annotate merge_top.py @ 0:33ed3c26b8c2 draft

planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb

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))