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annotate make_phylip_hooks.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 ea52b23f1141
children
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ea52b23f1141 Bug fixes for Draw variants, Phylip, and gd_d_tools
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1 #!/usr/bin/env python
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2
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3 def exec_before_job(app, inp_data=None, out_data=None, tool=None, param_dict=None):
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4 pass
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5
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6 def exec_after_process(app, inp_data=None, out_data=None, param_dict=None, tool=None, stdout=None, stderr=None):
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7 output_name = 'output1'
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8
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9 ## check for output
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10 try:
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11 first_output = out_data[output_name]
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12 except:
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13 return
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14
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15 ## check for collected datasets
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16 try:
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17 collected_dict = param_dict['__collected_datasets__']['primary'][output_name]
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18 except:
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19 return
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20
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21 if len(collected_dict.keys()) == 0:
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22 return
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23
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24 ## check for fasta file
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25 try:
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26 fasta_file = inp_data['fasta_input']
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27 except:
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28 return
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29
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30 ## find missing fasta header
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31 first_output_name = None
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32 with open(fasta_file.get_file_name()) as fh:
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33 for line in fh:
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34 if line[0] != '>':
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35 continue
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36 name = line[1:]
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37 name = name.strip()
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38 name = name.split()[0]
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39 name = name.replace('_', '-')
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40 if name not in collected_dict:
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41 first_output_name = name
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42 break
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44 ## fix name
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45 if first_output_name is not None:
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46 first_output.name = '%s (%s)' % (first_output.name, first_output_name)
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