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# ----------------------------------------------------------------------------
# Copyright (c) 2016-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
import skbio
from qiime2.sdk import Artifact
from qiime2.plugins.feature_classifier.actions import extract_reads
from q2_types.feature_data._format import DNAFASTAFormat
from . import FeatureClassifierTestPluginBase
class CutterTests(FeatureClassifierTestPluginBase):
package = 'q2_feature_classifier.tests'
def setUp(self):
super().setUp()
self.sequences = Artifact.import_data(
'FeatureData[Sequence]',
self.get_data_path('dna-sequences.fasta'))
self.mixed_sequences = Artifact.import_data(
'FeatureData[Sequence]',
self.get_data_path('dna-sequences-mixed.fasta'))
self.f_primer = 'AGAGA'
self.r_primer = 'GCTGC'
self.amplicons = ['ACGT', 'AAGT', 'ACCT', 'ACGG', 'ACTT']
def _test_results(self, results):
for i, result in enumerate(
skbio.io.read(str(results.reads.view(DNAFASTAFormat)),
format='fasta')):
self.assertEqual(str(result), self.amplicons[i])
def test_extract_reads_expected(self):
results = extract_reads(
self.sequences, f_primer=self.f_primer, r_primer=self.r_primer,
min_length=4)
self._test_results(results)
def test_extract_reads_expected_forward(self):
results = extract_reads(
self.sequences, f_primer=self.f_primer, r_primer=self.r_primer,
min_length=4, read_orientation='forward')
self._test_results(results)
def test_extract_mixed(self):
results = extract_reads(
self.mixed_sequences, f_primer=self.f_primer,
r_primer=self.r_primer, min_length=4)
self._test_results(results)
def test_extract_reads_expected_reverse(self):
reverse_sequences = Artifact.import_data(
'FeatureData[Sequence]',
self.get_data_path('dna-sequences-reverse.fasta'))
results = extract_reads(
reverse_sequences, f_primer=self.f_primer, r_primer=self.r_primer,
min_length=4, read_orientation='reverse')
self._test_results(results)
def test_extract_reads_manual_batch_size(self):
results = extract_reads(
self.sequences, f_primer=self.f_primer, r_primer=self.r_primer,
min_length=4, batch_size=10)
self._test_results(results)
def test_extract_reads_two_jobs(self):
results = extract_reads(
self.sequences, f_primer=self.f_primer, r_primer=self.r_primer,
min_length=4, n_jobs=2)
self._test_results(results)
def test_extract_reads_expected_degenerate_primers(self):
degenerate_f_primer = 'WWWWW'
degenerate_r_primer = 'SSSSS'
degenerate_sequences = Artifact.import_data(
'FeatureData[Sequence]',
self.get_data_path('dna-sequences-degenerate-primers.fasta'))
results = extract_reads(
degenerate_sequences, f_primer=degenerate_f_primer,
r_primer=degenerate_r_primer, min_length=4)
self._test_results(results)
def test_extract_reads_expected_trim_right(self):
"""Tests expected behavior of trim_right option"""
results = extract_reads(
self.sequences, f_primer=self.f_primer, r_primer=self.r_primer,
min_length=3, trim_right=1)
for i, result in enumerate(
skbio.io.read(str(results.reads.view(DNAFASTAFormat)),
format='fasta')):
self.assertEqual(str(result), self.amplicons[i][:-1])
def test_extract_reads_fail_identity(self):
with self.assertRaisesRegex(RuntimeError, "No matches found"):
extract_reads(
self.sequences, f_primer=self.f_primer, r_primer=self.r_primer,
min_length=4, identity=1)
def test_extract_reads_fail_min_length(self):
with self.assertRaisesRegex(RuntimeError, "No matches found"):
extract_reads(
self.sequences, f_primer=self.f_primer, r_primer=self.r_primer,
min_length=5)
def test_extract_reads_fail_max_length(self):
with self.assertRaisesRegex(RuntimeError, "No matches found"):
extract_reads(
self.sequences, f_primer=self.f_primer, r_primer=self.r_primer,
max_length=1)
def test_extract_reads_fail_trim_left_entire_read(self):
with self.assertRaisesRegex(RuntimeError, "No matches found"):
extract_reads(
self.sequences, f_primer=self.f_primer, r_primer=self.r_primer,
trim_left=4)
def test_extract_reads_fail_trim_right_entire_read(self):
with self.assertRaisesRegex(RuntimeError, "No matches found"):
extract_reads(
self.sequences, f_primer=self.f_primer, r_primer=self.r_primer,
trim_right=4)
def test_extract_reads_fail_trim_both_entire_read(self):
with self.assertRaisesRegex(RuntimeError, "No matches found"):
extract_reads(
self.sequences, f_primer=self.f_primer, r_primer=self.r_primer,
trim_left=2, trim_right=2)
def test_extract_reads_fail_min_len_greater_than_trunc_len(self):
with self.assertRaisesRegex(ValueError, "minimum length setting"):
extract_reads(
self.sequences, f_primer=self.f_primer, r_primer=self.r_primer,
trunc_len=1)
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