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59 lines
2.2 KiB
Python
59 lines
2.2 KiB
Python
#Dan Blankenberg
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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_filename1 = os.path.abspath(sys.argv[2].strip())
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output_filename2 = os.path.abspath(sys.argv[3].strip())
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distance_metric = sys.argv[4].strip()
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temp_ps_filename = hyphy_util.get_filled_temp_filename("")
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#Guess if this is a single or multiple FASTA input file
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found_blank = False
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is_multiple = False
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for line in open(input_filename):
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line = line.strip()
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if line == "": found_blank = True
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elif line.startswith(">") and found_blank:
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is_multiple = True
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break
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else: found_blank = False
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NJ_tree_shared_ibf = hyphy_util.get_filled_temp_filename(hyphy_util.NJ_tree_shared_ibf)
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#set up NJ_tree file
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NJ_tree_filename = hyphy_util.get_filled_temp_filename(hyphy_util.get_NJ_tree(NJ_tree_shared_ibf))
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#setup Config file
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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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if is_multiple:
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os.unlink(NJ_tree_filename)
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os.unlink(config_filename)
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NJ_tree_filename = hyphy_util.get_filled_temp_filename(hyphy_util.get_NJ_treeMF(NJ_tree_shared_ibf))
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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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print "Multiple Alignment Analyses"
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else: print "Single Alignment Analyses"
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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(NJ_tree_filename)
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os.unlink(config_filename)
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#Convert PS to PDF
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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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os.unlink(temp_ps_filename)
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