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comparison make_phylip_hooks.py @ 35:ea52b23f1141

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Bug fixes for Draw variants, Phylip, and gd_d_tools
author Richard Burhans <burhans@bx.psu.edu>
date Wed, 20 Nov 2013 13:46:10 -0500
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34:f739a296a339 35:ea52b23f1141
1 #!/usr/bin/env python
2
3 def exec_before_job(app, inp_data=None, out_data=None, tool=None, param_dict=None):
4 pass
5
6 def exec_after_process(app, inp_data=None, out_data=None, param_dict=None, tool=None, stdout=None, stderr=None):
7 output_name = 'output1'
8
9 ## check for output
10 try:
11 first_output = out_data[output_name]
12 except:
13 return
14
15 ## check for collected datasets
16 try:
17 collected_dict = param_dict['__collected_datasets__']['primary'][output_name]
18 except:
19 return
20
21 if len(collected_dict.keys()) == 0:
22 return
23
24 ## check for fasta file
25 try:
26 fasta_file = inp_data['fasta_input']
27 except:
28 return
29
30 ## find missing fasta header
31 first_output_name = None
32 with open(fasta_file.get_file_name()) as fh:
33 for line in fh:
34 if line[0] != '>':
35 continue
36 name = line[1:]
37 name = name.strip()
38 name = name.split()[0]
39 name = name.replace('_', '-')
40 if name not in collected_dict:
41 first_output_name = name
42 break
43
44 ## fix name
45 if first_output_name is not None:
46 first_output.name = '%s (%s)' % (first_output.name, first_output_name)
47