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comparison merge_top.py @ 1:65946f250c89 draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
author chemteam
date Thu, 28 Mar 2019 10:19:26 -0400
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children 1809414a9454
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0:77aaf9a68166 1:65946f250c89
1 import re
2 import sys
3
4
5 def combine_tops(top_text, itp_texts):
6 """
7 Search through parent topology top_text and replace
8 #include lines with the relevant child topologies
9 from the dictionary itp_texts
10 """
11 for itp in itp_texts:
12 # split on include string, then rejoin around itp file
13 spl = re.split('#include ".*{}"\n'.format(itp), top_text)
14 top_text = itp_texts[itp].join(spl)
15 return top_text
16
17
18 top = sys.argv[1] # parent topology file
19 itps_file = sys.argv[2] # file with list of child topologies (.itp files)
20
21 with open(itps_file) as f:
22 itps = f.read().split()
23
24 with open(top, 'r') as f:
25 top_text = f.read()
26
27 itp_texts = {} # create dictionary of child topologies
28 for itp in itps:
29 with open(itp, 'r') as f:
30 itp_texts[itp] = f.read()
31
32 for itp in itp_texts:
33 # child tops may also refer to each other; we need to check this
34 itp_texts[itp] = combine_tops(itp_texts[itp], itp_texts)
35
36 with open('top_output.top', 'w') as f:
37 # now combine all children into the parent
38 f.write(combine_tops(top_text, itp_texts))