MAINT: Removed 'move_files' function from 'reads.py' (#25)

bokulich-lab · Jan 11, 2024 · 898241c · 898241c
1 parent 94069c6
commit 898241c
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Showing 2 changed files with 15 additions and 55 deletions.
diff --git a/q2_amr/card/reads.py b/q2_amr/card/reads.py
@@ -74,13 +74,24 @@ def annotate_reads_card(
                 path=path_allele, samp_bin_name=samp, data_type="reads"
             )
             allele_frequency_list.append(allele_frequency)
+
             path_gene = os.path.join(samp_input_dir, "output.gene_mapping_data.txt")
             gene_frequency = read_in_txt(
                 path=path_gene, samp_bin_name=samp, data_type="reads"
             )
             gene_frequency_list.append(gene_frequency)
-            move_files(samp_input_dir, samp_allele_dir, "allele")
-            move_files(samp_input_dir, samp_gene_dir, "gene")
+
+            # Move mapping and stats files to the sample allele and gene directories
+            for map_type, des_dir in zip(
+                ["allele", "gene"], [samp_allele_dir, samp_gene_dir]
+            ):
+                files = [f"{map_type}_mapping_data.txt", "overall_mapping_stats.txt"]
+
+                for file in files:
+                    shutil.copy(
+                        os.path.join(samp_input_dir, "output." + file),
+                        os.path.join(des_dir, file),
+                    )
 
     allele_feature_table = create_count_table(allele_frequency_list)
     gene_feature_table = create_count_table(gene_frequency_list)
@@ -92,17 +103,6 @@ def annotate_reads_card(
     )
 
 
-def move_files(source_dir: str, des_dir: str, map_type: str):
-    shutil.move(
-        os.path.join(source_dir, f"output.{map_type}_mapping_data.txt"),
-        os.path.join(des_dir, f"{map_type}_mapping_data.txt"),
-    )
-    shutil.copy(
-        os.path.join(source_dir, "output.overall_mapping_stats.txt"),
-        os.path.join(des_dir, "overall_mapping_stats.txt"),
-    )
-
-
 def run_rgi_bwt(
     cwd: str,
     samp: str,

diff --git a/q2_amr/tests/card/test_reads.py b/q2_amr/tests/card/test_reads.py
@@ -13,7 +13,6 @@
 from q2_amr.card.reads import (
     annotate_reads_card,
     extract_sample_stats,
-    move_files,
     plot_sample_stats,
     run_rgi_bwt,
     visualize_annotation_stats,
@@ -147,11 +146,9 @@ def annotate_reads_card_test_body(self, read_type):
             # resulting CARD annotation objects
             for num in [0, 1]:
                 map_type = "allele" if num == 0 else "gene"
+                files = [f"{map_type}_mapping_data.txt", "overall_mapping_stats.txt"]
                 for samp in ["sample1", "sample2"]:
-                    for file in [
-                        f"{map_type}_mapping_data.txt",
-                        "overall_mapping_stats.txt",
-                    ]:
+                    for file in files:
                         self.assertTrue(
                             os.path.exists(os.path.join(str(result[num]), samp, file))
                         )
@@ -204,43 +201,6 @@ def test_exception_raised(self):
             run_rgi_bwt()
             self.assertEqual(str(cm.exception), expected_message)
 
-    def test_move_files_allele(self):
-        self.move_files_test_body("allele")
-
-    def test_move_files_gene(self):
-        self.move_files_test_body("gene")
-
-    def move_files_test_body(self, map_type):
-        with tempfile.TemporaryDirectory() as tmp:
-            source_dir = os.path.join(tmp, "source_dir")
-            des_dir = os.path.join(
-                tmp,
-                "des_dir",
-            )
-            os.makedirs(os.path.join(source_dir))
-            os.makedirs(os.path.join(des_dir))
-            mapping_data = self.get_data_path(f"output.{map_type}_mapping_data.txt")
-            mapping_stats = self.get_data_path("output.overall_mapping_stats.txt")
-            shutil.copy(mapping_data, source_dir)
-            shutil.copy(mapping_stats, source_dir)
-            move_files(source_dir, des_dir, map_type)
-            self.assertTrue(
-                os.path.exists(
-                    os.path.join(
-                        des_dir,
-                        f"{map_type}_mapping_data.txt",
-                    )
-                )
-            )
-            self.assertTrue(
-                os.path.exists(
-                    os.path.join(
-                        des_dir,
-                        "overall_mapping_stats.txt",
-                    )
-                )
-            )
-
     def test_extract_sample_stats(self):
         with tempfile.TemporaryDirectory() as tmp:
             mapping_stats_path = self.get_data_path("output.overall_mapping_stats.txt")