Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics
comparison phylographics/TreeVector.py @ 0:5b9a38ec4a39 draft default tip
First commit of old repositories
author | osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> |
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date | Tue, 11 Mar 2014 12:19:13 -0700 |
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-1:000000000000 | 0:5b9a38ec4a39 |
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1 #!/usr/bin/env python | |
2 | |
3 """ | |
4 Runs TreeVector on a newick file; | |
5 TODO: more documentation | |
6 """ | |
7 | |
8 import optparse, os, shutil, subprocess, sys, tempfile, re, string | |
9 | |
10 def stop_err( msg ): | |
11 sys.stderr.write( '%s\n' % msg ) | |
12 sys.exit() | |
13 | |
14 def __main__(): | |
15 #Parse Command Line | |
16 parser = optparse.OptionParser() | |
17 parser.add_option( '-i', '--input', dest='input', help='The sequence input file' ) | |
18 parser.add_option( '-s', '--shape', dest='shape', help='Branch shape' ) | |
19 parser.add_option( '-l', '--length', dest='length', help='Branch length' ) | |
20 parser.add_option( '-g', '--svg', dest='svg', help='Graph in SVG format' ) | |
21 parser.add_option( '-p', '--jarBin', dest='jarBin', default='', help='The path to where jars are stored' ) | |
22 parser.add_option( '-j', '--jarFile', dest='jarFile', help='The file name of the jar file to use') | |
23 parser.add_option( '-x', '--jvmArgs', dest='jvmArgs', help='Java JVM arguments, e.g -Xmx250m') | |
24 (options, args) = parser.parse_args() | |
25 if options.jarBin == None: | |
26 stop_err("Misssing option --jarBin") | |
27 elif options.jarFile == None: | |
28 stop_err("Misssing option --jarFile") | |
29 elif options.input == None: | |
30 stop_err("Misssing option --input") | |
31 params = [] | |
32 props = [] | |
33 if options.jvmArgs != None: | |
34 props.append(options.jvmArgs) | |
35 if options.shape != None and options.shape != 'None': | |
36 params.append('-%s' % options.shape) | |
37 if options.length != None and options.length != 'None': | |
38 params.append('-%s' % options.length) | |
39 if options.svg != None and options.svg != 'None': | |
40 params.append('-out %s' % options.svg) | |
41 # make temp directory | |
42 buffsize = 1048576 | |
43 tmp_dir = tempfile.mkdtemp() | |
44 # print("tmp_dir %s" % tmp_dir) | |
45 # generate commandline | |
46 cmd = 'java %s -jar %s %s %s' % (' '.join(props), os.path.join( options.jarBin, options.jarFile ), options.input, ' '.join(params)) | |
47 # print >> sys.stderr, cmd | |
48 # need to nest try-except in try-finally to handle 2.4 | |
49 try: | |
50 try: | |
51 proc = subprocess.Popen( args=cmd, shell=True, stderr=subprocess.PIPE ) | |
52 returncode = proc.wait() | |
53 stderr = proc.stderr.read() | |
54 if returncode != 0: | |
55 raise Exception, stderr | |
56 except Exception, e: | |
57 raise Exception, 'Error executing TeeVector. ' + str( e ) | |
58 except Exception, e: | |
59 stop_err( 'TreeVector failed.\n' + str( e ) ) | |
60 | |
61 if __name__=="__main__": __main__() |