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comparison tools/hyphy/hyphy_branch_lengths_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 commandline tree def and input multiple fasta alignment file and runs the branch length ananlysis
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 base_freq = sys.argv[5].strip()
18 model_options = sys.argv[6].strip()
19
20 #Set up Temporary files for hyphy run
21 #set up tree file
22 tree_filename = hyphy_util.get_filled_temp_filename(tree_contents)
23
24 #Guess if this is a single or multiple FASTA input file
25 found_blank = False
26 is_multiple = False
27 for line in open(input_filename):
28 line = line.strip()
29 if line == "": found_blank = True
30 elif line.startswith(">") and found_blank:
31 is_multiple = True
32 break
33 else: found_blank = False
34
35 #set up BranchLengths file
36 BranchLengths_filename = hyphy_util.get_filled_temp_filename(hyphy_util.BranchLengths)
37 if is_multiple:
38 os.unlink(BranchLengths_filename)
39 BranchLengths_filename = hyphy_util.get_filled_temp_filename(hyphy_util.BranchLengthsMF)
40 print "Multiple Alignment Analyses"
41 else: print "Single Alignment Analyses"
42
43 #setup Config file
44 config_filename = hyphy_util.get_branch_lengths_config_filename(input_filename, nuc_model, model_options, base_freq, tree_filename, output_filename, BranchLengths_filename)
45
46 #Run Hyphy
47 hyphy_cmd = "%s BASEPATH=%s USEPATH=/dev/null %s" % (HYPHY_EXECUTABLE, HYPHY_PATH, config_filename)
48 hyphy = os.popen(hyphy_cmd, 'r')
49 #print hyphy.read()
50 hyphy.close()
51
52 #remove temporary files
53 os.unlink(BranchLengths_filename)
54 os.unlink(tree_filename)
55 os.unlink(config_filename)