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