Activate resfinder and resfinderfg annotation

metagenopolis · Nov 19, 2024 · 026d42f · 026d42f
1 parent dbe9387
commit 026d42f
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Showing 18 changed files with 61 additions and 3 deletions.
diff --git a/meteor/merging.py b/meteor/merging.py
@@ -319,7 +319,11 @@ def execute(self) -> None:
                     "modules_completeness": ["msp_name", "mod_id"],
                     "modules": ["mod_id"],
                     "mustard_as_genes_sum": ["annotation"],
+                    "resfinder_as_genes_sum": ["annotation"],
+                    "resfinderfg_as_genes_sum": ["annotation"],
                     "mustard_as_msp_sum": ["annotation"],
+                    "resfinder_as_msp_sum": ["annotation"],
+                    "resfinderfg_as_msp_sum": ["annotation"],
                     "dbcan_as_genes_sum": ["annotation"],
                     "dbcan_as_msp_sum": ["annotation"],
                     "kegg_as_genes_sum": ["annotation"],

diff --git a/meteor/profiler.py b/meteor/profiler.py
@@ -155,7 +155,15 @@ def __post_init__(self):
         # Get functional db filenames
         if self.database_type == "complete":
             self.db_filenames = {}
-            for db in ["kegg", "mustard", "dbcan", "eggnog", "tigrfam"]:
+            for db in [
+                "kegg",
+                "mustard",
+                "dbcan",
+                "eggnog",
+                "tigrfam",
+                "resfinder",
+                "resfinderfg",
+            ]:
                 self.db_filenames[db] = (
                     self.meteor.ref_dir
                     / self.ref_config["reference_file"]["database_dir"]
@@ -646,8 +654,14 @@ def execute(self) -> None:
         )
         # Part 3: FUNCTIONAL PROFILING
         if self.database_type == "complete":
-            single_fun_db = ["mustard", "kegg", "dbcan"]
-            single_fun_by_msp_db = ["mustard", "kegg", "dbcan"]
+            single_fun_db = ["mustard", "kegg", "dbcan", "resfinder", "resfinderfg"]
+            single_fun_by_msp_db = [
+                "mustard",
+                "kegg",
+                "dbcan",
+                "resfinder",
+                "resfinderfg",
+            ]
             for db, db_filename in self.db_filenames.items():
                 # By sum of genes
                 if db in single_fun_db:

diff --git a/meteor/tests/test_merging/profiles/sample1/sample1_resfinder_as_genes_sum.tsv.xz b/meteor/tests/test_merging/profiles/sample1/sample1_resfinder_as_genes_sum.tsv.xz
diff --git a/meteor/tests/test_merging/profiles/sample1/sample1_resfinder_as_msp_sum.tsv.xz b/meteor/tests/test_merging/profiles/sample1/sample1_resfinder_as_msp_sum.tsv.xz
diff --git a/meteor/tests/test_merging/profiles/sample1/sample1_resfinderfg_as_genes_sum.tsv.xz b/meteor/tests/test_merging/profiles/sample1/sample1_resfinderfg_as_genes_sum.tsv.xz
diff --git a/meteor/tests/test_merging/profiles/sample1/sample1_resfinderfg_as_msp_sum.tsv.xz b/meteor/tests/test_merging/profiles/sample1/sample1_resfinderfg_as_msp_sum.tsv.xz
diff --git a/meteor/tests/test_merging/profiles/sample2/sample2_resfinder_as_genes_sum.tsv.xz b/meteor/tests/test_merging/profiles/sample2/sample2_resfinder_as_genes_sum.tsv.xz
diff --git a/meteor/tests/test_merging/profiles/sample2/sample2_resfinder_as_msp_sum.tsv.xz b/meteor/tests/test_merging/profiles/sample2/sample2_resfinder_as_msp_sum.tsv.xz
diff --git a/meteor/tests/test_merging/profiles/sample2/sample2_resfinderfg_as_genes_sum.tsv.xz b/meteor/tests/test_merging/profiles/sample2/sample2_resfinderfg_as_genes_sum.tsv.xz
diff --git a/meteor/tests/test_merging/profiles/sample2/sample2_resfinderfg_as_msp_sum.tsv.xz b/meteor/tests/test_merging/profiles/sample2/sample2_resfinderfg_as_msp_sum.tsv.xz
diff --git a/meteor/tests/test_merging/profiles/sample3/sample3_resfinder_as_genes_sum.tsv.xz b/meteor/tests/test_merging/profiles/sample3/sample3_resfinder_as_genes_sum.tsv.xz
diff --git a/meteor/tests/test_merging/profiles/sample3/sample3_resfinder_as_msp_sum.tsv.xz b/meteor/tests/test_merging/profiles/sample3/sample3_resfinder_as_msp_sum.tsv.xz
diff --git a/meteor/tests/test_merging/profiles/sample3/sample3_resfinderfg_as_genes_sum.tsv.xz b/meteor/tests/test_merging/profiles/sample3/sample3_resfinderfg_as_genes_sum.tsv.xz
diff --git a/meteor/tests/test_merging/profiles/sample3/sample3_resfinderfg_as_msp_sum.tsv b/meteor/tests/test_merging/profiles/sample3/sample3_resfinderfg_as_msp_sum.tsv
@@ -0,0 +1,24 @@
+annotation	value
+annotation	value
+aph	0
+dfra	0
+ldt	0
+tetM	0
+aac3_1	0
+aac6	0
+van	0
+ant	0
+erm	0
+blaa	0
+fos	0
+sul	0
+blac	0
+mcr	0
+tetX	0
+blab1	0
+blab3	0
+qnr	0
+blad	0
+aac3_2	0
+aac2	0
+arnm	0
diff --git a/meteor/tests/test_merging/profiles/sample3/sample3_resfinderfg_as_msp_sum.tsv.xz b/meteor/tests/test_merging/profiles/sample3/sample3_resfinderfg_as_msp_sum.tsv.xz
diff --git a/meteor/tests/test_profiler/catalogue/catalogue_reference.json b/meteor/tests/test_profiler/catalogue/catalogue_reference.json
@@ -30,6 +30,14 @@
     "tigrfam": {
       "filename": "catalogue_tigrfam.tsv",
       "version": "15.0"
+    },
+    "resfinder": {
+      "filename": "catalogue_resfinder.tsv",
+      "version": "2.4.0"
+    },
+    "resfinderfg": {
+      "filename": "catalogue_resfinderfg.tsv",
+      "version": "2.0"
     }
   }
 }
diff --git a/meteor/tests/test_profiler/catalogue/database/catalogue_resfinder.tsv b/meteor/tests/test_profiler/catalogue/database/catalogue_resfinder.tsv
@@ -0,0 +1,4 @@
+gene_id	gene_name	annotation
+3	gene_3	ARD1
+4	gene_4	ARD2
+8	gene_8	ARD2
diff --git a/meteor/tests/test_profiler/catalogue/database/catalogue_resfinderfg.tsv b/meteor/tests/test_profiler/catalogue/database/catalogue_resfinderfg.tsv
@@ -0,0 +1,4 @@
+gene_id	gene_name	annotation
+3	gene_3	ARD1
+4	gene_4	ARD2
+8	gene_8	ARD2