Mercurial > repos > pablocarb > synbiodesign
view rpviz/main.py @ 29:d854b21ada0c draft
planemo upload commit c56eddc745b70354680c2a2b605840ed72bb98ef
author | pablocarb |
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date | Wed, 07 Aug 2019 05:13:27 -0400 |
parents | fe78fd6b315a |
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# -*- coding: utf-8 -*- """ Created on Mon Jun 10 11:48:55 2019 @author: anael """ import argparse import os from .sbml2lists import sbml2list from .network2json import network2 from .py2html2 import html2 def arguments(): parser = argparse.ArgumentParser(description='Visualizing a network from sbml') parser.add_argument('inputfolder', help='Input folder with sbml files.') parser.add_argument('outfile', help='html file.') return parser def run(infolder,outfile,test=True): if test: folders=[infolder] else: folders=os.listdir(infolder) json_elements={} for f in folders: if test: file=f else: file=os.path.join(infolder,f) output=sbml2list(file) LR=output[0] Lreact=output[1] Lprod=output[2] name=output[3] species_smiles=output[4] images=output[5] species_names=output[6] species_links=output[7] #from smile2picture import picture #image=picture(species_smiles) json_elements[name]=network2(LR,Lreact,Lprod,name,species_smiles,images,species_names,species_links) html2(json_elements,outfile) if __name__ == '__main__': parser = arguments() arg = parser.parse_args() run(arg.inputfolder,arg.outfile)