def process_xml(xml_string):
tp = TripsProcessor(xml_string)
tp.get_complexes()
tp.get_phosphorylation()
tp.get_activating_mods()
return tp
def process_text(text):
html = trips_client.send_query(text)
xml = trips_client.get_xml(html)
with open('test.xml','w') as f:
f.write(xml)
return process_xml(xml)
def process_xml(xml_string):
tp = TripsProcessor(xml_string)
tp.get_complexes()
tp.get_phosphorylation()
tp.get_activating_mods()
return tp
if __name__ == '__main__':
input_fname = 'phosphorylate.xml'
if len(sys.argv) > 1:
input_fname = sys.argv[1]
try:
fh = open(input_fname, 'rt')
except IOError:
print 'Could not open file %s' % input_fname
sys.exit()
xml_string = fh.read()
tp = TripsProcessor(xml_string)
tp.get_complexes()
tp.get_phosphorylation()
