annotate rpviz/main.py @ 16:fe78fd6b315a draft

planemo upload commit 87db86a34f2d92eb2c9756bf9ee53ae2970554d5

# -*- 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)