Harrison
ae3732eba2
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Now allow for changing whether alignment is local or global and various scoring parameters Refactored directory structure Removed redundant aligned dict pattern for simple iterable Added unit tests
52 lines
1.6 KiB
Python
52 lines
1.6 KiB
Python
import pytest
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from Bio import SeqIO
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from bmlsa.aligner import align_many_to_one_ssw
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from bmlsa.cli import DEFAULT_ALIGNMENT_PARAMETERS
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from bmlsa.datatypes import AlignedSequence
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from collections.abc import Iterable
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@pytest.fixture
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def reference_sequence():
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return str(
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list(SeqIO.parse("tests/resources/NC_045512_coding.fasta", "fasta"))[0].seq
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)
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@pytest.fixture
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def queries():
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return [
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AlignedSequence(
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"ORF10",
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"ATGGGCTATATAAACGTTTTCGCTTTTCCGTTTACGATATATAGTCTACTCTTGTGCAGAAT"
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"GAATTCTCGTAACTACATAGCACAAGTAGATGTAGTTAACTTTAATCTCACATAG",
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start=29558,
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end=29674,
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)
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]
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def test_align_many_to_one_returns_data(reference_sequence, queries):
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results = align_many_to_one_ssw(
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reference_sequence, queries, **DEFAULT_ALIGNMENT_PARAMETERS["BLASTp"]
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)
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assert isinstance(results, Iterable)
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def test_align_many_to_one_returns_correct_data_structure(reference_sequence, queries):
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results = align_many_to_one_ssw(
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reference_sequence, queries, **DEFAULT_ALIGNMENT_PARAMETERS["BLASTp"]
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)
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for original, aligned_seq in results:
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assert isinstance(original, AlignedSequence)
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assert isinstance(aligned_seq, AlignedSequence)
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def test_align_many_to_one_returns_correct_data(reference_sequence, queries):
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results = align_many_to_one_ssw(
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reference_sequence, queries, **DEFAULT_ALIGNMENT_PARAMETERS["BLASTp"]
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)
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for original, aligned_seq in results:
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assert original.start == aligned_seq.start
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assert original.end == aligned_seq.end
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