[2] | 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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