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annotate phylographics/TreeVector.py @ 0:5b9a38ec4a39 draft default tip

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First commit of old repositories
author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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children
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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1 #!/usr/bin/env python
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2
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3 """
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4 Runs TreeVector on a newick file;
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5 TODO: more documentation
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6 """
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7
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8 import optparse, os, shutil, subprocess, sys, tempfile, re, string
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9
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10 def stop_err( msg ):
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11 sys.stderr.write( '%s\n' % msg )
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12 sys.exit()
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13
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14 def __main__():
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15 #Parse Command Line
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16 parser = optparse.OptionParser()
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17 parser.add_option( '-i', '--input', dest='input', help='The sequence input file' )
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18 parser.add_option( '-s', '--shape', dest='shape', help='Branch shape' )
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19 parser.add_option( '-l', '--length', dest='length', help='Branch length' )
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20 parser.add_option( '-g', '--svg', dest='svg', help='Graph in SVG format' )
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21 parser.add_option( '-p', '--jarBin', dest='jarBin', default='', help='The path to where jars are stored' )
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22 parser.add_option( '-j', '--jarFile', dest='jarFile', help='The file name of the jar file to use')
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23 parser.add_option( '-x', '--jvmArgs', dest='jvmArgs', help='Java JVM arguments, e.g -Xmx250m')
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24 (options, args) = parser.parse_args()
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25 if options.jarBin == None:
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26 stop_err("Misssing option --jarBin")
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27 elif options.jarFile == None:
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28 stop_err("Misssing option --jarFile")
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29 elif options.input == None:
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30 stop_err("Misssing option --input")
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31 params = []
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32 props = []
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33 if options.jvmArgs != None:
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34 props.append(options.jvmArgs)
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35 if options.shape != None and options.shape != 'None':
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36 params.append('-%s' % options.shape)
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37 if options.length != None and options.length != 'None':
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38 params.append('-%s' % options.length)
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39 if options.svg != None and options.svg != 'None':
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40 params.append('-out %s' % options.svg)
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41 # make temp directory
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42 buffsize = 1048576
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43 tmp_dir = tempfile.mkdtemp()
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44 # print("tmp_dir %s" % tmp_dir)
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45 # generate commandline
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46 cmd = 'java %s -jar %s %s %s' % (' '.join(props), os.path.join( options.jarBin, options.jarFile ), options.input, ' '.join(params))
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47 # print >> sys.stderr, cmd
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48 # need to nest try-except in try-finally to handle 2.4
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49 try:
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50 try:
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51 proc = subprocess.Popen( args=cmd, shell=True, stderr=subprocess.PIPE )
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52 returncode = proc.wait()
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53 stderr = proc.stderr.read()
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54 if returncode != 0:
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55 raise Exception, stderr
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56 except Exception, e:
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57 raise Exception, 'Error executing TeeVector. ' + str( e )
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58 except Exception, e:
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59 stop_err( 'TreeVector failed.\n' + str( e ) )
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60
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61 if __name__=="__main__": __main__()