remote control of IGV to jump to any number of loci in a file and screenshot the locus to a file

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3375 348d0f76-0448-11de-a6fe-93d51630548a

python/igvController.py

@@ -0,0 +1,74 @@
+# Echo server program
+import socket, re
+from os.path import join
+from time import sleep
+
+from farm_commands2 import *
+import os.path
+import sys
+from optparse import OptionParser
+from datetime import date
+import glob
+import operator
+import faiReader
+import math
+import shutil
+import string
+from madPipelineUtils import *
+
+HOST = 'vm0e0-052.broadinstitute.org'       # Symbolic name meaning the local host
+PORT = 60151                                # Arbitrary non-privileged port
+LOCAL_DIR = "/Users/depristo/Desktop/IGV_screenshots"
+
+def main():
+    global OPTIONS
+    usage = """usage: %prog [options] sites
+Automatically captures IGV PNG screenshots at each site in the file sites (of the form chrX:start-stop or chrX:pos) by connecting to 
+an IGV session.  See http://www.broadinstitute.org/igv/?q=PortCommands.  Make sure you enable ports in the IGV preferences"""
+    parser = OptionParser(usage=usage)
+    parser.add_option("-w", "--wait", dest="wait",
+                        action='store_true', default=False,
+                        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")
+    parser.add_option("", "--host", dest="host",
+                        type='string', default=HOST,
+                        help="The host running the port enabled IGV server")
+    parser.add_option("-d", "--dir", dest="dir",
+                        type='string', default=LOCAL_DIR,
+                        help="The local directory on the host machine that screenshots should be written to")
+    parser.add_option("-s", "--sort", dest="sort",
+                        type='string', default="base",
+                        help="The sort order for the bases, currently can be one of base, position, strand, quality, sample, and readGroup.")
+                        
+    (OPTIONS, args) = parser.parse_args()
+    if len(args) != 1:
+        parser.error("incorrect number of arguments")
+
+    sites = args[0]
+    #It might ignore the first line..
+    print "Be sure to turn on ports"
+    s = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
+
+    def sendCommand(cmd):
+        s.send(cmd)
+        print s.recv(512).trim()
+
+    s.connect((OPTIONS.host, PORT))
+    sendCommand("snapshotDirectory " + OPTIONS.dir + "\n")
+    c = 0
+    for line in open(sites):
+        site = line.split()[0]
+        print site
+        c+=1
+        sendCommand("goto %s\n" % site)
+        sendCommand("sort " + OPTIONS.sort + "\n")
+        if OPTIONS.wait: 
+            raw_input("Enter To Continue") 
+        else:
+            sendCommand("snapshot\n") # %s.png\n" % re.sub("-","_",re.sub(':', '_', site)))
+    print c
+
+            
+if __name__ == "__main__":
+    main()
+
+