refactor test code

oschwengers · Oct 24, 2023 · 7397830 · 7397830
1 parent ec327a6
commit 7397830
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Showing 8 changed files with 59 additions and 66 deletions.
diff --git a/test/test_args.py b/test/test_args.py
@@ -1,10 +1,10 @@
-from inspect import Parameter
 import os
-import pytest
 
 from pathlib import Path
 from subprocess import run
 
+import pytest
+
 from .conftest import FILES, SKIP_PARAMETERS
 
 

diff --git a/test/test_bakta_proteins.py b/test/test_bakta_proteins.py
@@ -3,6 +3,7 @@
 
 import pytest
 
+
 FILES = [
     'test.tsv',
     'test.hypotheticals.tsv',

diff --git a/test/test_crispr.py b/test/test_crispr.py
@@ -3,8 +3,6 @@
 from pathlib import Path
 from subprocess import run
 
-import pytest
-
 
 CRISPR_ARRAYS = [
     {
@@ -19,8 +17,6 @@
 ]
 
 
-
-
 def test_crispr_arrays(tmpdir):
     proc = run(
         [

diff --git a/test/test_edge_features.py b/test/test_edge_features.py
@@ -3,8 +3,6 @@
 from pathlib import Path
 from subprocess import run
 
-import pytest
-
 from bakta import constants as bc
 
 

diff --git a/test/test_nt_sequences.py b/test/test_nt_sequences.py
@@ -3,10 +3,8 @@
 from pathlib import Path
 from subprocess import run
 
-import pytest
-
-cds = 'TTGACTACGCCATTGAAAAAGATTGTGATTGTCGGCGGCGGTGCTGGTGGGCTGGAAATGGCAACACAGCTGGGGCATAAGCTGGGACGCAAGAAAAAAGCCAAAATTACGCTGGTCGATCGTAACCACAGCCATCTGTGGAAACCGCTGCTGCACGAAGTGGCGACTGGCTCGCTTGATGAAGGCGTCGATGCGTTGAGCTATCTGGCCCATGCGCGCAATCATGGTTTCCAGTTCCAGCTGGGTTCCGTCATTGATATTGATCGTGAAGCGAAAACAATCACTATTGCAGAACTGCGCGATGAGAAAGGTGAACTGCTGGTTCCGGAACGTAAAATCGCCTATGACACCCTGGTAATGGCGCTGGGTAGCACCTCTAACGATTTCAATACGCCAGGTGTCAAAGAGAACTGCATTTTCCTCGATAACCCGCACCAGGCGCGTCGCTTTCACCAGGAGATGCTGAATCTCTTCCTGAAATACTCCGCCAACCTGGGCGCAAATGGCAAAGTGAACATTGCGATTGTCGGCGGCGGCGCGACGGGTGTAGAACTCTCCGCTGAATTGCACAACGCGGTCAAGCAACTGCACAGCTACGGTTACAAAGGCCTGACCAACGAAGCCCTGAACGTAACGCTGGTAGAAGCGGGAGAACGTATTTTGCCTGCATTACCGCCACGTATCTCTGCTGCGGCCCACAACGAGCTAACGAAACTTGGCGTTCGCGTGCTGACGCAAACCATGGTCACCAGTGCTGATGAAGGCGGCCTGCACACTAAAGATGGCGAATATATTGAGGCTGATCTGATGGTGTGGGCAGCCGGGATCAAAGCGCCAGACTTCCTGAAAGATATCGGTGGTCTTGAAACTAACCGTATCAACCAGCTGGTGGTGGAACCGACGCTGCAAACCACCCGCGATCCAGACATTTACGCTATTGGCGACTGCGCGTCATGCCCGCGTCCGGAAGGGGGCTTTGTTCCGCCGCGTGCTCAGGCTGCACACCAGATGGCGACTTGCGCAATGAACAACATTCTGGCGCAGATGAATGGTAAGCCGCTGAAAAATTATCAGTATAAAGATCATGGTTCGCTGGTATCGCTGTCGAACTTCTCCACCGTTGGTAGCCTGATGGGTAACCTGACGCGCGGCTCAATGATGATTGAAGGACGAATTGCGCGCTTTGTATATATCTCGCTATACCGAATGCATCAGATTGCGCTGCATGGTTACTTTAAAACCGGATTAATGATGCTGGTGGGGAGTATTAACCGCGTTATCCGTCCGCGTTTGAAGTTGCATTAA'
-sorf = 'ATGGTGAATACCGGCGGCAATAAACGTCAGGTGCCGGCGAAACGTCAGAATCGTGGCTCCCGTAATTCCAAAGATGATGGCGGCTAA'
+CDS = 'TTGACTACGCCATTGAAAAAGATTGTGATTGTCGGCGGCGGTGCTGGTGGGCTGGAAATGGCAACACAGCTGGGGCATAAGCTGGGACGCAAGAAAAAAGCCAAAATTACGCTGGTCGATCGTAACCACAGCCATCTGTGGAAACCGCTGCTGCACGAAGTGGCGACTGGCTCGCTTGATGAAGGCGTCGATGCGTTGAGCTATCTGGCCCATGCGCGCAATCATGGTTTCCAGTTCCAGCTGGGTTCCGTCATTGATATTGATCGTGAAGCGAAAACAATCACTATTGCAGAACTGCGCGATGAGAAAGGTGAACTGCTGGTTCCGGAACGTAAAATCGCCTATGACACCCTGGTAATGGCGCTGGGTAGCACCTCTAACGATTTCAATACGCCAGGTGTCAAAGAGAACTGCATTTTCCTCGATAACCCGCACCAGGCGCGTCGCTTTCACCAGGAGATGCTGAATCTCTTCCTGAAATACTCCGCCAACCTGGGCGCAAATGGCAAAGTGAACATTGCGATTGTCGGCGGCGGCGCGACGGGTGTAGAACTCTCCGCTGAATTGCACAACGCGGTCAAGCAACTGCACAGCTACGGTTACAAAGGCCTGACCAACGAAGCCCTGAACGTAACGCTGGTAGAAGCGGGAGAACGTATTTTGCCTGCATTACCGCCACGTATCTCTGCTGCGGCCCACAACGAGCTAACGAAACTTGGCGTTCGCGTGCTGACGCAAACCATGGTCACCAGTGCTGATGAAGGCGGCCTGCACACTAAAGATGGCGAATATATTGAGGCTGATCTGATGGTGTGGGCAGCCGGGATCAAAGCGCCAGACTTCCTGAAAGATATCGGTGGTCTTGAAACTAACCGTATCAACCAGCTGGTGGTGGAACCGACGCTGCAAACCACCCGCGATCCAGACATTTACGCTATTGGCGACTGCGCGTCATGCCCGCGTCCGGAAGGGGGCTTTGTTCCGCCGCGTGCTCAGGCTGCACACCAGATGGCGACTTGCGCAATGAACAACATTCTGGCGCAGATGAATGGTAAGCCGCTGAAAAATTATCAGTATAAAGATCATGGTTCGCTGGTATCGCTGTCGAACTTCTCCACCGTTGGTAGCCTGATGGGTAACCTGACGCGCGGCTCAATGATGATTGAAGGACGAATTGCGCGCTTTGTATATATCTCGCTATACCGAATGCATCAGATTGCGCTGCATGGTTACTTTAAAACCGGATTAATGATGCTGGTGGGGAGTATTAACCGCGTTATCCGTCCGCGTTTGAAGTTGCATTAA'
+SORF = 'ATGGTGAATACCGGCGGCAATAAACGTCAGGTGCCGGCGAAACGTCAGAATCGTGGCTCCCGTAATTCCAAAGATGATGGCGGCTAA'
 
 
 def test_bakta_cds_nt_sequence(tmpdir):
@@ -30,7 +28,7 @@ def test_bakta_cds_nt_sequence(tmpdir):
 
     for feat in results['features']:
         if(feat['contig'] != 'dummy'):
-            assert feat['nt'] == cds
+            assert feat['nt'] == CDS
 
 
 def test_bakta_sorf_nt_sequence(tmpdir):
@@ -53,4 +51,4 @@ def test_bakta_sorf_nt_sequence(tmpdir):
         results = json.load(fh)
 
     for feat in results['features']:
-        assert feat['nt'] == sorf
+        assert feat['nt'] == SORF
diff --git a/test/test_sORF.py b/test/test_sORF.py
@@ -5,39 +5,39 @@
 from bakta.features import s_orf as bu
 
 
-contig_1 = {
+CONTIG_1 = {
     'id': 1,
     'description': 'no sORFs',
     'sequence': 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG'
 }
-contig_2 = {
+CONTIG_2 = {
     'id': 2,
     'description': 'out of limits',
     'sequence': 'ATGAAAAAATAGGGGATGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGTAG'
 }
-contig_3 = {
+CONTIG_3 = {
     'id': 3,
     'description': 'two sORFs',
     'sequence': 'ATGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGTAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGATGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGTAG'
 }
 
-genome_1 = {
-    'contigs': [contig_1]
+GENOME_1 = {
+    'contigs': [CONTIG_1]
 }
-genome_2 = {
-    'contigs': [contig_2]
+GENOME_2 = {
+    'contigs': [CONTIG_2]
 }
-genome_3 = {
-    'contigs': [contig_3]
+GENOME_3 = {
+    'contigs': [CONTIG_3]
 }
 
 
 @pytest.mark.parametrize(
     "genome, expected",
     [
-        (genome_1, 0),
-        (genome_2, 0),
-        (genome_3, 2)
+        (GENOME_1, 0),
+        (GENOME_2, 0),
+        (GENOME_3, 2)
     ]
 )
 def test_sORF(genome, expected):

diff --git a/test/test_sig_peps.py b/test/test_sig_peps.py
@@ -3,25 +3,25 @@
 from bakta.features import signal_peptides as bsp
 
 
-one_twentyone_fwd = {'start': 1, 'stop': 21, 'strand': '+'}
-one_twentyone_rev = {'start': 1, 'stop': 21, 'strand': '-'}
-four_fifteen_fwd = {'start': 4, 'stop': 15, 'strand': '+'}
-four_fifteen_rev = {'start': 4, 'stop': 15, 'strand': '-'}
+ONE_TWENTYONE_FWD = {'start': 1, 'stop': 21, 'strand': '+'}
+ONE_TWENTYONE_REV = {'start': 1, 'stop': 21, 'strand': '-'}
+FOUR_FIFTEEN_FWD = {'start': 4, 'stop': 15, 'strand': '+'}
+FOUR_FIFTEEN_REV = {'start': 4, 'stop': 15, 'strand': '-'}
 
 
 @pytest.mark.parametrize(
     "orf, start_aa, stop_aa, expected",
     [
         # Forward strand
-        (one_twentyone_fwd, 1, 3, (1,9)),   # ORF spans whole sequence length, signal peptide starts at AA 1
-        (one_twentyone_fwd, 2, 7, (4,21)),  # ORF spans whole sequence length, signal peptide stops at last AA
-        (four_fifteen_fwd, 1, 3, (4,12)),   # ORF does not span whole sequence length, signal peptide starts at AA 1
-        (four_fifteen_fwd, 2, 4, (7,15)),   # ORF does not span whole sequence length, signal peptide stops at last AA
+        (ONE_TWENTYONE_FWD, 1, 3, (1,9)),   # ORF spans whole sequence length, signal peptide starts at AA 1
+        (ONE_TWENTYONE_FWD, 2, 7, (4,21)),  # ORF spans whole sequence length, signal peptide stops at last AA
+        (FOUR_FIFTEEN_FWD, 1, 3, (4,12)),   # ORF does not span whole sequence length, signal peptide starts at AA 1
+        (FOUR_FIFTEEN_FWD, 2, 4, (7,15)),   # ORF does not span whole sequence length, signal peptide stops at last AA
         # Reverse strand
-        (one_twentyone_rev, 1, 3, (13,21)), # ORF spans whole sequence length, signal peptide starts at AA 1
-        (one_twentyone_rev, 3, 7, (1,15)),  # ORF spans whole sequence length, signal peptide stops at last AA
-        (four_fifteen_rev, 1, 2, (10,15)),  # ORF does not span whole sequence length, signal peptide starts at AA 1
-        (four_fifteen_rev, 2, 3, (7,12))    # ORF does not span whole sequence length, signal peptide in the middle of ORF
+        (ONE_TWENTYONE_REV, 1, 3, (13,21)), # ORF spans whole sequence length, signal peptide starts at AA 1
+        (ONE_TWENTYONE_REV, 3, 7, (1,15)),  # ORF spans whole sequence length, signal peptide stops at last AA
+        (FOUR_FIFTEEN_REV, 1, 2, (10,15)),  # ORF does not span whole sequence length, signal peptide starts at AA 1
+        (FOUR_FIFTEEN_REV, 2, 3, (7,12))    # ORF does not span whole sequence length, signal peptide in the middle of ORF
     ]
 )
 def test_start_stop(orf, start_aa, stop_aa, expected):

diff --git a/test/test_user_proteins.py b/test/test_user_proteins.py
@@ -12,74 +12,74 @@
 SEQUENCE = 'MRADEEPGDLSAVAQDYLKVIWTAQEWSQDKVSTKMLAERIGVSASTASESIRKLAEQGLVDHEKYGAVTLTDSGRRAALAMVRRHRLLETFLVNELGYRWDEVHDEA'
 
 
-aa_min = {
+AA_MIN = {
     'id': 'min',
     'description': '~~~product~~~',
     'sequence': SEQUENCE
 }
-aa_min_gene = {
+AA_MIN_GENE = {
     'id': 'min',
     'description': 'gene~~~product~~~',
     'sequence': SEQUENCE
 }
-aa_min_dbxref = {
+AA_MIN_DBXREF = {
     'id': 'min',
     'description': 'gene~~~product~~~db-1:id-1',
     'sequence': SEQUENCE
 }
-aa_min_dbxrefs = {
+AA_MIN_DBXREFS = {
     'id': 'min',
     'description': 'gene~~~product~~~db-1:id-1,db-2:id-2',
     'sequence': SEQUENCE
 }
-aa_full = {
+AA_FULL = {
     'id': 'full',
     'description': '90.0~~~80.0~~~80.0~~~gene~~~product~~~db-1:id-1,db-2:id-2',
     'sequence': SEQUENCE
 }
 
 
-aa_wrong_1 = {
+AA_WRONG_1 = {
     'id': 'low-cols',
     'description': '~~~product',
     'sequence': SEQUENCE
 }
-aa_wrong_2 = {
+AA_WRONG_2 = {
     'id': 'high-cols',
     'description': '90~~~80~~~80~~~gene~~~product~~~dbxref:dbxref~~~',
     'sequence': SEQUENCE
 }
-aa_wrong_3 = {
+AA_WRONG_3 = {
     'id': 'no-product',
     'description': 'gene~~~~~~dbxref:dbxref',
     'sequence': SEQUENCE
 }
-aa_wrong_4 = {
+AA_WRONG_4 = {
     'id': 'no-product-full',
     'description': '90~~~80~~~80~~~gene~~~~~~dbxref:dbxref',
     'sequence': SEQUENCE
 }
-aa_wrong_5 = {
+AA_WRONG_5 = {
     'id': 'wrong-dbxref',
     'description': 'gene~~~product~~~dbxrefdbxref',
     'sequence': SEQUENCE
 }
-aa_wrong_6 = {
+AA_WRONG_6 = {
     'id': 'wrong-dbxref-full',
     'description': '90~~~80~~~80~~~gene~~~product~~~dbxrefdbxref',
     'sequence': SEQUENCE
 }
-aa_wrong_7 = {
+AA_WRONG_7 = {
     'id': 'wrong-id',
     'description': 'ninety~~~80~~~80~~~gene~~~product~~~dbxref:dbxref',
     'sequence': SEQUENCE
 }
-aa_wrong_8 = {
+AA_WRONG_8 = {
     'id': 'wrong-min-query-cov',
     'description': '90~~~eighty~~~80~~~gene~~~product~~~dbxref:dbxref',
     'sequence': SEQUENCE
 }
-aa_wrong_9 = {
+AA_WRONG_9 = {
     'id': 'wrong-min-model-cov',
     'description': '90~~~80~~~eighty~~~gene~~~product~~~dbxref:dbxref',
     'sequence': SEQUENCE
@@ -89,15 +89,15 @@
 @pytest.mark.parametrize(
     "parameters",
     [
-        (aa_wrong_1),
-        (aa_wrong_2),
-        (aa_wrong_3),
-        (aa_wrong_4),
-        (aa_wrong_5),
-        (aa_wrong_6),
-        (aa_wrong_7),
-        (aa_wrong_8),
-        (aa_wrong_9)
+        AA_WRONG_1,
+        AA_WRONG_2,
+        AA_WRONG_3,
+        AA_WRONG_4,
+        AA_WRONG_5,
+        AA_WRONG_6,
+        AA_WRONG_7,
+        AA_WRONG_8,
+        AA_WRONG_9
     ]
 )
 def test_wrong_user_proteins_io(tmpdir, parameters):
@@ -114,11 +114,11 @@ def test_wrong_user_proteins_io(tmpdir, parameters):
 @pytest.mark.parametrize(
     "parameters",
     [
-        (aa_min),
-        (aa_min_gene),
-        (aa_min_dbxref),
-        (aa_min_dbxrefs),
-        (aa_full)
+        AA_MIN,
+        AA_MIN_GENE,
+        AA_MIN_DBXREF,
+        AA_MIN_DBXREFS,
+        AA_FULL
     ]
 )
 def test_user_proteins_io(parameters, tmpdir):