Mercurial > repos > chemteam > gmx_sim
view merge_top.py @ 0:1a5960636405 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
author | chemteam |
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date | Mon, 07 Oct 2019 12:48:44 -0400 |
parents | |
children | 2e219a2d9327 |
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import re import sys def combine_tops(top_text, itp_texts): """ Search through parent topology top_text and replace #include lines with the relevant child topologies from the dictionary itp_texts """ for itp in itp_texts: # split on include string, then rejoin around itp file spl = re.split('#include ".*{}"\n'.format(itp), top_text) top_text = itp_texts[itp].join(spl) return top_text top = sys.argv[1] # parent topology file itps_file = sys.argv[2] # file with list of child topologies (.itp files) with open(itps_file) as f: itps = f.read().split() with open(top, 'r') as f: top_text = f.read() itp_texts = {} # create dictionary of child topologies for itp in itps: with open(itp, 'r') as f: itp_texts[itp] = f.read() for itp in itp_texts: # child tops may also refer to each other; we need to check this itp_texts[itp] = combine_tops(itp_texts[itp], itp_texts) with open('top_output.top', 'w') as f: # now combine all children into the parent f.write(combine_tops(top_text, itp_texts))