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annotate raxml.py @ 36:51cd0307fb70

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Phylip's extra ouputs are now stored in the job working directory
author Richard Burhans <burhans@bx.psu.edu>
date Wed, 20 Nov 2013 16:32:01 -0500
parents a631c2f6d913
children
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1 #!/usr/bin/env python
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2
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3 import random
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4 import sys
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5 import shutil
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6 import gd_util
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7
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8 ################################################################################
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9
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10 if len(sys.argv) != 3:
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11 gd_util.die('Usage')
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13 input, output = sys.argv[1:]
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14 random.seed()
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15
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16 ################################################################################
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17
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18 prog = 'raxmlHPC'
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20 args = [ prog ]
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21
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22 ## required: -s sequenceFileName -n outputFileName -m substitutionModel
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23 ## we supply -s, -n (they are not allowed from user)
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25 args.append('-s') # name of the alignment data file in PHYLIP format
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26 args.append(input)
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28 args.append('-n') # name of the output file
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29 args.append('fake')
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30
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31 ## default options
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32 args.append('-m') # substitutionModel
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33 args.append('GTRGAMMA') # GTR + Optimization of substitution rates + GAMMA model of rate
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34 # heterogeneity (alpha parameter will be estimated)
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36 args.append('-N') # number of alternative runs on distinct starting trees
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37 args.append(1000)
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38
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39 args.append('-f') # select algorithm
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40 args.append('a') # rapid Bootstrap analysis and search for
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41 # best-scoring ML tree in one program run
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43 args.append('-x') # integer random seed and turn on rapid bootstrapping
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44 args.append(random.randint(0,100000000000000))
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46 args.append('-p') # random seed for parsimony inferences
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47 args.append(random.randint(0,100000000000000))
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49 gd_util.run_program(prog, args)
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50 shutil.copy2('RAxML_bipartitions.fake', output)
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51 sys.exit(0)