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annotate phylogenies/beast.py @ 0:5b9a38ec4a39 draft default tip

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author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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1 #!/usr/bin/python
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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2 """
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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3 This program makes a new copy of a BEAST XML config file and changes the name of the log and tree files.
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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4 The names have to be changed since Galaxy does not support dynamic output file names.
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5 The new XML file name must not be the same as the original!!!
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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6 Script prints unique filename.
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7
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8
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9 Usage: python beast.py XMLFILE SAVE_DIRECTORY
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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10 """
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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11
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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12 import sys
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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13 import time
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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14 from xml.etree.ElementTree import ElementTree
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15
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16 beastDOM = ElementTree()
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17 beastDOM.parse(sys.argv[1])
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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18 logs = beastDOM.findall('mcmc/log')
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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19 for log in logs:
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20 if log.get('id', False) == "fileLog":
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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21 log.set('fileName', 'data.log')
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22
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23 logs = beastDOM.findall('mcmc/logTree')
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24 for log in logs:
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25 if log.get('id', False) == "treeFileLog":
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26 log.set('fileName', 'data.trees')
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27
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28 if len(sys.argv) > 2:
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29 directory = sys.argv[2]
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30 else:
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31 directory = ""
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32
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33 filename = directory + "/" + str(time.time()) + '.xml'
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34 beastDOM.write(filename)
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35 print filename