[2] | 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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