--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phylographics/TreeVector.py	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,61 @@
+#!/usr/bin/env python
+
+"""
+Runs TreeVector on a newick file;
+TODO: more documentation
+"""
+
+import optparse, os, shutil, subprocess, sys, tempfile, re, string
+
+def stop_err( msg ):
+    sys.stderr.write( '%s\n' % msg )
+    sys.exit()
+
+def __main__():
+    #Parse Command Line
+    parser = optparse.OptionParser()
+    parser.add_option( '-i', '--input', dest='input', help='The sequence input file' )
+    parser.add_option( '-s', '--shape', dest='shape', help='Branch shape' )
+    parser.add_option( '-l', '--length', dest='length', help='Branch length' )
+    parser.add_option( '-g', '--svg', dest='svg', help='Graph in SVG format' )
+    parser.add_option( '-p', '--jarBin', dest='jarBin', default='', help='The path to where jars are stored' )
+    parser.add_option( '-j', '--jarFile', dest='jarFile', help='The file name of the jar file to use')
+    parser.add_option( '-x', '--jvmArgs', dest='jvmArgs', help='Java JVM arguments, e.g -Xmx250m')
+    (options, args) = parser.parse_args()
+    if options.jarBin == None:
+       stop_err("Misssing option --jarBin")
+    elif options.jarFile == None:
+       stop_err("Misssing option --jarFile")
+    elif options.input == None:
+       stop_err("Misssing option --input")
+    params = []
+    props = []
+    if options.jvmArgs != None:
+        props.append(options.jvmArgs)
+    if options.shape != None and options.shape != 'None':
+       params.append('-%s' % options.shape)
+    if options.length != None and options.length != 'None':
+       params.append('-%s' % options.length)
+    if options.svg != None and options.svg != 'None':
+       params.append('-out %s' % options.svg)
+    # make temp directory
+    buffsize = 1048576
+    tmp_dir = tempfile.mkdtemp()
+    # print("tmp_dir %s" % tmp_dir)
+    # generate commandline
+    cmd = 'java %s -jar %s %s %s' % (' '.join(props), os.path.join( options.jarBin, options.jarFile ), options.input, ' '.join(params))
+    # print >> sys.stderr, cmd 
+    # need to nest try-except in try-finally to handle 2.4
+    try:
+        try:
+            proc = subprocess.Popen( args=cmd, shell=True, stderr=subprocess.PIPE )
+            returncode = proc.wait()
+            stderr = proc.stderr.read()
+            if returncode != 0:
+                raise Exception, stderr
+        except Exception, e:
+            raise Exception, 'Error executing TeeVector. ' + str( e )
+    except Exception, e:
+        stop_err( 'TreeVector failed.\n' + str( e ) )
+
+if __name__=="__main__": __main__()