2024-03-20: adding first tests

requirements.txt

@@ -0,0 +1,2 @@
+IMGTgeneDL>=0.5.2
+importlib-resources>=1.1.0

setup.cfg

@@ -17,11 +17,9 @@ operating system :: OS Independent
 [options]
 package_dir =
     = src
-packages = find:
+packages = find_packages()
 python_requires = >=3.9
-install_requires =
-    IMGTgeneDL>=0.5.2
-    importlib-resources>=1.1.0
+install_requires = [line.strip() for line in open('requirements.txt')]
 
 [options.packages.find]
 where = src

tests/test_shared_functions.py

@@ -0,0 +1,130 @@
+import os
+import pytest
+import subprocess
+from Stitchr import stitchrfunctions as fxn
+
+def empty_file(file_name):
+    with open(file_name, 'w') as out_file:
+        out_file.write('')
+    return file_name
+
+
+def test_downloaded_data_handling():
+    # Need to have data downloaded to test various functions; arbitrarily use canine and mouse
+    # dl_cmd = 'stitchrdl -s dog'
+    # subprocess.call(dl_cmd, shell=True)
+    # dl_cmd = 'stitchrdl -s mouse'
+    # subprocess.call(dl_cmd, shell=True)
+    assert 'DOG' in fxn.find_species_covered()
+    assert 'MOUSE' in fxn.find_species_covered()
+
+    tmp_file = empty_file('temp_dog.txt')
+    assert fxn.infer_species(tmp_file) == 'DOG'
+    os.remove(tmp_file)
+
+    tmp_file = empty_file('temp_dog_mouse.txt')
+    assert fxn.infer_species(tmp_file) == ''
+    os.remove(tmp_file)
+
+
+def test_file_handling():
+    in_header, in_seq = ['test_header', 'ACGT']
+    tmp_file = 'temp.fasta'
+    with open(tmp_file, 'w') as out_file:
+        out_file.write(fxn.fastafy(in_header, in_seq))
+
+    with fxn.opener(tmp_file) as in_file:
+        for header, seq, null in fxn.read_fa(in_file):
+            assert in_header == header and in_seq == seq, "Failed FASTA handling."
+
+    os.remove(tmp_file)
+
+
+def test_get_chain():
+    assert fxn.get_chain('TRAV', 'TRAJ') == 'TRA'
+    assert fxn.get_chain('TRDV', 'TRAJ') == 'TRA'
+    assert fxn.get_chain('TRBV', 'TRBJ') == 'TRB'
+    assert fxn.get_chain('TRDV', 'TRDJ') == 'TRD'
+    assert fxn.get_chain('TRGV', 'TRGJ') == 'TRG'
+    assert fxn.get_chain('IGHV', 'IGHJ') == 'IGH'
+    assert fxn.get_chain('IGLV', 'IGLJ') == 'IGL'
+    assert fxn.get_chain('IGKV', 'IGKJ') == 'IGK'
+    assert not fxn.get_chain('TRAV', 'TRAJ') == 'TRB'
+    with pytest.raises(ValueError):
+        fxn.get_chain('TRAV', 'TRBJ')
+
+
+def test_get_imgt_data():
+    assert fxn.get_imgt_data('TRA', list(fxn.regions.values()), 'DOG')
+
+    with pytest.raises(ValueError):
+        fxn.get_imgt_data('TEST', list(fxn.regions.values()), 'DOG')
+
+    with pytest.raises(IOError):
+        fxn.get_imgt_data('TRA', list(fxn.regions.values()), 'UNICORN')
+
+    imgt_dat = fxn.get_imgt_data('TRA', list(fxn.regions.values()), 'MOUSE')
+    assert [isinstance(x, dict) for x in imgt_dat]
+    assert list(imgt_dat[0].keys()) == ['LEADER', 'VARIABLE', 'JOINING', 'CONSTANT']
+    assert list(imgt_dat[1].keys())[0].startswith('TR')
+
+    preferred = fxn.get_preferred_alleles('templates/preferred-alleles/mouse_c57-bl6_example.tsv',
+                                          list(fxn.regions.values()), imgt_dat[0], imgt_dat[2], 'TRA')
+    assert preferred['LEADER']['TRAV15D-3'] == '02'
+
+
+
+aa = ['*', 'A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y']
+def test_translation_handling():
+    codon_file = os.path.join(fxn.data_dir, 'kazusa', 'DOG.txt')
+    assert fxn.get_codon_frequencies(codon_file)
+    codon_freqs = fxn.get_codon_frequencies(codon_file)
+    assert [x for x in aa if x in codon_freqs.keys()] == aa
+    assert [x for x in aa if x in list(set(fxn.codons.values()))] == aa
+    assert fxn.get_optimal_codons(codon_file, 'DOG')
+    codons = fxn.get_optimal_codons(codon_file, 'DOG')
+
+    assert (fxn.translate_nt('AAAAACAAGAATACAACCACGACTAGAAGCAGGAGTATAATCATGATTCAACACCAGCATCCAC'
+                             'CCCCGCCTCGACGCCGGCGTCTACTCCTGCTTGAAGACGAGGATGCAGCCGCGGCTGGAGGCGG'
+                             'GGGTGTAGTCGTGGTTTAATACTAGTATTCATCCTCGTCTTGATGCTGGTGTTTATTCTTGTTT') ==
+            'KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSS*CWCLFLF')
+    assert fxn.translate_nt('naaaaa') == 'xK'
+    with pytest.raises(OSError):
+        fxn.translate_nt('123')
+
+    assert (fxn.rev_translate(''.join(aa).replace('*', ''), codons) ==
+            'GCCTGCGACGAGTTCGGCCACATCAAGCTGATGAACCCCCAGAGGAGCACCGTGTGGTAC')
+
+
+def test_misc_str_handling():
+    assert fxn.strip_functionality('()[]test') == 'test'
+    assert fxn.tidy_n_term('aaacccggg') == ('aaacccggg', 'KPG')
+    assert fxn.tidy_n_term('aaacccgggtt') == ('aaacccggg', 'KPG')
+    assert fxn.find_stop('0123456789') == 10
+    assert fxn.find_stop('01234*6789') == 5
+    assert fxn.dna_check('acgt')
+    assert not fxn.dna_check('dna')
+    assert fxn.check_suffix_prefix('thisdoesnt', 'overlap') == ''
+    assert fxn.check_suffix_prefix('thisdoes', 'doesthough') == 'does'
+
+
+def test_linker_handling():
+    assert fxn.get_linker_dict()
+    linkers = fxn.get_linker_dict()
+    assert linkers['P2A'] == 'GGCAGCGGCGCCACCAACTTCAGCCTGCTGAAGCAGGCCGGCGACGTGGAGGAGAACCCCGGCCCC'
+    linker_seq = fxn.get_linker_seq('P2A', linkers)
+    assert linker_seq == 'GGCAGCGGCGCCACCAACTTCAGCCTGCTGAAGCAGGCCGGCGACGTGGAGGAGAACCCCGGCCCC'
+
+
+# TODO STILL
+    # def get_additional_genes(imgt_data, imgt_functionality):
+    # def tidy_c_term(c_term_nt, skip, c_region_motifs, c_gene):
+    # def determine_v_interface(cdr3aa, n_term_nuc, n_term_amino):
+    # def find_cdr3_c_term(cdr3_chunk, j_seq, strict):
+    # def determine_j_interface(cdr3_cterm_aa, c_term_nuc, c_term_amino, gl_nt_j_len, j_warning_threshold):
+    # def get_j_motifs(species):
+    # def get_c_motifs(species):
+    # def find_v_overlap(v_germline, nt_cdr3):
+    # def find_j_overlap(nt_cdr3, j_germline):
+
+    # def tweak_thimble_input(stitch_dict): # Todo move to a thimble test file?