Mercurial > repos > chemteam > gmx_editconf

annotate merge_top.py @ 2:004232c5336f draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit d75a4b4a47d2a74aacb6d3ff90755f9a5289cfb1"
author chemteam
date Wed, 18 Dec 2019 15:25:03 -0500
parents 7b23265126b0
children 3b8a9d5ced85
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7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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1 import re
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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2 import sys
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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5 def combine_tops(top_text, itp_texts):
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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6 """
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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7 Search through parent topology top_text and replace
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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8 #include lines with the relevant child topologies
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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9 from the dictionary itp_texts
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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10 """
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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11 for itp in itp_texts:
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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12 # split on include string, then rejoin around itp file
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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13 spl = re.split('#include ".*{}"\n'.format(itp), top_text)
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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14 top_text = itp_texts[itp].join(spl)
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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15 return top_text
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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18 top = sys.argv[1] # parent topology file
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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19 itps_file = sys.argv[2] # file with list of child topologies (.itp files)
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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21 with open(itps_file) as f:
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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22 itps = f.read().split()
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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24 with open(top, 'r') as f:
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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25 top_text = f.read()
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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27 itp_texts = {} # create dictionary of child topologies
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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28 for itp in itps:
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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29 with open(itp, 'r') as f:
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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30 itp_texts[itp] = f.read()
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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32 for itp in itp_texts:
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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33 # child tops may also refer to each other; we need to check this
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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34 itp_texts[itp] = combine_tops(itp_texts[itp], itp_texts)
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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36 with open('top_output.top', 'w') as f:
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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37 # now combine all children into the parent
7b23265126b0 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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38 f.write(combine_tops(top_text, itp_texts))