Merge branch 'main' into 26_change_read_in_text

bokulich-lab · Jan 16, 2024 · c9a49ed · c9a49ed
2 parents ed4331d + c0ca96d
commit c9a49ed
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Showing 5 changed files with 38 additions and 21 deletions.
diff --git a/.github/workflows/black.yaml b/.github/workflows/black.yaml
@@ -1,13 +1,13 @@
-name: Lint
+name: Black
 
 on: [push, pull_request]
 
 jobs:
-  lint:
+  black:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
       - uses: psf/black@stable
         with:
           version: "23.12.1"
-          args: ". --check --extend-exclude '.*_version\.py$'"
+          options: ". --check --extend-exclude '.*_version\\.py$' --verbose"
diff --git a/q2_amr/card/reads.py b/q2_amr/card/reads.py
@@ -90,8 +90,11 @@ def annotate_reads_card(
             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"]
-
+                files = [f"{map_type}_mapping_data.txt"]
+                # mapping statistics only go to the allele directories
+                files.append(
+                    "overall_mapping_stats.txt"
+                ) if map_type == "allele" else None
                 for file in files:
                     shutil.copy(
                         os.path.join(samp_input_dir, "output." + file),

diff --git a/q2_amr/plugin_setup.py b/q2_amr/plugin_setup.py
@@ -14,7 +14,7 @@
 )
 from q2_types.sample_data import SampleData
 from q2_types_genomics.per_sample_data import MAGs
-from qiime2.core.type import Bool, Choices, Int, Range, Str
+from qiime2.core.type import Bool, Choices, Int, Properties, Range, Str, TypeMap
 from qiime2.plugin import Citations, Plugin
 
 from q2_amr import __version__
@@ -118,21 +118,41 @@
     citations=[citations["alcock_card_2023"]],
 )
 
+P_aligner, T_allele_annotation, T_gene_annotation = TypeMap(
+    {
+        Str
+        % Choices("kma"): (
+            SampleData[CARDAlleleAnnotation % Properties("kma")],
+            SampleData[CARDGeneAnnotation % Properties("kma")],
+        ),
+        Str
+        % Choices("bowtie2"): (
+            SampleData[CARDAlleleAnnotation % Properties("bowtie2")],
+            SampleData[CARDGeneAnnotation % Properties("bowtie2")],
+        ),
+        Str
+        % Choices("bwa"): (
+            SampleData[CARDAlleleAnnotation % Properties("bwa")],
+            SampleData[CARDGeneAnnotation % Properties("bwa")],
+        ),
+    }
+)
+
 plugin.methods.register_function(
     function=annotate_reads_card,
     inputs={
         "reads": SampleData[PairedEndSequencesWithQuality | SequencesWithQuality],
         "card_db": CARDDatabase,
     },
     parameters={
-        "aligner": Str % Choices(["kma", "bowtie2", "bwa"]),
+        "aligner": P_aligner,
         "threads": Int % Range(0, None, inclusive_start=False),
         "include_wildcard": Bool,
         "include_other_models": Bool,
     },
     outputs=[
-        ("amr_allele_annotation", SampleData[CARDAlleleAnnotation]),
-        ("amr_gene_annotation", SampleData[CARDGeneAnnotation]),
+        ("amr_allele_annotation", T_allele_annotation),
+        ("amr_gene_annotation", T_gene_annotation),
         ("allele_feature_table", FeatureTable[Frequency]),
         ("gene_feature_table", FeatureTable[Frequency]),
     ],
@@ -196,11 +216,9 @@
 
 plugin.visualizers.register_function(
     function=visualize_annotation_stats,
-    inputs={"amr_reads_annotation": CARDGeneAnnotation | CARDAlleleAnnotation},
+    inputs={"amr_reads_annotation": SampleData[CARDAlleleAnnotation]},
     parameters={},
-    input_descriptions={
-        "amr_reads_annotation": "AMR annotation mapped on alleles or genes."
-    },
+    input_descriptions={"amr_reads_annotation": "AMR annotations on the allele level."},
     parameter_descriptions={},
     name="Visualize mapping statistics.",
     description="Visualize mapping statistics of an annotate-reads-card output.",

diff --git a/q2_amr/tests/card/test_reads.py b/q2_amr/tests/card/test_reads.py
@@ -147,7 +147,10 @@ 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"]
+                files = [f"{map_type}_mapping_data.txt"]
+                files.append(
+                    "overall_mapping_stats.txt"
+                ) if map_type == "allele" else None
                 for samp in ["sample1", "sample2"]:
                     for file in files:
                         self.assertTrue(

diff --git a/q2_amr/types/_format.py b/q2_amr/types/_format.py
@@ -421,14 +421,7 @@ class CARDGeneAnnotationDirectoryFormat(MultiDirValidationMixin, model.Directory
     gene = model.FileCollection(
         r".+(gene_mapping_data.txt)$", format=CARDGeneAnnotationFormat
     )
-    stats = model.FileCollection(
-        r".+(overall_mapping_stats.txt)$", format=CARDAnnotationStatsFormat
-    )
 
     @gene.set_path_maker
     def gene_path_maker(self, sample_id):
         return "%s/gene_mapping_data.txt" % sample_id
-
-    @stats.set_path_maker
-    def stats_path_maker(self, sample_id):
-        return "%s/overall_mapping_stats.txt" % sample_id