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comparison tools/hyphy/hyphy_nj_tree_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 #Dan Blankenberg
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_filename1 = os.path.abspath(sys.argv[2].strip())
15 output_filename2 = os.path.abspath(sys.argv[3].strip())
16 distance_metric = sys.argv[4].strip()
17 temp_ps_filename = hyphy_util.get_filled_temp_filename("")
18
19 #Guess if this is a single or multiple FASTA input file
20 found_blank = False
21 is_multiple = False
22 for line in open(input_filename):
23 line = line.strip()
24 if line == "": found_blank = True
25 elif line.startswith(">") and found_blank:
26 is_multiple = True
27 break
28 else: found_blank = False
29
30 NJ_tree_shared_ibf = hyphy_util.get_filled_temp_filename(hyphy_util.NJ_tree_shared_ibf)
31
32 #set up NJ_tree file
33 NJ_tree_filename = hyphy_util.get_filled_temp_filename(hyphy_util.get_NJ_tree(NJ_tree_shared_ibf))
34 #setup Config file
35 config_filename = hyphy_util.get_nj_tree_config_filename(input_filename, distance_metric, output_filename1, temp_ps_filename, NJ_tree_filename)
36 if is_multiple:
37 os.unlink(NJ_tree_filename)
38 os.unlink(config_filename)
39 NJ_tree_filename = hyphy_util.get_filled_temp_filename(hyphy_util.get_NJ_treeMF(NJ_tree_shared_ibf))
40 config_filename = hyphy_util.get_nj_treeMF_config_filename(input_filename, output_filename1, temp_ps_filename, distance_metric, NJ_tree_filename)
41 print "Multiple Alignment Analyses"
42 else: print "Single Alignment Analyses"
43
44
45 #Run Hyphy
46 hyphy_cmd = "%s BASEPATH=%s USEPATH=/dev/null %s" % (HYPHY_EXECUTABLE, HYPHY_PATH, config_filename)
47 hyphy = os.popen(hyphy_cmd, 'r')
48 #print hyphy.read()
49 hyphy.close()
50
51 #remove temporary files
52 os.unlink(NJ_tree_filename)
53 os.unlink(config_filename)
54
55
56 #Convert PS to PDF
57 if os.path.getsize(temp_ps_filename)>0: temp = os.popen("ps2pdf %s %s" % (temp_ps_filename, output_filename2), 'r').close()
58 os.unlink(temp_ps_filename)