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import numpy as np
from ont_fast5_api.fast5_file import Fast5File
from ont_fast5_api.analysis_tools.basecall_1d import Basecall1DTools
from test.helpers import TestFast5ApiHelper
class TestBasecall1DTools(TestFast5ApiHelper):
def test_001_put_and_retrieve(self):
fname = self.generate_temp_filename()
dtypes = [('mean', float),
('start', float),
('stdv', float),
('length', float),
('called_state', '<U5'),
('move', int)]
data1 = np.zeros(10, dtype=dtypes)
data1['mean'] = [10.0, 15.0, 8.5, 7.2, 13.6, 9.4, 11.8, 10.1, 4.2, 10.9]
data1['stdv'] = [0.7, 0.9, 1.0, 1.1, 0.75, 0.6, 0.83, 1.12, 9.45, 2.9]
data1['start'] = [0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9]
data1['length'] = [0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1]
data1['move'] = [1, 1, 0, 1, 0, 2, 1, 1, 1, 0]
data1['called_state'] = ['AAAAA', 'AAAAT', 'AAAAT', 'AAATC', 'AAATC',
'ATCCG', 'TCCGT', 'CCGTT', 'CGTTA', 'CGTTA']
data2 = data1[::-1]
seq1 = 'AAAAATCCGTTA'
seq2 = 'TAACGGATTTTT'
qstring1 = 'blahblahblah'
qstring2 = 'halbhalbhalb'
with Fast5File(fname, mode='w') as fh:
fh.add_channel_info({'channel_number': 1,
'sampling_rate': 4000,
'digitisation': 8192,
'range': 819.2,
'offset': 0})
fh.add_read(12, 'unique_snowflake', 12345, 1000, 0, 120.75)
attrs = {'name': 'test', 'version': 0, 'time_stamp': 'just now'}
fh.add_analysis('basecall_1d', 'Basecall_1D_000', attrs)
with Basecall1DTools(fh, group_name='Basecall_1D_000') as basecall:
basecall.add_event_data('template', data1)
basecall.add_event_data('complement', data2)
basecall.add_called_sequence('template', 'template', seq1, qstring1)
basecall.add_called_sequence('complement', 'complement', seq2, qstring2)
with Fast5File(fname, mode='r') as fh:
with Basecall1DTools(fh, group_name='Basecall_1D_000') as basecall:
events1 = basecall.get_event_data('template')
np.testing.assert_array_equal(events1, data1)
events2 = basecall.get_event_data('complement')
np.testing.assert_array_equal(events2, data2)
n1, s1, q1 = basecall.get_called_sequence('template')
self.assertEqual(n1, 'template')
self.assertEqual(s1, seq1)
self.assertEqual(q1, qstring1)
n2, s2, q2 = basecall.get_called_sequence('complement')
self.assertEqual(n2, 'complement')
self.assertEqual(s2, seq2)
self.assertEqual(q2, qstring2)
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