MAINT: change function load_card_db to load all files globally inst…

…ead of locally (#66)
bokulich-lab · Jun 20, 2024 · 5ace3a6 · 5ace3a6
1 parent 75d4efa
commit 5ace3a6
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Showing 6 changed files with 6 additions and 15 deletions.
diff --git a/q2_amr/card/mags.py b/q2_amr/card/mags.py
@@ -24,7 +24,7 @@ def annotate_mags_card(
     amr_annotations = CARDAnnotationDirectoryFormat()
     frequency_list = []
     with tempfile.TemporaryDirectory() as tmp:
-        load_card_db(tmp=tmp, card_db=card_db)
+        load_card_db(card_db=card_db)
         for samp_bin in list(manifest.index):
             bin_dir = os.path.join(str(amr_annotations), samp_bin[0], samp_bin[1])
             os.makedirs(bin_dir, exist_ok=True)
@@ -79,7 +79,6 @@ def run_rgi_main(
         alignment_tool,
         "--input_type",
         "contig",
-        "--local",
     ]
     if include_loose:
         cmd.append("--include_loose")

diff --git a/q2_amr/card/reads.py b/q2_amr/card/reads.py
@@ -40,7 +40,6 @@ def annotate_reads_card(
     amr_gene_annotation = CARDGeneAnnotationDirectoryFormat()
     with tempfile.TemporaryDirectory() as tmp:
         load_card_db(
-            tmp=tmp,
             card_db=card_db,
             fasta=True,
             include_other_models=include_other_models,
@@ -126,7 +125,6 @@ def run_rgi_bwt(
         f"{cwd}/{samp}/output",
         "-n",
         str(threads),
-        "--local",
         "--clean",
         "--aligner",
         aligner,

diff --git a/q2_amr/card/tests/test_mags.py b/q2_amr/card/tests/test_mags.py
@@ -78,7 +78,6 @@ def test_run_rgi_main(self):
                     "DIAMOND",
                     "--input_type",
                     "contig",
-                    "--local",
                     "--include_loose",
                     "--include_nudge",
                     "--low_quality",

diff --git a/q2_amr/card/tests/test_reads.py b/q2_amr/card/tests/test_reads.py
@@ -105,7 +105,6 @@ def annotate_reads_card_test_body(self, read_type):
             # Expected call object for mock_run_rgi_load
             exp_calls_mock_load = [
                 call(
-                    tmp=tmp_dir,
                     card_db=ANY,
                     fasta=True,
                     include_other_models=False,
@@ -174,7 +173,6 @@ def test_run_rgi_bwt(self):
                     "path_tmp/sample1/output",
                     "-n",
                     "8",
-                    "--local",
                     "--clean",
                     "--aligner",
                     "bowtie2",

diff --git a/q2_amr/card/tests/test_utils.py b/q2_amr/card/tests/test_utils.py
@@ -80,7 +80,6 @@ def test_load_card_db_fasta(self):
             # Run load_card_db two times with include_other_models set to True and False
             for parameters in [False, True]:
                 load_card_db(
-                    tmp="path_tmp",
                     card_db=card_db,
                     kmer_db=kmer_db,
                     kmer=True,
@@ -95,12 +94,11 @@ def test_load_card_db_fasta(self):
 
             expected_calls = [
                 call(
-                    [
+                    cmd=[
                         "rgi",
                         "load",
                         "--card_json",
                         os.path.join(str(card_db), "card.json"),
-                        "--local",
                         f"--card_annotation{flag}",
                         os.path.join(
                             str(card_db), f"card_database_v3.2.5{parameter}.fasta"
@@ -118,7 +116,7 @@ def test_load_card_db_fasta(self):
                         "--kmer_size",
                         "61",
                     ],
-                    "path_tmp",
+                    cwd=None,
                     verbose=True,
                 )
                 for flag, parameter in zip(flags, parameters)

diff --git a/q2_amr/card/utils.py b/q2_amr/card/utils.py
@@ -25,7 +25,6 @@ def run_command(cmd, cwd, verbose=True):
 
 
 def load_card_db(
-    tmp,
     card_db,
     kmer_db=None,
     kmer: bool = False,
@@ -36,8 +35,8 @@ def load_card_db(
     # Get path to card.json
     path_card_json = os.path.join(str(card_db), "card.json")
 
-    # Base command that only loads card.json into the local database
-    cmd = ["rgi", "load", "--card_json", path_card_json, "--local"]
+    # Base command that only loads card.json
+    cmd = ["rgi", "load", "--card_json", path_card_json]
 
     # Define suffixes for card fasta file
     models = ("_all", "_all_models") if include_other_models is True else ("", "")
@@ -83,7 +82,7 @@ def load_card_db(
 
     # Run command
     try:
-        run_command(cmd, tmp, verbose=True)
+        run_command(cmd=cmd, cwd=None, verbose=True)
     except subprocess.CalledProcessError as e:
         raise Exception(
             f"An error was encountered while running rgi, "