kaizhao86

from PyQt4 import Qt,QtCore,QtGui
import operator,os,sys,sqlite3,time



def joinMsats(parent,conn,c,MAXGAP,MINFLANK):
    
    c.execute("CREATE INDEX IF NOT EXISTS iML1 on msatLocations(readname)")
    c.execute("CREATE INDEX IF NOT EXISTS iML2 on msatLocations(readname,start)")
    parent.emit(QtCore.SIGNAL("log"),"%s Starting to join msat loci"%time.strftime('%I:%M%p'))

kaizhao86

import Bio.SeqIO,fnmatch,gzip,itertools,math,numpy,os,re,sqlite3,subprocess,sys,tarfile,xlsxwriter
from multiprocessing import Pool  #used for simple multicore processing, yeehaw!
conn = sqlite3.connect("limb-nouveau.sqlite3",check_same_thread=False); 
#this allows sqlite to work in a multithreaded environment
c=conn.cursor()

PATH = "/home/zhaok/Data/20140702_limb/"

#For each of our enhancer near genes of interest, make a new table that are for orthologs in non-mouse species, 
c.execute("DROP TABLE IF EXISTS enhancerOrthologs")

kaizhao86

import Bio.SeqIO,gzip,fnmatch,itertools,math,numpy,os,re,sqlite3,subprocess,sys,tarfile,xlsxwriter
"""
This program reads in our list of known mouse enhancers (from publications), Gli3-binding sites, 
and H3k27ac marks. For the k27ac marks, we merge adjacent CHIP-seq binding positions
"""

conn = sqlite3.connect("limb-nouveau.sqlite3")
  #Connect to local sqlite3 database
c=conn.cursor()

kaizhao86

Use the following Hayes AT command through the diag com port:

AT$NWGPSSTART=3,1,4,250,50,255

kaizhao86

#saves lots of history
#Incorporates Ubuntu's default .bashrc and bash_completion (need to install separately)


PS1='\u@\h \W \$ '
stty stop undef # to unmap ctrl-s
shopt -s histappend
HISTFILESIZE=1000000
HISTSIZE=1000000
HISTCONTROL=ignoreboth

kaizhao86

#taken from who knows where. 

# no annoying audible bell, please
vbell on

# detach on hangup
autodetach on

# don't display the copyright page
startup_message off