added new amrfinder directory and moved types to card directory

bokulich-lab · Jun 28, 2024 · d33e0cb · d33e0cb
1 parent 5ace3a6
commit d33e0cb
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Showing 74 changed files with 92 additions and 25 deletions.
diff --git a/q2_amr/types/tests/__init__.py → q2_amr/amrfinderplus/__init__.py b/q2_amr/types/tests/__init__.py → q2_amr/amrfinderplus/__init__.py
diff --git a/q2_amr/amrfinderplus/tests/__init__.py b/q2_amr/amrfinderplus/tests/__init__.py
@@ -0,0 +1,7 @@
+# ----------------------------------------------------------------------------
+# Copyright (c) 2019-2023, QIIME 2 development team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# ----------------------------------------------------------------------------
diff --git a/q2_amr/amrfinderplus/types/__init__.py b/q2_amr/amrfinderplus/types/__init__.py
@@ -0,0 +1,9 @@
+# ----------------------------------------------------------------------------
+# Copyright (c) 2019-2023, QIIME 2 development team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# ----------------------------------------------------------------------------
+
+__all__ = []
diff --git a/q2_amr/amrfinderplus/types/_format.py b/q2_amr/amrfinderplus/types/_format.py
@@ -0,0 +1,7 @@
+# ----------------------------------------------------------------------------
+# Copyright (c) 2019-2023, QIIME 2 development team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# ----------------------------------------------------------------------------
diff --git a/q2_amr/amrfinderplus/types/_transformer.py b/q2_amr/amrfinderplus/types/_transformer.py
@@ -0,0 +1,7 @@
+# ----------------------------------------------------------------------------
+# Copyright (c) 2019-2023, QIIME 2 development team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# ----------------------------------------------------------------------------
diff --git a/q2_amr/amrfinderplus/types/_type.py b/q2_amr/amrfinderplus/types/_type.py
@@ -0,0 +1,10 @@
+# ----------------------------------------------------------------------------
+# Copyright (c) 2019-2023, QIIME 2 development team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# ----------------------------------------------------------------------------
+from qiime2.core.type import SemanticType
+
+AMRFinderPlusDatabase = SemanticType("AMRFinderPlusDatabase")
diff --git a/q2_amr/amrfinderplus/types/tests/__init__.py b/q2_amr/amrfinderplus/types/tests/__init__.py
@@ -0,0 +1,7 @@
+# ----------------------------------------------------------------------------
+# Copyright (c) 2019-2023, QIIME 2 development team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# ----------------------------------------------------------------------------
diff --git a/q2_amr/amrfinderplus/types/tests/test_types_formats_transformers.py b/q2_amr/amrfinderplus/types/tests/test_types_formats_transformers.py
@@ -0,0 +1,7 @@
+# ----------------------------------------------------------------------------
+# Copyright (c) 2019-2023, QIIME 2 development team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# ----------------------------------------------------------------------------
diff --git a/q2_amr/card/database.py b/q2_amr/card/database.py
@@ -9,11 +9,11 @@
 import requests
 from tqdm import tqdm
 
-from q2_amr.card.utils import colorify, run_command
-from q2_amr.types._format import (
+from q2_amr.card.types._format import (
     CARDDatabaseDirectoryFormat,
     CARDKmerDatabaseDirectoryFormat,
 )
+from q2_amr.card.utils import colorify, run_command
 
 
 def fetch_card_db() -> (CARDDatabaseDirectoryFormat, CARDKmerDatabaseDirectoryFormat):

diff --git a/q2_amr/card/heatmap.py b/q2_amr/card/heatmap.py
@@ -8,8 +8,8 @@
 import pkg_resources
 import q2templates
 
+from q2_amr.card.types import CARDAnnotationDirectoryFormat
 from q2_amr.card.utils import run_command
-from q2_amr.types import CARDAnnotationDirectoryFormat
 
 
 def heatmap(

diff --git a/q2_amr/card/mags.py b/q2_amr/card/mags.py
@@ -6,8 +6,8 @@
 import pandas as pd
 from q2_types.per_sample_sequences import MultiMAGSequencesDirFmt
 
+from q2_amr.card.types import CARDAnnotationDirectoryFormat, CARDDatabaseDirectoryFormat
 from q2_amr.card.utils import create_count_table, load_card_db, read_in_txt, run_command
-from q2_amr.types import CARDAnnotationDirectoryFormat, CARDDatabaseDirectoryFormat
 
 
 def annotate_mags_card(

diff --git a/q2_amr/card/partition.py b/q2_amr/card/partition.py
@@ -5,15 +5,15 @@
 import numpy as np
 from qiime2.util import duplicate
 
-from q2_amr.card.utils import copy_files
-from q2_amr.types import (
+from q2_amr.card.types import (
     CARDAlleleAnnotationDirectoryFormat,
     CARDAnnotationDirectoryFormat,
     CARDGeneAnnotationDirectoryFormat,
     CARDMAGsKmerAnalysisDirectoryFormat,
     CARDReadsAlleleKmerAnalysisDirectoryFormat,
     CARDReadsGeneKmerAnalysisDirectoryFormat,
 )
+from q2_amr.card.utils import copy_files
 
 
 def collate_mags_annotations(

diff --git a/q2_amr/card/reads.py b/q2_amr/card/reads.py
@@ -10,12 +10,12 @@
     SingleLanePerSampleSingleEndFastqDirFmt,
 )
 
-from q2_amr.card.utils import create_count_table, load_card_db, read_in_txt, run_command
-from q2_amr.types import (
+from q2_amr.card.types import (
     CARDAlleleAnnotationDirectoryFormat,
     CARDDatabaseDirectoryFormat,
     CARDGeneAnnotationDirectoryFormat,
 )
+from q2_amr.card.utils import create_count_table, load_card_db, read_in_txt, run_command
 
 
 def annotate_reads_card(

diff --git a/q2_amr/card/tests/test_database.py b/q2_amr/card/tests/test_database.py
@@ -8,7 +8,10 @@
 from qiime2.plugin.testing import TestPluginBase
 
 from q2_amr.card.database import download_with_progress_bar, fetch_card_db, preprocess
-from q2_amr.types import CARDDatabaseDirectoryFormat, CARDKmerDatabaseDirectoryFormat
+from q2_amr.card.types import (
+    CARDDatabaseDirectoryFormat,
+    CARDKmerDatabaseDirectoryFormat,
+)
 
 
 class TestAnnotateMagsCard(TestPluginBase):

diff --git a/q2_amr/card/tests/test_heatmap.py b/q2_amr/card/tests/test_heatmap.py
@@ -10,7 +10,7 @@
     heatmap,
     run_rgi_heatmap,
 )
-from q2_amr.types import CARDAnnotationDirectoryFormat
+from q2_amr.card.types import CARDAnnotationDirectoryFormat
 
 
 class TestHeatmap(TestPluginBase):

diff --git a/q2_amr/card/tests/test_mags.py b/q2_amr/card/tests/test_mags.py
@@ -7,7 +7,7 @@
 from qiime2.plugin.testing import TestPluginBase
 
 from q2_amr.card.mags import annotate_mags_card, run_rgi_main
-from q2_amr.types import CARDAnnotationDirectoryFormat, CARDDatabaseDirectoryFormat
+from q2_amr.card.types import CARDAnnotationDirectoryFormat, CARDDatabaseDirectoryFormat
 
 
 class TestAnnotateMagsCard(TestPluginBase):

diff --git a/q2_amr/card/tests/test_partition.py b/q2_amr/card/tests/test_partition.py
@@ -13,7 +13,7 @@
     partition_reads_allele_annotations,
     partition_reads_gene_annotations,
 )
-from q2_amr.types import (
+from q2_amr.card.types import (
     CARDAlleleAnnotationDirectoryFormat,
     CARDAnnotationDirectoryFormat,
     CARDGeneAnnotationDirectoryFormat,

diff --git a/q2_amr/card/tests/test_reads.py b/q2_amr/card/tests/test_reads.py
@@ -10,7 +10,7 @@
 from qiime2.plugin.testing import TestPluginBase
 
 from q2_amr.card.reads import annotate_reads_card, run_rgi_bwt
-from q2_amr.types import (
+from q2_amr.card.types import (
     CARDAlleleAnnotationDirectoryFormat,
     CARDDatabaseDirectoryFormat,
     CARDGeneAnnotationDirectoryFormat,

diff --git a/q2_amr/card/tests/test_utils.py b/q2_amr/card/tests/test_utils.py
@@ -6,14 +6,17 @@
 import pandas as pd
 from qiime2.plugin.testing import TestPluginBase
 
+from q2_amr.card.types import (
+    CARDDatabaseDirectoryFormat,
+    CARDKmerDatabaseDirectoryFormat,
+)
 from q2_amr.card.utils import (
     colorify,
     copy_files,
     create_count_table,
     load_card_db,
     read_in_txt,
 )
-from q2_amr.types import CARDDatabaseDirectoryFormat, CARDKmerDatabaseDirectoryFormat
 
 
 class TestAnnotateReadsCARD(TestPluginBase):

diff --git a/q2_amr/types/__init__.py → q2_amr/card/types/__init__.py b/q2_amr/types/__init__.py → q2_amr/card/types/__init__.py
diff --git a/q2_amr/types/_format.py → q2_amr/card/types/_format.py b/q2_amr/types/_format.py → q2_amr/card/types/_format.py
diff --git a/q2_amr/types/_transformer.py → q2_amr/card/types/_transformer.py b/q2_amr/types/_transformer.py → q2_amr/card/types/_transformer.py
@@ -18,9 +18,9 @@
 from q2_types.genome_data import GenesDirectoryFormat, ProteinsDirectoryFormat
 from skbio import DNA, Protein
 
-from q2_amr.types import CARDAnnotationDirectoryFormat
+from q2_amr.card.types import CARDAnnotationDirectoryFormat
+from q2_amr.plugin_setup import plugin
 
-from ..plugin_setup import plugin
 from ._format import (
     CARDAlleleAnnotationDirectoryFormat,
     CARDAnnotationJSONFormat,

diff --git a/q2_amr/types/_type.py → q2_amr/card/types/_type.py b/q2_amr/types/_type.py → q2_amr/card/types/_type.py
diff --git a/q2_amr/card/types/tests/__init__.py b/q2_amr/card/types/tests/__init__.py
@@ -0,0 +1,7 @@
+# ----------------------------------------------------------------------------
+# Copyright (c) 2019-2023, QIIME 2 development team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# ----------------------------------------------------------------------------
diff --git a/...ypes/tests/data/61mer_analysis.allele.txt → ...ypes/tests/data/61mer_analysis.allele.txt b/...ypes/tests/data/61mer_analysis.allele.txt → ...ypes/tests/data/61mer_analysis.allele.txt
diff --git a/.../types/tests/data/61mer_analysis.gene.txt → .../types/tests/data/61mer_analysis.gene.txt b/.../types/tests/data/61mer_analysis.gene.txt → .../types/tests/data/61mer_analysis.gene.txt
diff --git a/...tests/data/61mer_analysis_rgi_summary.txt → ...tests/data/61mer_analysis_rgi_summary.txt b/...tests/data/61mer_analysis_rgi_summary.txt → ...tests/data/61mer_analysis_rgi_summary.txt
diff --git a/q2_amr/types/tests/data/DNA_fasta.fasta → q2_amr/card/types/tests/data/DNA_fasta.fasta b/q2_amr/types/tests/data/DNA_fasta.fasta → q2_amr/card/types/tests/data/DNA_fasta.fasta
diff --git a/q2_amr/types/tests/data/DNA_fasta_-.fasta → ...r/card/types/tests/data/DNA_fasta_-.fasta b/q2_amr/types/tests/data/DNA_fasta_-.fasta → ...r/card/types/tests/data/DNA_fasta_-.fasta
diff --git a/...nnotation/sample1/allele_mapping_data.txt → ...nnotation/sample1/allele_mapping_data.txt b/...nnotation/sample1/allele_mapping_data.txt → ...nnotation/sample1/allele_mapping_data.txt
diff --git a/...otation/sample1/overall_mapping_stats.txt → ...otation/sample1/overall_mapping_stats.txt b/...otation/sample1/overall_mapping_stats.txt → ...otation/sample1/overall_mapping_stats.txt
diff --git a/..._annotation/sample1/sorted.length_100.bam → ..._annotation/sample1/sorted.length_100.bam b/..._annotation/sample1/sorted.length_100.bam → ..._annotation/sample1/sorted.length_100.bam
diff --git a/...nnotation/sample2/allele_mapping_data.txt → ...nnotation/sample2/allele_mapping_data.txt b/...nnotation/sample2/allele_mapping_data.txt → ...nnotation/sample2/allele_mapping_data.txt
diff --git a/...otation/sample2/overall_mapping_stats.txt → ...otation/sample2/overall_mapping_stats.txt b/...otation/sample2/overall_mapping_stats.txt → ...otation/sample2/overall_mapping_stats.txt
diff --git a/..._annotation/sample2/sorted.length_100.bam → ..._annotation/sample2/sorted.length_100.bam b/..._annotation/sample2/sorted.length_100.bam → ..._annotation/sample2/sorted.length_100.bam
diff --git a/...de3-a957-7e8bf837f30d/amr_annotation.json → ...de3-a957-7e8bf837f30d/amr_annotation.json b/...de3-a957-7e8bf837f30d/amr_annotation.json → ...de3-a957-7e8bf837f30d/amr_annotation.json
diff --git a/...4de3-a957-7e8bf837f30d/amr_annotation.txt → ...4de3-a957-7e8bf837f30d/amr_annotation.txt b/...4de3-a957-7e8bf837f30d/amr_annotation.txt → ...4de3-a957-7e8bf837f30d/amr_annotation.txt
diff --git a/...c4a-a53b-4df6999815dd/amr_annotation.json → ...c4a-a53b-4df6999815dd/amr_annotation.json b/...c4a-a53b-4df6999815dd/amr_annotation.json → ...c4a-a53b-4df6999815dd/amr_annotation.json
diff --git a/...4c4a-a53b-4df6999815dd/amr_annotation.txt → ...4c4a-a53b-4df6999815dd/amr_annotation.txt b/...4c4a-a53b-4df6999815dd/amr_annotation.txt → ...4c4a-a53b-4df6999815dd/amr_annotation.txt
diff --git a/...9f9-875e-620f333a9293/amr_annotation.json → ...9f9-875e-620f333a9293/amr_annotation.json b/...9f9-875e-620f333a9293/amr_annotation.json → ...9f9-875e-620f333a9293/amr_annotation.json
diff --git a/...49f9-875e-620f333a9293/amr_annotation.txt → ...49f9-875e-620f333a9293/amr_annotation.txt b/...49f9-875e-620f333a9293/amr_annotation.txt → ...49f9-875e-620f333a9293/amr_annotation.txt
diff --git a/..._annotation/sample1/gene_mapping_data.txt → ..._annotation/sample1/gene_mapping_data.txt b/..._annotation/sample1/gene_mapping_data.txt → ..._annotation/sample1/gene_mapping_data.txt
diff --git a/..._annotation/sample2/gene_mapping_data.txt → ..._annotation/sample2/gene_mapping_data.txt b/..._annotation/sample2/gene_mapping_data.txt → ..._annotation/sample2/gene_mapping_data.txt
diff --git a/...mple1/bin1/61mer_analysis_rgi_summary.txt → ...mple1/bin1/61mer_analysis_rgi_summary.txt b/...mple1/bin1/61mer_analysis_rgi_summary.txt → ...mple1/bin1/61mer_analysis_rgi_summary.txt
diff --git a/...de3-a957-7e8bf837f30d/61mer_analysis.json → ...de3-a957-7e8bf837f30d/61mer_analysis.json b/...de3-a957-7e8bf837f30d/61mer_analysis.json → ...de3-a957-7e8bf837f30d/61mer_analysis.json
diff --git a/...8bf837f30d/61mer_analysis_rgi_summary.txt → ...8bf837f30d/61mer_analysis_rgi_summary.txt b/...8bf837f30d/61mer_analysis_rgi_summary.txt → ...8bf837f30d/61mer_analysis_rgi_summary.txt
diff --git a/...c4a-a53b-4df6999815dd/61mer_analysis.json → ...c4a-a53b-4df6999815dd/61mer_analysis.json b/...c4a-a53b-4df6999815dd/61mer_analysis.json → ...c4a-a53b-4df6999815dd/61mer_analysis.json
diff --git a/...f6999815dd/61mer_analysis_rgi_summary.txt → ...f6999815dd/61mer_analysis_rgi_summary.txt b/...f6999815dd/61mer_analysis_rgi_summary.txt → ...f6999815dd/61mer_analysis_rgi_summary.txt
diff --git a/...9f9-875e-620f333a9293/61mer_analysis.json → ...9f9-875e-620f333a9293/61mer_analysis.json b/...9f9-875e-620f333a9293/61mer_analysis.json → ...9f9-875e-620f333a9293/61mer_analysis.json
diff --git a/...0f333a9293/61mer_analysis_rgi_summary.txt → ...0f333a9293/61mer_analysis_rgi_summary.txt b/...0f333a9293/61mer_analysis_rgi_summary.txt → ...0f333a9293/61mer_analysis_rgi_summary.txt
diff --git a/...nalysis/sample1/61mer_analysis.allele.txt → ...nalysis/sample1/61mer_analysis.allele.txt b/...nalysis/sample1/61mer_analysis.allele.txt → ...nalysis/sample1/61mer_analysis.allele.txt
diff --git a/...kmer_analysis/sample1/61mer_analysis.json → ...kmer_analysis/sample1/61mer_analysis.json b/...kmer_analysis/sample1/61mer_analysis.json → ...kmer_analysis/sample1/61mer_analysis.json
diff --git a/...nalysis/sample2/61mer_analysis.allele.txt → ...nalysis/sample2/61mer_analysis.allele.txt b/...nalysis/sample2/61mer_analysis.allele.txt → ...nalysis/sample2/61mer_analysis.allele.txt
diff --git a/...kmer_analysis/sample2/61mer_analysis.json → ...kmer_analysis/sample2/61mer_analysis.json b/...kmer_analysis/sample2/61mer_analysis.json → ...kmer_analysis/sample2/61mer_analysis.json
diff --git a/..._analysis/sample1/61mer_analysis.gene.txt → ..._analysis/sample1/61mer_analysis.gene.txt b/..._analysis/sample1/61mer_analysis.gene.txt → ..._analysis/sample1/61mer_analysis.gene.txt
diff --git a/..._analysis/sample2/61mer_analysis.gene.txt → ..._analysis/sample2/61mer_analysis.gene.txt b/..._analysis/sample2/61mer_analysis.gene.txt → ..._analysis/sample2/61mer_analysis.gene.txt
diff --git a/q2_amr/types/tests/data/card_test.json → q2_amr/card/types/tests/data/card_test.json b/q2_amr/types/tests/data/card_test.json → q2_amr/card/types/tests/data/card_test.json
diff --git a/q2_amr/types/tests/data/card_test_dna.fasta → ...card/types/tests/data/card_test_dna.fasta b/q2_amr/types/tests/data/card_test_dna.fasta → ...card/types/tests/data/card_test_dna.fasta
diff --git a/.../types/tests/data/card_test_protein.fasta → .../types/tests/data/card_test_protein.fasta b/.../types/tests/data/card_test_protein.fasta → .../types/tests/data/card_test_protein.fasta
diff --git a/q2_amr/types/tests/data/empty_dict.json → q2_amr/card/types/tests/data/empty_dict.json b/q2_amr/types/tests/data/empty_dict.json → q2_amr/card/types/tests/data/empty_dict.json
diff --git a/...s/data/index-for-model-sequences-test.txt → ...s/data/index-for-model-sequences-test.txt b/...s/data/index-for-model-sequences-test.txt → ...s/data/index-for-model-sequences-test.txt
diff --git a/q2_amr/types/tests/data/kmer_json_test.json → ...card/types/tests/data/kmer_json_test.json b/q2_amr/types/tests/data/kmer_json_test.json → ...card/types/tests/data/kmer_json_test.json
diff --git a/q2_amr/types/tests/data/kmer_txt_test.txt → ...r/card/types/tests/data/kmer_txt_test.txt b/q2_amr/types/tests/data/kmer_txt_test.txt → ...r/card/types/tests/data/kmer_txt_test.txt
diff --git a/...types/tests/data/mags_61mer_analysis.json → ...types/tests/data/mags_61mer_analysis.json b/...types/tests/data/mags_61mer_analysis.json → ...types/tests/data/mags_61mer_analysis.json
diff --git a/...ypes/tests/data/reads_61mer_analysis.json → ...ypes/tests/data/reads_61mer_analysis.json b/...ypes/tests/data/reads_61mer_analysis.json → ...ypes/tests/data/reads_61mer_analysis.json
diff --git a/q2_amr/types/tests/data/rgi_output.json → q2_amr/card/types/tests/data/rgi_output.json b/q2_amr/types/tests/data/rgi_output.json → q2_amr/card/types/tests/data/rgi_output.json
diff --git a/q2_amr/types/tests/data/rgi_output.txt → q2_amr/card/types/tests/data/rgi_output.txt b/q2_amr/types/tests/data/rgi_output.txt → q2_amr/card/types/tests/data/rgi_output.txt
diff --git a/q2_amr/types/tests/data/rgi_output_dna.fna → .../card/types/tests/data/rgi_output_dna.fna b/q2_amr/types/tests/data/rgi_output_dna.fna → .../card/types/tests/data/rgi_output_dna.fna
diff --git a/...r/types/tests/data/rgi_output_protein.fna → ...d/types/tests/data/rgi_output_protein.fna b/...r/types/tests/data/rgi_output_protein.fna → ...d/types/tests/data/rgi_output_protein.fna
diff --git a/.../types/tests/data/tabulated_df_allele.txt → .../types/tests/data/tabulated_df_allele.txt b/.../types/tests/data/tabulated_df_allele.txt → .../types/tests/data/tabulated_df_allele.txt
diff --git a/...mr/types/tests/data/tabulated_df_mags.txt → ...rd/types/tests/data/tabulated_df_mags.txt b/...mr/types/tests/data/tabulated_df_mags.txt → ...rd/types/tests/data/tabulated_df_mags.txt
diff --git a/.../tests/test_types_formats_transformers.py → .../tests/test_types_formats_transformers.py b/.../tests/test_types_formats_transformers.py → .../tests/test_types_formats_transformers.py
@@ -24,12 +24,12 @@
 from qiime2.plugin.testing import TestPluginBase
 from skbio import DNA, Protein
 
-from q2_amr.types import (
+from q2_amr.card.types import (
     CARDAlleleAnnotationDirectoryFormat,
     CARDDatabaseDirectoryFormat,
     CARDGeneAnnotationDirectoryFormat,
 )
-from q2_amr.types._format import (
+from q2_amr.card.types._format import (
     CARDAnnotationDirectoryFormat,
     CARDAnnotationTXTFormat,
     CARDDatabaseFormat,
@@ -47,7 +47,7 @@
     CARDWildcardIndexFormat,
     GapDNAFASTAFormat,
 )
-from q2_amr.types._transformer import (
+from q2_amr.card.types._transformer import (
     _read_from_card_file,
     card_annotation_df_to_fasta,
     extract_sequence,
@@ -56,7 +56,7 @@
 
 
 class AMRTypesTestPluginBase(TestPluginBase):
-    package = "q2_amr.types.tests"
+    package = "q2_amr.card.types.tests"
 
     def setUp(self):
         super().setUp()

diff --git a/q2_amr/plugin_setup.py b/q2_amr/plugin_setup.py
@@ -43,14 +43,14 @@
     partition_reads_gene_annotations,
 )
 from q2_amr.card.reads import annotate_reads_card
-from q2_amr.types import (
+from q2_amr.card.types import (
     CARDAnnotationJSONFormat,
     CARDAnnotationTXTFormat,
     CARDDatabase,
     CARDDatabaseDirectoryFormat,
     CARDDatabaseFormat,
 )
-from q2_amr.types._format import (
+from q2_amr.card.types._format import (
     CARDAlleleAnnotationDirectoryFormat,
     CARDAlleleAnnotationFormat,
     CARDAnnotationDirectoryFormat,
@@ -71,7 +71,7 @@
     CARDWildcardIndexFormat,
     GapDNAFASTAFormat,
 )
-from q2_amr.types._type import (
+from q2_amr.card.types._type import (
     CARDAlleleAnnotation,
     CARDAnnotation,
     CARDGeneAnnotation,
@@ -524,4 +524,4 @@
     CARDReadsAlleleKmerAnalysisDirectoryFormat,
 )
 
-importlib.import_module("q2_amr.types._transformer")
+importlib.import_module("q2_amr.card.types._transformer")
diff --git a/setup.py b/setup.py
@@ -28,7 +28,7 @@
             "assets/rgi/annotation_stats/*",
             "assets/rgi/heatmap/*",
         ],
-        "q2_amr.types.tests": [
+        "q2_amr.card.types.tests": [
             "data/*",
             "data/*/*/*",
             "data/*/*/*/*",