13575009990

Committed 27 Feb 2025 08:11PM UTC coverage: 36.409% (+36.4%) from 0.0%

Build # 13575009990

Build Type

Pull #90

github

Committed by

web-flow

Commit Message

Merge 2912168c2 into 0ad54ba86

Pull Request Pull Request #90: Rnahybrid add targetbreaking

Run Details

350 of 410 new or added lines in 9 files covered. (85.37%)

1472 of 4043 relevant lines covered (36.41%)

0.36 hits per line

Source File
Press 'n' to go to next uncovered line, 'b' for previous

95.0

/Misc/Applications/RNAhybrid/tests/test_rnahybrid.py

import sys
from os.path import dirname, join
sys.path.append(dirname(__file__) + '/../')

from unittest import TestCase, main
from input import read_CT_file, disentangle_knots

def getFP(filepath):
    return join(dirname(__file__), filepath)

class TestRNAhybrid(TestCase):
    def setUp(self):
        self.CTsars = disentangle_knots(next(read_CT_file(getFP('data/SARS-CoV-2_Full_Length_Secondary_Structure_Map.ct')))[2], verbose=None)['nested']
        # Pairs are stored as opening: closing base pair positions, i.e. opening < closing.
        # To ease access, we enrich this dict by also adding in closing: opening information.
        self.CTsars.update({c: o for o, c in self.CTsars.items()})

    def tearDown(self):
        pass

    def test_getOriginalPairs(self):
        exp = {839: 851, 840: 850, 841: 849, 842: 848, 854: 943, 855: 942, 856: 941, 857: 940, 862: 906,  # assert that: i < j
               848: 842, 850: 840, 852: 838, 853: 837  # duplicate pairs where j < i
              }

        novel_target_pairing_partners = [int(x) for x in '839,840,841,842,843,845,846,847,848,850,852,853,854,855,856,857,858,859,862'.split(',')]
        obs = {o: c for o, c in {x: self.CTsars.get(x, -1) for x in novel_target_pairing_partners}.items() if c != -1}
        self.assertEqual(exp, obs)


if __name__ == '__main__':
    main()

1	import sys	1✔
2	from os.path import dirname, join	1✔
3	sys.path.append(dirname(__file__) + '/../')	1✔
4
5	from unittest import TestCase, main	1✔
6	from input import read_CT_file, disentangle_knots	1✔
7
8	def getFP(filepath):	1✔
9	return join(dirname(__file__), filepath)	1✔
10
11	class TestRNAhybrid(TestCase):	1✔
12	def setUp(self):	1✔
13	self.CTsars = disentangle_knots(next(read_CT_file(getFP('data/SARS-CoV-2_Full_Length_Secondary_Structure_Map.ct')))[2], verbose=None)['nested']	1✔
14	# Pairs are stored as opening: closing base pair positions, i.e. opening < closing.
15	# To ease access, we enrich this dict by also adding in closing: opening information.
16	self.CTsars.update({c: o for o, c in self.CTsars.items()})	1✔
17
18	def tearDown(self):	1✔
19	pass	1✔
20
21	def test_getOriginalPairs(self):	1✔
22	exp = {839: 851, 840: 850, 841: 849, 842: 848, 854: 943, 855: 942, 856: 941, 857: 940, 862: 906, # assert that: i < j	1✔
23	848: 842, 850: 840, 852: 838, 853: 837 # duplicate pairs where j < i
24	}
25
26	novel_target_pairing_partners = [int(x) for x in '839,840,841,842,843,845,846,847,848,850,852,853,854,855,856,857,858,859,862'.split(',')]	1✔
27	obs = {o: c for o, c in {x: self.CTsars.get(x, -1) for x in novel_target_pairing_partners}.items() if c != -1}	1✔
28	self.assertEqual(exp, obs)	1✔
29
30
31	if __name__ == '__main__':	1✔
NEW 32	main()	×

jlab / fold-grammars / 13575009990

Source File Press 'n' to go to next uncovered line, 'b' for previous

Source File
Press 'n' to go to next uncovered line, 'b' for previous