xml_parser.py

import xml.etree.ElementTree as ET
import numpy as np
'''
XML file has tag called "reactivity". Take value from "reactivity" 
and put it into a variable (list)

Set NaN values to 0
'''

filename = 'HCV_IRES_IVT_RNA_0mg_DMS1.xml'

tree = ET.parse(filename)
root = tree.getroot()

for reactivity_tag in root.iter('reactivity'):
    # Get the text string from the xml file
    reactivity_string = reactivity_tag.text
    
    # Separate the string by commas
    reactive_list = [i.strip()for i in reactivity_string.split(',')]
    
    # Convert to numpy array
    reactive_list = np.array(reactive_list)
    reactive_list = reactive_list.astype(float)
    reactive_list[np.isnan(reactive_list)] = 0
    
    print(reactive_list)