hanfeisun

(setenv "PATH" (concat (getenv "PATH") ":/usr/local/bin:/Applications/Racket5/bin/:/usr/texbin/"))
(setenv "CLASSPATH" ":/Users/hanfei/Documents/Sandbox/TIJ/TIJS/TIJ-3rd-edition-code")


(if x-resource-name
    (progn
      (set-face-attribute 'default nil :font "inconsolata-18")
      ))
(if (not (equal emacs-version "23.4.1"))
    (progn

hanfeisun

import pysam
import os

t = "./865_rep1_treat.bam"
tb = "865_rep1_peaks.bed"

sorted_prefix = lambda path: path + ".sorted"
sorted_path = lambda path: sorted_prefix(path) + ".bam"

hanfeisun

import sys
import os
from ConfigParser import SafeConfigParser
from jinja2 import Environment, PackageLoader
from chilin.qc import MappingQC, PeakcallingQC

jinja_env = env = Environment(loader=PackageLoader('chilin', 'templates'))

def check_conf(conf):
    if True:

hanfeisun

from chilin.dc import jinja_env, PathFinder

class QC_Controller(object):
    def __init__(self, conf):
        self.pathfinder = PathFinder(conf)
        self.template = jinja_env.get_template(pathfinder.qc_template)
        self.has_run = False
    def run(self):
        pass
    def check(self):

hanfeisun

#!/usr/bin/python2.7

import os
import sys
import argparse
from math import sqrt
from collections import Counter
from itertools import tee, ifilterfalse, ifilter

import pysam

hanfeisun

#include <stdio.h>
#include <stdlib.h>
#define SHIFT 4
#define MSK 0x0F
#define UNT 1
#define N 300000000
#define print(X) for (i=1;i<1+N;i++) {printf("%d\t%d\n",i,(X)[i]);}


unsigned char aln[1+N];

hanfeisun

def create_workflow(args, conf):
    """
    :type conf:ChiLinConfig 
    """
    root_workflow = Workflow("Main")
    ShellCommand("prepare","mkdir -p {output}",output = conf.target_dir).attach_to(root_workflow)

    groom_workflow = attach(root_workflow, Workflow("Groom"))
    rawQC_workflow = attach(root_workflow, Workflow("RawQC"))
    map_workflow = attach(root_workflow, Workflow("ReadsMapping"))

hanfeisun

def _peaks_parse(input):
    total = 0
    fc20n = 0
    fc10n = 0
    peaks_info = {}
    with open(input) as peaks_xls:
        for line in peaks_xls:
            if line.startswith('# tags after filtering in treatment'):
                # tags after filtering in treatment: 13438948
                peaks_info["uniloc"] = int(line.strip().split(":")[1])

hanfeisun

def parseFactorByAntibody(geoPost):
    targetFlds = ["CHIP_ANTIBODY", "ANTIBODY", "CHIP", "ANTIBODY_SOURCE", "ANTIBODY_ANTIBODYDESCRIPTION",
                  "ANTIBODY_TARGETDESCRIPTION"]
    #1. try to get the values
    for t in targetFlds:
        tmp = getFromPost(geoPost, t).strip()
        if not tmp:
            continue
        tmp = tmp.upper().replace("ANTI-", " ").replace("ANTI", " ").strip()
        if len(tmp) < 10 and tmp != "":

hanfeisun

#!/bin/bash
sudo date 03050001

# Replace the following line with any application you need to run
open /Applications/Merriam-Webster\ 4.0/Merriam-Webster\ Dictionary.app

# sleep 60

# Set back to the current time using apple service (network needed)
sudo ntpdate -u time.apple.com