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import numpy as np
from ont_fast5_api.fast5_file import Fast5File
from ont_fast5_api.analysis_tools.basecall_2d import Basecall2DTools
from test.helpers import TestFast5ApiHelper
class TestBasecall2DTools(TestFast5ApiHelper):
def test_001_put_and_retrieve(self):
fname = self.generate_temp_filename()
dtypes = [('template', int), ('complement', int)]
data1 = np.zeros(10, dtype=dtypes)
data1['template'] = [0, 1, 2, 2, 3, 4, 5, 6, 7, 8]
data1['complement'] = [9, 8, 7, 6, 5, 4, 3, 2, 1, 0]
dtypes.append(('model_state', '<U5'))
data2 = np.zeros(10, dtype=dtypes)
data2['template'] = data1['template']
data2['complement'] = data1['complement']
data2['model_state'] = ['AAAAA', 'AAAAT', 'AAATC', 'AAATC', 'ATCCG',
'TCCGT', 'CCGTT', 'CGTTA', 'CGTTA', 'GTTAC']
seq = 'AAAAATCCGTTAC'
qstring = 'blahblahblahb'
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_2d', 'Basecall_2D_000', attrs)
with Basecall2DTools(fh, group_name='Basecall_2D_000') as basecall:
basecall.add_prior_alignment(data1)
basecall.add_2d_call_alignment(data2)
basecall.add_called_sequence("2D", 'test_2d', seq, qstring)
with Fast5File(fname, mode='r') as fh:
with Basecall2DTools(fh, group_name='Basecall_2D_000') as basecall:
hp_align = basecall.get_prior_alignment()
np.testing.assert_array_equal(hp_align, data1)
bc2d = basecall.get_2d_call_alignment()
np.testing.assert_array_equal(bc2d, data2)
n, s, q = basecall.get_called_sequence("2D")
self.assertEqual(n, 'test_2d')
self.assertEqual(s, seq)
self.assertEqual(q, qstring)
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