88 lines
3.3 KiB
Python
Executable File
88 lines
3.3 KiB
Python
Executable File
# Echo server program
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import socket, re
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from os.path import join
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from time import sleep
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from farm_commands2 import *
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import os.path
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import sys
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from optparse import OptionParser
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from datetime import date
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import glob
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import operator
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import faiReader
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import math
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import shutil
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import string
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import time
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from madPipelineUtils import *
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HOST = 'vm0e0-052.broadinstitute.org' # Symbolic name meaning the local host
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PORT = 60151 # Arbitrary non-privileged port
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LOCAL_DIR = "/Users/depristo/Desktop/IGV_screenshots"
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SLEEP_TIME = 1
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def main():
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global OPTIONS
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usage = """usage: %prog [options] sites
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Automatically captures IGV PNG screenshots at each site in the file sites (of the form chrX:start-stop or chrX:pos or a VCF file) by connecting to
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an IGV session. See http://www.broadinstitute.org/igv/?q=PortCommands. Make sure you enable ports in the IGV preferences"""
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parser = OptionParser(usage=usage)
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parser.add_option("-w", "--wait", dest="wait",
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action='store_true', default=False,
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help="If provided, instead of taking screenshots we will prompt the user on the command line to press return and then jump to the new location")
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parser.add_option("", "--host", dest="host",
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type='string', default=HOST,
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help="The host running the port enabled IGV server")
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parser.add_option("-d", "--dir", dest="dir",
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type='string', default=LOCAL_DIR,
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help="The local directory on the host machine that screenshots should be written to")
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parser.add_option("-s", "--sort", dest="sort",
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type='string', default="base",
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help="The sort order for the bases, currently can be one of base, position, strand, quality, sample, and readGroup.")
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parser.add_option("-p", "--prefix", dest="prefix",
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type='string', default="",
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help="A prefix to add before the contig name before sending the command to IGV. Useful for dealing with b36 -> hg18 issues")
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(OPTIONS, args) = parser.parse_args()
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if len(args) != 1:
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parser.error("incorrect number of arguments")
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sites = args[0]
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#It might ignore the first line..
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print "Be sure to turn on ports"
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s = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
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def sendCommand(cmd):
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s.send(cmd)
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print cmd.strip(), '=>', s.recv(512).strip()
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s.connect((OPTIONS.host, PORT))
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sendCommand("snapshotDirectory " + OPTIONS.dir + "\n")
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c = 0
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for line in open(sites):
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parts = line.split()
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if sites.find(".vcf") != -1 and parts[0][0] != "#":
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site = OPTIONS.prefix + ':'.join(parts[0:2])
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else:
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site = parts[0]
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print site
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c+=1
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sendCommand("goto %s\n" % site)
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sendCommand("sort " + OPTIONS.sort + "\n")
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if OPTIONS.wait:
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raw_input("Enter To Continue")
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else:
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print 'sleep', SLEEP_TIME, 'secs'
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time.sleep(SLEEP_TIME)
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sendCommand("snapshot\n") # %s.png\n" % re.sub("-","_",re.sub(':', '_', site)))
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print c
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if __name__ == "__main__":
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main()
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