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