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