'''
To run test from top directory:
➜ python3 -m khipu.test
'''
import urllib.request
# import numpy as np
from khipu import __version__
from .model import Khipu
from .extended import *
from .utils import *
from .epdsConstructor import epdsConstructor
url= 'https://github.com/shuzhao-li/khipu/raw/main/testdata/ecoli_pos.tsv'
def test_read_url(url=url):
flist = get_peaklist_from_url(url)
subnetworks, peak_dict, edge_dict = peaks_to_networks(flist,
adduct_search_patterns = adduct_search_patterns,
isotope_search_patterns = isotope_search_patterns,
rt_tolerance = 1, # 1 sec
)
return subnetworks, peak_dict, edge_dict
def get_peaklist_from_url(url):
print("Retrieving test data from GitHub.")
data = urllib.request.urlopen(url).read().decode('utf-8')
flist = read_features_from_text(data, id_col=0, mz_col=1, rtime_col=2, intensity_cols=(3, 9))
return flist
[docs]def test1():
'''Test khipu construction process and plots
'''
print('''
#########################
# Test 1 #
#########################
''')
subnetworks, peak_dict, edge_dict = test_read_url()
big = [g for g in subnetworks if g.size()>15]
WV = Weavor(peak_dict, isotope_search_patterns, adduct_search_patterns,
mz_tolerance_ppm=5, mode='pos')
print(WV.mzgrid)
print("\n\n")
print("Example khipu of one empirical compound from demo data.")
KP = khipu_diagnosis(big[ 1 ])
print("Input network edges: ")
print(KP.input_network.edges(data=True))
KP.build_khipu(WV)
print(KP.sorted_mz_peak_ids, "\n")
KP.show_trimming()
print("\n\n")
KP.build_diagnostic_tree_full()
print("\n\n")
KP.build_diagnostic_tree_clean()
print("Looking at khipu: ")
KP.print()
print("\n\n")
print("Rotated way to look at khipu: ")
KP.print2()
print("\n\n")
KP.build_khipu_tree()
unassigned_peaks = [v for x,v in peak_dict.items() if x not in KP.nodes_to_use]
mztree = build_centurion_tree(unassigned_peaks)
KP.extended_search(mztree, extended_adducts)
print("extended khipu with additional adducts: ")
KP.print()
print("Feature intensities: ")
print(KP.get_khipu_intensities())
# KP.plot_khipu_diagram()
print("\n\n")
print("Multiple example khipus: ")
print("======================== \n")
for g in big[ -6: ]:
KP = Khipu(g)
KP.build_khipu(WV)
print(KP.sorted_mz_peak_ids, "\n")
KP.print_khipu()
print('\n\n')
print("\n\n")
print("Build and export JSON file of full list of khipus: ")
print("================================================== \n")
khipu_list = graphs_to_khipu_list(
subnetworks, WV, mz_tolerance_ppm=5)
# khipu_list = extend_khipu_list(khipu_list, peaks, adduct_search_patterns_extended)
print("\n\n ~~~~~~ Got %d khipus ~~~~~~~ \n\n" %len(khipu_list))
empCpds = export_empCpd_khipu_list(khipu_list)
outfile = 'khipu_test_empricalCompounds.json'
with open(outfile, 'w', encoding='utf-8') as f:
json.dump(empCpds, f, ensure_ascii=False, indent=2)
[docs]def test2(mz_tolerance_ppm = 5, mode = 'pos'):
'''Test epdsConstructor wrapper class
'''
print('''
#########################
# Test 2 #
#########################
''')
adduct_patterns = adduct_search_patterns
if mode == 'neg':
adduct_patterns = adduct_search_patterns_neg
list_peaks = get_peaklist_from_url(url)
ECCON = epdsConstructor(list_peaks, mode=mode)
dict_empCpds = ECCON.peaks_to_epdDict(
isotope_search_patterns,
adduct_patterns,
extended_adducts,
mz_tolerance_ppm,
rt_tolerance=2,
charges=[1, 2, 3],
has_parent_masstrack=False,
)
outfile = 'khipu_test2.json'
with open(outfile, 'w', encoding='utf-8') as f:
json.dump(dict_empCpds, f, ensure_ascii=False, indent=2)
#
# -----------------------------------------------------------------------------
#
if __name__ == '__main__':
print("\n\n~~~~ testing Khipu (%s) ~~~\n" %__version__)
test1()
test2()