.BioMart.plantsmart28") | |
library("biomaRt") | |
# Annotate genomic intervals in bed format using ChIPpeakAnno | |
# This script was designed for Arabidopsis, but can be easily changed for | |
# any other organism available through biomaRt |
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################################################################################ | |
# | |
# R.nanorc -- nano syntax-highlighting file for R | |
# | |
# Origin: This file is part of the pkgutils package for R. | |
# | |
# Usage: This file should be placed in a directory such as /usr/share/nano/ (on | |
# Ubuntu 12.04). That nano uses syntax highlighting at all might need to be | |
# enabled separately. | |
# |
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#!/bin/sh | |
parse_yaml() { | |
local prefix=$2 | |
local s='[[:space:]]*' w='[a-zA-Z0-9_]*' fs=$(echo @|tr @ '\034') | |
sed -ne "s|^\($s\)\($w\)$s:$s\"\(.*\)\"$s\$|\1$fs\2$fs\3|p" \ | |
-e "s|^\($s\)\($w\)$s:$s\(.*\)$s\$|\1$fs\2$fs\3|p" $1 | | |
awk -F$fs '{ | |
indent = length($1)/2; | |
vname[indent] = $2; | |
for (i in vname) {if (i > indent) {delete vname[i]}} |