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56 lines
1.9 KiB
Python
56 lines
1.9 KiB
Python
#Guru
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#takes fasta alignments, a distance metric and builds neighbor joining trees
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import os, sys
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from galaxy import eggs
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from galaxy.tools.util import hyphy_util
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#Retrieve hyphy path, this will need to be the same across the cluster
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tool_data = sys.argv.pop()
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HYPHY_PATH = os.path.join( tool_data, "HYPHY" )
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HYPHY_EXECUTABLE = os.path.join( HYPHY_PATH, "HYPHY" )
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#Read command line arguments
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input_filename = os.path.abspath(sys.argv[1].strip())
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output_filename = os.path.abspath(sys.argv[2].strip())
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tree_contents = sys.argv[3].strip()
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nuc_model = sys.argv[4].strip()
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analysis = sys.argv[5].strip()
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if tree_contents == "":
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print >> sys.stderr, "Please specify a valid tree definition."
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sys.exit()
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tree_filename = hyphy_util.get_filled_temp_filename(tree_contents)
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if analysis == "local":
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fitter_filename = hyphy_util.get_filled_temp_filename(hyphy_util.SimpleLocalFitter)
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else:
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fitter_filename = hyphy_util.get_filled_temp_filename(hyphy_util.SimpleGlobalFitter)
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tabwriter_filename = hyphy_util.get_filled_temp_filename(hyphy_util.TabWriter)
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FastaReader_filename = hyphy_util.get_filled_temp_filename(hyphy_util.FastaReader)
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#setup Config file
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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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#Run Hyphy
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hyphy_cmd = "%s BASEPATH=%s USEPATH=/dev/null %s" % (HYPHY_EXECUTABLE, HYPHY_PATH, config_filename)
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hyphy = os.popen(hyphy_cmd, 'r')
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#print hyphy.read()
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hyphy.close()
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#remove temporary files
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os.unlink(fitter_filename)
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os.unlink(tabwriter_filename)
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os.unlink(tree_filename)
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os.unlink(FastaReader_filename)
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os.unlink(config_filename)
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if nuc_model == "000000":
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model = "F81"
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elif nuc_model == "010010":
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model = "HKY85"
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else:
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model = "REV"
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print "Analysis: %s; Model: %s; Tree: %s" %(analysis, model, tree_contents)
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