aligner class tests complete coverage

tests/test_aligner.py

@@ -0,0 +1,77 @@
+import pytest
+import os
+import locidex.classes.aligner
+from locidex.constants import BLAST_TABLE_COLS
+from dataclasses import dataclass
+
+PACKAGE_ROOT = os.path.dirname(locidex.__file__)
+@dataclass
+class Datasets:
+    def __init__(self, tmpdir):
+        self.align_inputs = {'thrA':{'thrA':{
+                                'locus_name': 'thrA', 
+                                'ref_id': '43', 
+                                'ref_seq': 'gtgctgggccgtaatggttccgactattccgccgccgtgctggccgcctgtttacgcgctgactgctgtgaaatctggactgacgtcgatggcgtgtatacctgtgacccgcgccaggtgccggacgccagactgctgaaatcgatgtcctaccaggaagcgatggaactctcttacttcggcgccaaagtccttcaccctcgcaccataacgcctatcgcccagttccagatcccctgtctgattaaaaataccggtaatccgcaggcgccaggaacgctgatcggcgcgtccagcgacgatgataatctgccggttaaagggatctctaaccttaacaacatggcgatgtttagcgtctccggcccgggaatgaaagggatgattgggatggcggcgcgtgttttcgccgccatgtctcgcgccgggatctcggtggtgctcattacccagtcctcctctgagtacagcatcagcttctgtgtgccgcagagtgactgc', 
+                                'ext_seq': 'gtgctgggccgtaatggttccgactattccgccgccgtgctggccgcctgtttacgcgctgactgctgtgaaatctggactgacgtcgatggcgtgtatacctgtgacccgcgccaggtgccggacgccaggctgttgaaatcgatgtcctaccaggaagcgatggagctctcttacttcggcgctaaagtccttcaccctcgcaccataacgcctatcgcccagttccagatcccctgtctgattaaaaataccggcaatccgcaggcgccaggaacgctgatcggcgcgtccagcgacgatgataatctgccggttaaagggatctctaaccttaacaacatggcgatgtttagcgtctccggcccgggaatgaaagggatgattgggatggcggcgcgtgttttcgccgccatgtctcgcgccgggatctcggtggtgctcattacccagtcctcctctgagtacagcatcagcttctgtgtgccgcagagtgactgc', 
+                                'file': tmpdir
+                            }},
+                            'hemD':{'hemD': {
+                                'locus_name': 'hemD', 
+                                'ref_id': '16', 
+                                'ref_seq': 'gcgacgttgacggaaaacgatctggtttttgccctttcacagcacgccgtcgcctttgcccacgcccaactccagcgagatggtcgaaactggcctgcgtcgccgcgctatttcgcgattggtcgcaccacggcgctcgcccttcataccgttagcgggttcgatattcgttatccattggatcgggaaatcagcgaagtcttgctacaattacctgaattacaaaatattgcgggcaaacgcgcgctgattttgcgtggcaatggcggtcgcggtcgcgaactgctgggcgaaaccctgacagctcgcggagccgaagtcagtttttgtgaatgttatcaacgaagtgcgaaacattacgatggcgcagaagaggcgatgcgctggcacactcgcggcgtaacgacgcttgttgtcaccagcggcgagatgttgcaa', 
+                                'ext_seq': 'gcaacgctgacggaaaacgatctggtttttgccctttcacagcactccgtcgcctttgctcacgcccagctccagcgggatggacgaaactggcctgcgtcgccgcgctatttctcgattggccgcaccacggcgctcgcccttcataccgttagcgggttcgatattcgttatccattggatcgggaaatcagcgaagccttgctacaattacctgaattacaaaatattgcgggcaaacgcgcgctgattttgcgtggcaatggcggccgcgaactgctgggcgaaaccctgacagttcgcggagccgaagtcagtttttgtgaatgttatcaacgatgtgcgaaacattacgatggcgcggaagaagcgatgcgctggcatactcgcggcgtaacaacgcttgttgttaccagcggcgagatgttgcaa', 
+                                'file': tmpdir
+                            }}
+                            }
+
+@pytest.fixture
+def aligner_class_fixture():
+    return locidex.classes.aligner.aligner(trim_fwd=True,trim_rev=True,ext_fwd=False, ext_rev=False,fill=False, snps_only=False)
+
+def test_perform_alignment_call_variants(tmpdir, aligner_class_fixture):
+    seq_id = 'thrA'; ref_id='43'
+    ext_seq_data=Datasets(tmpdir).align_inputs[seq_id]     
+    result = locidex.classes.aligner.perform_alignment(ext_seq_data, tmpdir, 1)
+    alignment = ext_seq_data[seq_id]['alignment']
+    variants = aligner_class_fixture.call_seq(seq_id,alignment[ref_id],alignment[seq_id])
+    assert list(variants.keys())==['id', 'matched_bases', 'num_diff', 'coverage', 'seq']
+    assert variants['num_diff'] == 5, 'Expected value 5 for sequence differences'
+    assert variants['coverage'] == 100, 'Expected value 100 for reference coverage'
+
+    aligned_sequences_str=result[0][0] #identical to alignment variable, but needed to test parser
+    aligned_sequences_dict = locidex.classes.aligner.parse_align(aligned_sequences_str)
+    assert list(aligned_sequences_dict.keys()) == [ref_id, seq_id]
+    assert all([True if 'alignment' in ext_seq_data[key] else False for key in ext_seq_data ]), 'Missing alignment results in locidex.classes.aligner object'
+    assert len(ext_seq_data[seq_id]['alignment'].keys()) == 2, 'Should have two sequences (ref and query)'
+    assert len(ext_seq_data[seq_id]['alignment'][ref_id]) == 501, 'Length should be 501 bp'
+    assert len(ext_seq_data[seq_id]['alignment'][seq_id]) == 501, 'Length should be 501 bp'
+    assert list(ext_seq_data[seq_id].keys()) == ['locus_name', 'ref_id', 'ref_seq', 'ext_seq', 'file', 'alignment'], 'Keys do not match'
+
+def test_perform_seq_transform_trim_extend_gapfill(aligner_class_fixture):
+    tseq = aligner_class_fixture.transform_seq( 'GTGGCAATGGCGGT',
+                                                'GCGTGGCAATG---')
+    assert tseq == 'GCGTGGCAATGGGT', f'Unexpected result {tseq}'
+    tseq = aligner_class_fixture.trim_ends('ATGT--','ATGTAA', trim_fwd=False,trim_rev=False)
+    assert 'ATGTAA' == tseq, f'Unexpected result {tseq}'
+    tseq = aligner_class_fixture.trim_ends('--GTAA','ATGTAA', trim_fwd=False,trim_rev=True)
+    assert 'ATGTAA' == tseq, f'Unexpected result {tseq}'
+    tseq = aligner_class_fixture.trim_ends('--GT--','ATGTAA', trim_fwd=True,trim_rev=True)
+    assert '--GT--' == tseq, f'Unexpected result {tseq}'
+    tseq = aligner_class_fixture.extend('GCGTAA','-AGTCC',ext_fwd=False, ext_rev=False)
+    assert '-AGTCC' == tseq, f'Unexpected result {tseq}'
+    tseq = aligner_class_fixture.extend('GCGTAA','GAGTC-',ext_fwd=False, ext_rev=True)
+    assert 'GAGTCA' == tseq, f'Unexpected result {tseq}'
+    tseq = aligner_class_fixture.extend('GCGTAA','-AGTCC',ext_fwd=True, ext_rev=True)
+    assert 'GAGTCC' == tseq, f'Unexpected result {tseq}'
+    tseq = aligner_class_fixture.gap_fill('ATGTAA','AT--AA')
+    assert 'ATGTAA' == tseq, f'Unexpected result {tseq}'
+
+def test_coverage_and_identity(aligner_class_fixture):
+    coverage = aligner_class_fixture.calc_coverage('GCGTAACCAT','GCGTAACC--')
+    assert coverage == 80, "Expected different coverage value between two sequences"
+    coverage = aligner_class_fixture.calc_coverage('GCGTAACCAT','-CGTA-CCA-')
+    assert coverage == 70, "Expected different coverage value between two sequences"
+    identity = aligner_class_fixture.count_identity('GCGTAACCAT','GCGTAACC--')
+    assert identity == [8,2], "Expected different match and difference value in list"
+    identity = aligner_class_fixture.count_identity('GCGTAACCAT','-CGTAACCGG')
+    assert identity == [7,3], "Expected different match and difference value in list"