style: pre-commit reformatting

Danderson123 · Aug 14, 2024 · 3ae42d7 · 3ae42d7
1 parent d308ee3
commit 3ae42d7
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Showing 2 changed files with 9 additions and 9 deletions.
diff --git a/amira_prototype/__main__.py b/amira_prototype/__main__.py
@@ -320,7 +320,10 @@ def parse_fastq(fastq_file):
                 # Iterate over the lines in the file
                 for identifier, sequence, quality in parse_fastq_lines(fh):
                     # Add the identifier and sequence to the results dictionary
-                    results[identifier.replace("\n", "")] = {"sequence": sequence, "quality": quality}
+                    results[identifier.replace("\n", "")] = {
+                        "sequence": sequence,
+                        "quality": quality,
+                    }
             return results
         except OSError:
             pass

diff --git a/tests/test_gene_mer_graph.py b/tests/test_gene_mer_graph.py
@@ -1,7 +1,7 @@
 import unittest
 from collections import Counter
 
-from amira_prototype.__main__ import parse_fastq, write_fastq
+from amira_prototype.__main__ import parse_fastq
 from amira_prototype.construct_edge import Edge
 from amira_prototype.construct_graph import GeneMerGraph
 from amira_prototype.construct_node import Node
@@ -5874,12 +5874,11 @@ def test___get_closest_allele(self):
     def test___path_finding_between_junctions(self):
         # setup
         import json
-        with open("tests/test_paths.json") as i:
+
+        with open("tests/test_path_calls.json") as i:
             calls = json.load(i)
         graph = GeneMerGraph(calls, 3)
         graph.filter_graph(3, 1)
-        fastq_data = parse_fastq("tests/test_1.fastq.gz")
-        graph.generate_gml("tests/test", 3, 1, 1)
         # get the potential start nodes
         potential_bubble_starts = graph.identify_potential_bubble_starts()
         max_distance = graph.get_kmerSize() * 3
@@ -5899,12 +5898,12 @@ def test___path_finding_between_junctions(self):
     def test___get_minhashes_for_paths_same_path(self):
         # setup
         import json
+
         with open("tests/test_path_calls.json") as i:
             calls = json.load(i)
         with open("tests/test_path_positions.json") as i:
             positions = json.load(i)
         graph = GeneMerGraph(calls, 3, positions)
-        graph.filter_graph(3, 1)
         fastq_data = parse_fastq("tests/test_1.fastq.gz")
         # get the potential start nodes
         potential_bubble_starts = graph.identify_potential_bubble_starts()
@@ -5919,9 +5918,7 @@ def test___get_minhashes_for_paths_same_path(self):
             filtered_paths = graph.filter_paths_between_bubble_starts(unique_paths)
             sorted_filtered_paths = sorted(filtered_paths, key=lambda x: len(x[0]), reverse=True)
             # execution
-            path_minimizers = graph.get_minhashes_for_paths(
-                sorted_filtered_paths, fastq_data, 1
-            )
+            path_minimizers = graph.get_minhashes_for_paths(sorted_filtered_paths, fastq_data, 1)
             min1 = path_minimizers[tuple([n[0] for n in sorted_filtered_paths[0][0]])]
             min2 = path_minimizers[tuple([n[0] for n in sorted_filtered_paths[1][0]])]
             # assertion