Mercurial > repos > xuebing > sharplabtool

comparison tools/hyphy/hyphy_dnds_wrapper.py @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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-1:000000000000 0:9071e359b9a3
1 #Guru
2 #takes fasta alignments, a distance metric and builds neighbor joining trees
3 import os, sys
4 from galaxy import eggs
5 from galaxy.tools.util import hyphy_util
6
7 #Retrieve hyphy path, this will need to be the same across the cluster
8 tool_data = sys.argv.pop()
9 HYPHY_PATH = os.path.join( tool_data, "HYPHY" )
10 HYPHY_EXECUTABLE = os.path.join( HYPHY_PATH, "HYPHY" )
11
12 #Read command line arguments
13 input_filename = os.path.abspath(sys.argv[1].strip())
14 output_filename = os.path.abspath(sys.argv[2].strip())
15 tree_contents = sys.argv[3].strip()
16 nuc_model = sys.argv[4].strip()
17 analysis = sys.argv[5].strip()
18
19 if tree_contents == "":
20 print >> sys.stderr, "Please specify a valid tree definition."
21 sys.exit()
22
23 tree_filename = hyphy_util.get_filled_temp_filename(tree_contents)
24
25 if analysis == "local":
26 fitter_filename = hyphy_util.get_filled_temp_filename(hyphy_util.SimpleLocalFitter)
27 else:
28 fitter_filename = hyphy_util.get_filled_temp_filename(hyphy_util.SimpleGlobalFitter)
29
30 tabwriter_filename = hyphy_util.get_filled_temp_filename(hyphy_util.TabWriter)
31 FastaReader_filename = hyphy_util.get_filled_temp_filename(hyphy_util.FastaReader)
32 #setup Config file
33 config_filename = hyphy_util.get_dnds_config_filename(fitter_filename, tabwriter_filename, "Universal", tree_filename, input_filename, nuc_model, output_filename, FastaReader_filename)
34
35 #Run Hyphy
36 hyphy_cmd = "%s BASEPATH=%s USEPATH=/dev/null %s" % (HYPHY_EXECUTABLE, HYPHY_PATH, config_filename)
37 hyphy = os.popen(hyphy_cmd, 'r')
38 #print hyphy.read()
39 hyphy.close()
40
41 #remove temporary files
42 os.unlink(fitter_filename)
43 os.unlink(tabwriter_filename)
44 os.unlink(tree_filename)
45 os.unlink(FastaReader_filename)
46 os.unlink(config_filename)
47
48 if nuc_model == "000000":
49 model = "F81"
50 elif nuc_model == "010010":
51 model = "HKY85"
52 else:
53 model = "REV"
54
55 print "Analysis: %s; Model: %s; Tree: %s" %(analysis, model, tree_contents)