From 6844065f3e90358471c0fc67b041fdfd321773a9 Mon Sep 17 00:00:00 2001
From: VinzentRisch <100149044+VinzentRisch@users.noreply.github.com>
Date: Mon, 16 Oct 2023 16:41:51 +0200
Subject: [PATCH] FIX: Fixed q2-amr failing, if no ARGs are detected (#9)

-Fixed the problem of q2-amr failing if no ARGs are detected with annotate_reads_card or annotate_mags_card methods. Now the user is informed that no ARGs where detected and no further output is produced.
-Removed mapq, mapped and coverage parameters from annotate_reads_card method.
-Added CARDGeneAnnotationDirectoryFormat/CARDGeneAnnotationDirectoryFormat-> qiime2.Metadata transformer .
-Fixed bug in heatmap method. Parameters clus and cat can not be used at the same time.
---
 q2_amr/assets/rgi/heatmap/index.html          |  22 ++-
 q2_amr/card/heatmap.py                        | 102 ++++++++++++
 q2_amr/card/mags.py                           |  39 +++--
 q2_amr/card/reads.py                          |  70 ++------
 q2_amr/card/utils.py                          |  32 ++++
 q2_amr/plugin_setup.py                        |  99 ++++++-----
 q2_amr/tests/card/test_database.py            |  22 +--
 q2_amr/tests/card/test_heatmap.py             | 113 +++++++++++++
 q2_amr/tests/card/test_mags.py                |  94 +++++++----
 q2_amr/tests/card/test_reads.py               | 157 +++++-------------
 q2_amr/tests/card/test_utils.py               |  72 +++++++-
 q2_amr/tests/data/output.mags.txt             |   5 +
 q2_amr/types/_transformer.py                  |  39 ++++-
 q2_amr/types/_type.py                         |   8 +-
 ...mr_annotation.json => amr_annotation.json} |   0
 ..._amr_annotation.txt => amr_annotation.txt} |   0
 ...mr_annotation.json => amr_annotation.json} |   0
 ..._amr_annotation.txt => amr_annotation.txt} |   4 +-
 ...pping_data.txt => allele_mapping_data.txt} |   0
 ...mapping_data.txt => gene_mapping_data.txt} |   0
 ...ng_stats.txt => overall_mapping_stats.txt} |   0
 ...pping_data.txt => allele_mapping_data.txt} |   0
 ...mapping_data.txt => gene_mapping_data.txt} |   0
 ...ng_stats.txt => overall_mapping_stats.txt} |   0
 .../tests/test_types_formats_transformers.py  |  10 ++
 25 files changed, 608 insertions(+), 280 deletions(-)
 create mode 100644 q2_amr/card/heatmap.py
 create mode 100644 q2_amr/tests/card/test_heatmap.py
 create mode 100644 q2_amr/tests/data/output.mags.txt
 rename q2_amr/types/tests/data/annotate_mags_output/sample1/bin1/{sample1_bin1_amr_annotation.json => amr_annotation.json} (100%)
 rename q2_amr/types/tests/data/annotate_mags_output/sample1/bin1/{sample1_bin1_amr_annotation.txt => amr_annotation.txt} (100%)
 rename q2_amr/types/tests/data/annotate_mags_output/sample2/bin1/{sample2_bin1_amr_annotation.json => amr_annotation.json} (100%)
 rename q2_amr/types/tests/data/annotate_mags_output/sample2/bin1/{sample2_bin1_amr_annotation.txt => amr_annotation.txt} (96%)
 rename q2_amr/types/tests/data/annotate_reads_output/sample1/{sample1.allele_mapping_data.txt => allele_mapping_data.txt} (100%)
 rename q2_amr/types/tests/data/annotate_reads_output/sample1/{sample1.gene_mapping_data.txt => gene_mapping_data.txt} (100%)
 rename q2_amr/types/tests/data/annotate_reads_output/sample1/{sample1.overall_mapping_stats.txt => overall_mapping_stats.txt} (100%)
 rename q2_amr/types/tests/data/annotate_reads_output/sample2/{sample2.allele_mapping_data.txt => allele_mapping_data.txt} (100%)
 rename q2_amr/types/tests/data/annotate_reads_output/sample2/{sample2.gene_mapping_data.txt => gene_mapping_data.txt} (100%)
 rename q2_amr/types/tests/data/annotate_reads_output/sample2/{sample2.overall_mapping_stats.txt => overall_mapping_stats.txt} (100%)

diff --git a/q2_amr/assets/rgi/heatmap/index.html b/q2_amr/assets/rgi/heatmap/index.html
index 722c6f6..3e92f86 100644
--- a/q2_amr/assets/rgi/heatmap/index.html
+++ b/q2_amr/assets/rgi/heatmap/index.html
@@ -1,10 +1,10 @@
-{% extends 'tabbed.html' %}
+{% extends 'base.html' %}
 
-{% block tabcontent %}
+{% block content %}
 
   <div class="row">
     <div class="col-lg-12">
-      <h3>Downloads</h3>
+      <h4>Downloads</h4>
     </div>
   </div>
 
@@ -16,15 +16,27 @@ <h3>Downloads</h3>
           </div>
       </div>
   </div>
-  <br>
+
+<br>
 
 <div class="row">
   <div class="col-lg-6">
-    <h3>My Picture</h3>
+    <h4>CARD annotation: heatmap</h4>
     <img src="rgi_data/heatmap.png" alt="My Picture">
   </div>
 </div>
 
+<br>
+
+<div class="row mt-4">
+    <div class="col-lg-12">
+        <p>Displayed is a heatmap of annotate-mags-card output. <br>
+            Yellow represents a perfect hit, teal represents a <br>
+            strict hit, purple represents no hit.</p>
+    </div>
+</div>
+
+
 {% endblock %}
 
 {% block footer %}
diff --git a/q2_amr/card/heatmap.py b/q2_amr/card/heatmap.py
new file mode 100644
index 0000000..02e583d
--- /dev/null
+++ b/q2_amr/card/heatmap.py
@@ -0,0 +1,102 @@
+import glob
+import os
+import shutil
+import subprocess
+import tempfile
+from distutils.dir_util import copy_tree
+
+import pkg_resources
+import q2templates
+
+from q2_amr.card.utils import run_command
+from q2_amr.types import CARDAnnotationDirectoryFormat
+
+
+def heatmap(
+    output_dir: str,
+    amr_annotation: CARDAnnotationDirectoryFormat,
+    clus: str = None,
+    cat: str = None,
+    display: str = "plain",
+    frequency: bool = False,
+):
+    TEMPLATES = pkg_resources.resource_filename("q2_amr", "assets")
+    annotation_dir = str(amr_annotation)
+    with tempfile.TemporaryDirectory() as tmp:
+        results_dir = os.path.join(tmp, "results")
+        json_files_dir = os.path.join(tmp, "json_files")
+        os.makedirs(results_dir)
+        os.makedirs(json_files_dir)
+        for json_file in glob.glob(os.path.join(annotation_dir, "*", "*", "*.json")):
+            sample, bin_name, _ = json_file.split(os.path.sep)[-3:]
+            destination_path = os.path.join(json_files_dir, f"{sample}_{bin_name}")
+            shutil.copy(json_file, destination_path)
+
+        run_rgi_heatmap(tmp, json_files_dir, clus, cat, display, frequency)
+        change_names(results_dir)
+        copy_tree(os.path.join(TEMPLATES, "rgi", "heatmap"), output_dir)
+        copy_tree(results_dir, os.path.join(output_dir, "rgi_data"))
+    context = {"tabs": [{"title": "Heatmap", "url": "index.html"}]}
+    index = os.path.join(TEMPLATES, "rgi", "heatmap", "index.html")
+    templates = [index]
+    q2templates.render(templates, output_dir, context=context)
+
+
+class InvalidParameterCombinationError(Exception):
+    def __init__(self, message="Invalid parameter combination"):
+        self.message = message
+        super().__init__(self.message)
+
+
+def run_rgi_heatmap(tmp, json_files_dir, clus, cat, display, frequency):
+    cmd = [
+        "rgi",
+        "heatmap",
+        "--input",
+        json_files_dir,
+        "--output",
+        f"{tmp}/results/heatmap",
+        "--display",
+        display,
+    ]
+    if (clus == "both" or clus == "genes") and cat:
+        raise InvalidParameterCombinationError(
+            "If the parameter clus is set to genes "
+            "or both it is not possible to use the "
+            "cat parameter"
+        )
+    if clus:
+        cmd.extend(["--clus", clus])
+    if cat:
+        cmd.extend(["--cat", cat])
+    if frequency:
+        cmd.append("--frequency")
+    try:
+        run_command(cmd, tmp, verbose=True)
+    except subprocess.CalledProcessError as e:
+        raise Exception(
+            "An error was encountered while running rgi, "
+            f"(return code {e.returncode}), please inspect "
+            "stdout and stderr to learn more."
+        )
+
+
+def change_names(results_dir):
+    """
+    This function changes the names of the output files of the "rgi heatmap" function.
+    The output files are called heatmap-*.extension with * being the number of samples
+    included in the heatmap. The files are changed to heatmap.extension so that they
+    can be accessed in the index.html file more easily.
+
+    Parameters:
+    - results_dir (str): The directory where the files are stored.
+    """
+    extensions = [".eps", ".csv", ".png"]
+    files = os.listdir(results_dir)
+    for filename in files:
+        if os.path.splitext(filename)[1] in extensions:
+            file_ext = os.path.splitext(filename)[1]
+            new_filename = "heatmap" + file_ext
+            old_path = os.path.join(results_dir, filename)
+            new_path = os.path.join(results_dir, new_filename)
+            os.rename(old_path, new_path)
diff --git a/q2_amr/card/mags.py b/q2_amr/card/mags.py
index 45057e0..3198775 100644
--- a/q2_amr/card/mags.py
+++ b/q2_amr/card/mags.py
@@ -6,7 +6,12 @@
 import pandas as pd
 from q2_types_genomics.per_sample_data import MultiMAGSequencesDirFmt
 
-from q2_amr.card.utils import load_preprocess_card_db, run_command
+from q2_amr.card.utils import (
+    create_count_table,
+    load_preprocess_card_db,
+    read_in_txt,
+    run_command,
+)
 from q2_amr.types import CARDAnnotationDirectoryFormat, CARDDatabaseFormat
 
 
@@ -14,15 +19,15 @@ def annotate_mags_card(
     mag: MultiMAGSequencesDirFmt,
     card_db: CARDDatabaseFormat,
     alignment_tool: str = "BLAST",
-    input_type: str = "contig",
     split_prodigal_jobs: bool = False,
     include_loose: bool = False,
     include_nudge: bool = False,
     low_quality: bool = False,
-    num_threads: int = 1,
-) -> CARDAnnotationDirectoryFormat:
+    threads: int = 1,
+) -> (CARDAnnotationDirectoryFormat, pd.DataFrame):
     manifest = mag.manifest.view(pd.DataFrame)
     amr_annotations = CARDAnnotationDirectoryFormat()
+    frequency_list = []
     with tempfile.TemporaryDirectory() as tmp:
         load_preprocess_card_db(tmp, card_db, "load")
         for samp_bin in list(manifest.index):
@@ -33,24 +38,34 @@ def annotate_mags_card(
                 tmp,
                 input_sequence,
                 alignment_tool,
-                input_type,
                 split_prodigal_jobs,
                 include_loose,
                 include_nudge,
                 low_quality,
-                num_threads,
+                threads,
+            )
+            txt_path = os.path.join(bin_dir, "amr_annotation.txt")
+            json_path = os.path.join(bin_dir, "amr_annotation.json")
+
+            shutil.move(f"{tmp}/output.txt", txt_path)
+            shutil.move(f"{tmp}/output.json", json_path)
+            samp_bin_name = os.path.join(samp_bin[0], samp_bin[1])
+            frequency_df = read_in_txt(
+                path=txt_path, col_name="ARO", samp_bin_name=samp_bin_name
             )
-            shutil.move(f"{tmp}/output.txt", f"{bin_dir}/amr_annotation.txt")
-            shutil.move(f"{tmp}/output.json", f"{bin_dir}/amr_annotation.json")
-    print("a")
-    return amr_annotations
+            if frequency_df is not None:
+                frequency_list.append(frequency_df)
+        feature_table = create_count_table(df_list=frequency_list)
+    return (
+        amr_annotations,
+        feature_table,
+    )
 
 
 def run_rgi_main(
     tmp,
     input_sequence: str,
     alignment_tool: str = "BLAST",
-    input_type: str = "contig",
     split_prodigal_jobs: bool = False,
     include_loose: bool = False,
     include_nudge: bool = False,
@@ -69,7 +84,7 @@ def run_rgi_main(
         "--alignment_tool",
         alignment_tool,
         "--input_type",
-        input_type,
+        "contig",
         "--local",
     ]
     if include_loose:
diff --git a/q2_amr/card/reads.py b/q2_amr/card/reads.py
index 1fc0dab..a1a5a65 100644
--- a/q2_amr/card/reads.py
+++ b/q2_amr/card/reads.py
@@ -3,7 +3,6 @@
 import subprocess
 import tempfile
 from distutils.dir_util import copy_tree
-from functools import reduce
 from typing import Union
 
 import altair as alt
@@ -15,7 +14,12 @@
     SingleLanePerSampleSingleEndFastqDirFmt,
 )
 
-from q2_amr.card.utils import load_preprocess_card_db, run_command
+from q2_amr.card.utils import (
+    create_count_table,
+    load_preprocess_card_db,
+    read_in_txt,
+    run_command,
+)
 from q2_amr.types import (
     CARDAlleleAnnotationDirectoryFormat,
     CARDDatabaseFormat,
@@ -30,10 +34,6 @@ def annotate_reads_card(
     card_db: CARDDatabaseFormat,
     aligner: str = "kma",
     threads: int = 1,
-    include_baits: bool = False,
-    mapq: float = None,
-    mapped: float = None,
-    coverage: float = None,
 ) -> (
     CARDAlleleAnnotationDirectoryFormat,
     CARDGeneAnnotationDirectoryFormat,
@@ -65,15 +65,19 @@ def annotate_reads_card(
                 rev=rev,
                 aligner=aligner,
                 threads=threads,
-                include_baits=include_baits,
-                mapq=mapq,
-                mapped=mapped,
-                coverage=coverage,
             )
-            allele_frequency = read_in_txt(samp_input_dir, "allele")
-            allele_frequency_list.append(allele_frequency)
-            gene_frequency = read_in_txt(samp_input_dir, "gene")
-            gene_frequency_list.append(gene_frequency)
+            path_allele = os.path.join(samp_input_dir, "output.allele_mapping_data.txt")
+            allele_frequency = read_in_txt(
+                path=path_allele, col_name="ARO Accession", samp_bin_name=samp
+            )
+            if allele_frequency is not None:
+                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, col_name="ARO Accession", samp_bin_name=samp
+            )
+            if gene_frequency is not None:
+                gene_frequency_list.append(gene_frequency)
             move_files(samp_input_dir, samp_allele_dir, "allele")
             move_files(samp_input_dir, samp_gene_dir, "gene")
 
@@ -98,32 +102,6 @@ def move_files(source_dir: str, des_dir: str, map_type: str):
     )
 
 
-def create_count_table(df_list: list) -> pd.DataFrame:
-    df_merged = reduce(
-        lambda left, right: pd.merge(left, right, on="ARO Accession", how="outer"),
-        df_list,
-    )
-    df_transposed = df_merged.transpose()
-    df_transposed = df_transposed.fillna(0)
-    df_transposed.columns = df_transposed.iloc[0]
-    df_transposed = df_transposed.drop("ARO Accession")
-    df_transposed.columns.name = None
-    df_transposed.index.name = "sample_id"
-    return df_transposed
-
-
-def read_in_txt(samp_dir: str, map_type: str):
-    df = pd.read_csv(
-        os.path.join(samp_dir, f"output.{map_type}_mapping_data.txt"), sep="\t"
-    )
-    df = df[["ARO Accession"]]
-    df = df.astype(str)
-    samp = os.path.basename(samp_dir)
-    df[samp] = df.groupby("ARO Accession")["ARO Accession"].transform("count")
-    df = df.drop_duplicates(subset=["ARO Accession"])
-    return df
-
-
 def run_rgi_bwt(
     cwd: str,
     samp: str,
@@ -131,10 +109,6 @@ def run_rgi_bwt(
     rev: str,
     aligner: str,
     threads: int,
-    include_baits: bool,
-    mapq: float,
-    mapped: float,
-    coverage: float,
 ):
     cmd = [
         "rgi",
@@ -152,14 +126,6 @@ def run_rgi_bwt(
     ]
     if rev:
         cmd.extend(["--read_two", rev])
-    if include_baits:
-        cmd.append("--include_baits")
-    if mapq:
-        cmd.extend(["--mapq", str(mapq)])
-    if mapped:
-        cmd.extend(["--mapped", str(mapped)])
-    if coverage:
-        cmd.extend(["--coverage", str(coverage)])
     try:
         run_command(cmd, cwd, verbose=True)
     except subprocess.CalledProcessError as e:
diff --git a/q2_amr/card/utils.py b/q2_amr/card/utils.py
index 602e0a8..99415d5 100644
--- a/q2_amr/card/utils.py
+++ b/q2_amr/card/utils.py
@@ -1,5 +1,8 @@
 import json
 import subprocess
+from functools import reduce
+
+import pandas as pd
 
 EXTERNAL_CMD_WARNING = (
     "Running external command line application(s). "
@@ -44,3 +47,32 @@ def load_preprocess_card_db(tmp, card_db, operation):
             f"(return code {e.returncode}), please inspect "
             "stdout and stderr to learn more."
         )
+
+
+def read_in_txt(path: str, col_name: str, samp_bin_name: str):
+    df = pd.read_csv(path, sep="\t")
+    if df.empty:
+        return None
+    df = df[[col_name]]
+    df = df.astype(str)
+    df[samp_bin_name] = df.groupby(col_name)[col_name].transform("count")
+    df = df.drop_duplicates(subset=[col_name])
+    return df
+
+
+def create_count_table(df_list: list) -> pd.DataFrame:
+    if not df_list:
+        raise ValueError(
+            "RGI did not identify any AMR genes. No output can be created."
+        )
+    df = reduce(
+        lambda left, right: pd.merge(left, right, on=left.columns[0], how="outer"),
+        df_list,
+    )
+    df = df.transpose()
+    df = df.fillna(0)
+    df.columns = df.iloc[0]
+    df = df.drop(df.index[0])
+    df.columns.name = None
+    df.index.name = "sample_id"
+    return df
diff --git a/q2_amr/plugin_setup.py b/q2_amr/plugin_setup.py
index 37d4db5..84efb88 100644
--- a/q2_amr/plugin_setup.py
+++ b/q2_amr/plugin_setup.py
@@ -7,18 +7,19 @@
 # ----------------------------------------------------------------------------
 import importlib
 
-from q2_types.feature_table import FeatureTable, Frequency
+from q2_types.feature_table import FeatureTable, PresenceAbsence
 from q2_types.per_sample_sequences import (
     PairedEndSequencesWithQuality,
     SequencesWithQuality,
 )
 from q2_types.sample_data import SampleData
 from q2_types_genomics.per_sample_data import MAGs
-from qiime2.core.type import Bool, Choices, Float, Int, Range, Str
+from qiime2.core.type import Bool, Choices, Int, Range, Str
 from qiime2.plugin import Citations, Plugin
 
 from q2_amr import __version__
 from q2_amr.card.database import fetch_card_db
+from q2_amr.card.heatmap import heatmap
 from q2_amr.card.mags import annotate_mags_card
 from q2_amr.card.reads import annotate_reads_card, visualize_annotation_stats
 from q2_amr.types import (
@@ -45,9 +46,9 @@
     version=__version__,
     website="https://github.com/bokulich-lab/q2-amr",
     package="q2_amr",
-    description="This is a QIIME 2 plugin that annotates microbiome sequence data with "
+    description="This is a QIIME 2 plugin that annotates sequence data with "
     "antimicrobial resistance gene information from CARD.",
-    short_description="This is a QIIME 2 plugin that annotates microbiome sequence "
+    short_description="This is a QIIME 2 plugin that annotates sequence "
     "data with antimicrobial resistance gene information from CARD.",
 )
 plugin.methods.register_function(
@@ -62,7 +63,7 @@
         "phenotypes."
     },
     name="Download CARD data.",
-    description=("Downloads the CARD database from the CARD website."),
+    description=("Download the latest version of the CARD database."),
     citations=[citations["alcock_card_2023"]],
 )
 
@@ -71,32 +72,35 @@
     inputs={"mag": SampleData[MAGs], "card_db": CARDDatabase},
     parameters={
         "alignment_tool": Str % Choices(["BLAST", "DIAMOND"]),
-        "input_type": Str % Choices(["contig", "protein"]),
         "split_prodigal_jobs": Bool,
         "include_loose": Bool,
         "include_nudge": Bool,
         "low_quality": Bool,
-        "num_threads": Int % Range(1, 9),
+        "threads": Int % Range(0, None, inclusive_start=False),
     },
-    outputs=[("amr_annotations", SampleData[CARDAnnotation])],
+    outputs=[
+        ("amr_annotations", SampleData[CARDAnnotation]),
+        ("feature_table", FeatureTable[PresenceAbsence]),
+    ],
     input_descriptions={
-        "mag": "MAG to be annotated with CARD.",
+        "mag": "MAGs to be annotated with CARD.",
         "card_db": "CARD Database.",
     },
     parameter_descriptions={
         "alignment_tool": "Specify alignment tool BLAST or DIAMOND.",
-        "input_type": "Specify data input type contig or protein.",
-        "split_prodigal_jobs": "Run multiple prodigal jobs simultaneously for contigs "
-        "in a fasta file.",
+        "split_prodigal_jobs": "Run multiple prodigal jobs simultaneously for contigs"
+        " in one sample",
         "include_loose": "Include loose hits in addition to strict and perfect hits .",
         "include_nudge": "Include hits nudged from loose to strict hits.",
         "low_quality": "Use for short contigs to predict partial genes.",
-        "num_threads": "Number of threads (CPUs) to use in the BLAST search.",
+        "threads": "Number of threads (CPUs) to use in the BLAST search.",
     },
-    output_descriptions={"amr_annotations": "AMR Annotation as .txt and .json file."},
-    name="Annotate MAGs with antimicrobial resistance gene information from CARD.",
-    description="Annotate MAGs with antimicrobial resistance gene information from "
-    "CARD.",
+    output_descriptions={
+        "amr_annotations": "AMR annotation as .txt and .json file.",
+        "feature_table": "Presence and absence table of ARGs in all samples.",
+    },
+    name="Annotate MAGs with antimicrobial resistance genes from CARD.",
+    description="Annotate MAGs with antimicrobial resistance genes from CARD.",
     citations=[citations["alcock_card_2023"]],
 )
 
@@ -109,40 +113,54 @@
     },
     parameters={
         "aligner": Str % Choices(["kma", "bowtie2", "bwa"]),
-        "include_baits": Bool,
-        "mapq": Float % Range(0, None, inclusive_start=True),
-        "mapped": Float % Range(0, None, inclusive_start=True),
-        "coverage": Float % Range(0, None, inclusive_start=True),
         "threads": Int % Range(0, None, inclusive_start=False),
     },
     outputs=[
-        ("amr_allele_annotation", CARDAlleleAnnotation),
-        ("amr_gene_annotation", CARDGeneAnnotation),
-        ("allele_feature_table", FeatureTable[Frequency]),
-        ("gene_feature_table", FeatureTable[Frequency]),
+        ("amr_allele_annotation", SampleData[CARDAlleleAnnotation]),
+        ("amr_gene_annotation", SampleData[CARDGeneAnnotation]),
+        ("allele_feature_table", FeatureTable[PresenceAbsence]),
+        ("gene_feature_table", FeatureTable[PresenceAbsence]),
     ],
     input_descriptions={
-        "reads": "Paired or single end metagenomic reads.",
+        "reads": "Paired or single end reads.",
         "card_db": "CARD Database",
     },
     parameter_descriptions={
         "aligner": "Specify alignment tool.",
-        "include_baits": "Include baits.",
-        "mapq": "Filter reads based on MAPQ score.",
-        "mapped": "Filter reads based on mapped reads.",
-        "coverage": "Filter reads based on coverage of reference sequence.",
         "threads": "Number of threads (CPUs) to use.",
     },
     output_descriptions={
         "amr_allele_annotation": "AMR annotation mapped on alleles.",
         "amr_gene_annotation": "AMR annotation mapped on genes.",
-        "allele_feature_table": "Samples combined into one frequency count table.",
-        "gene_feature_table": "Samples combined into one frequency count table.",
+        "allele_feature_table": "Presence and absence table of ARGs in all samples for"
+        " allele mapping.",
+        "gene_feature_table": "Presence and absence table of ARGs in all samples for "
+        "gene mapping.",
+    },
+    name="Annotate reads with antimicrobial resistance genes from CARD.",
+    description="Annotate reads with antimicrobial resistance genes from CARD.",
+    citations=[citations["alcock_card_2023"]],
+)
+
+plugin.visualizers.register_function(
+    function=heatmap,
+    inputs={"amr_annotation": SampleData[CARDAnnotation]},
+    parameters={
+        "cat": Str % Choices(["drug_class", "resistance_mechanism", "gene_family"]),
+        "clus": Str % Choices(["samples", "genes", "both"]),
+        "display": Str % Choices(["plain", "fill", "text"]),
+        "frequency": Bool,
+    },
+    input_descriptions={"amr_annotation": "AMR Annotations from MAGs"},
+    parameter_descriptions={
+        "cat": "The option to organize resistance genes based on a category.",
+        "clus": "Option to use SciPy's hierarchical clustering algorithm to cluster "
+        "rows (AMR genes) or columns (samples).",
+        "display": "Specify display options for categories",
+        "frequency": "Represent samples based on resistance profile.",
     },
-    name="Annotate metagenomic reads with antimicrobial resistance gene information "
-    "from CARD.",
-    description="Annotate metagenomic reads with antimicrobial resistance gene "
-    "information from CARD.",
+    name="Create heatmap from annotate-mags-card output.",
+    description=("Create heatmap from annotate-mags-card output."),
     citations=[citations["alcock_card_2023"]],
 )
 
@@ -155,7 +173,7 @@
     },
     parameter_descriptions={},
     name="Visualize mapping statistics.",
-    description="Visualize mapping statistics.",
+    description="Visualize mapping statistics of an annotate-reads-card output.",
     citations=[citations["alcock_card_2023"]],
 )
 
@@ -168,13 +186,14 @@
     CARDDatabase, artifact_format=CARDDatabaseDirectoryFormat
 )
 plugin.register_semantic_type_to_format(
-    CARDAnnotation, artifact_format=CARDAnnotationDirectoryFormat
+    SampleData[CARDAnnotation], artifact_format=CARDAnnotationDirectoryFormat
 )
 plugin.register_semantic_type_to_format(
-    CARDAlleleAnnotation, artifact_format=CARDAlleleAnnotationDirectoryFormat
+    SampleData[CARDAlleleAnnotation],
+    artifact_format=CARDAlleleAnnotationDirectoryFormat,
 )
 plugin.register_semantic_type_to_format(
-    CARDGeneAnnotation, artifact_format=CARDGeneAnnotationDirectoryFormat
+    SampleData[CARDGeneAnnotation], artifact_format=CARDGeneAnnotationDirectoryFormat
 )
 
 plugin.register_formats(
diff --git a/q2_amr/tests/card/test_database.py b/q2_amr/tests/card/test_database.py
index 8cae7af..e4ec9b7 100644
--- a/q2_amr/tests/card/test_database.py
+++ b/q2_amr/tests/card/test_database.py
@@ -12,26 +12,28 @@
 class TestAnnotateMagsCard(TestPluginBase):
     package = "q2_amr.tests"
 
-    @patch("requests.get")
-    def test_fetch_card_db(self, mock_requests):
+    def test_fetch_card_db(self):
         f = open(self.get_data_path("card.tar.bz2"), "rb")
         mock_response = MagicMock(raw=f)
-        mock_requests.return_value = mock_response
-        obs = fetch_card_db()
+        with patch("requests.get") as mock_requests:
+            mock_requests.return_value = mock_response
+            obs = fetch_card_db()
         self.assertTrue(os.path.exists(os.path.join(str(obs), "card.json")))
         self.assertIsInstance(obs, CARDDatabaseDirectoryFormat)
         mock_requests.assert_called_once_with(
             "https://card.mcmaster.ca/latest/data", stream=True
         )
 
-    @patch("requests.get", side_effect=requests.ConnectionError)
-    def test_fetch_card_data_connection_error(self, mock_requests):
-        with self.assertRaisesRegex(
+    def test_fetch_card_data_connection_error(self):
+        with patch(
+            "requests.get", side_effect=requests.ConnectionError
+        ), self.assertRaisesRegex(
             requests.ConnectionError, "Network connectivity problems."
         ):
             fetch_card_db()
 
-    @patch("tarfile.open", side_effect=tarfile.ReadError)
-    def test_fetch_card_data_tarfile_read_error(self, mock_requests):
-        with self.assertRaisesRegex(tarfile.ReadError, "Tarfile is invalid."):
+    def test_fetch_card_data_tarfile_read_error(self):
+        with patch(
+            "tarfile.open", side_effect=tarfile.ReadError
+        ), self.assertRaisesRegex(tarfile.ReadError, "Tarfile is invalid."):
             fetch_card_db()
diff --git a/q2_amr/tests/card/test_heatmap.py b/q2_amr/tests/card/test_heatmap.py
new file mode 100644
index 0000000..44aee61
--- /dev/null
+++ b/q2_amr/tests/card/test_heatmap.py
@@ -0,0 +1,113 @@
+import os
+import tempfile
+from unittest.mock import patch
+
+from qiime2.plugin.testing import TestPluginBase
+
+from q2_amr.card.heatmap import (
+    InvalidParameterCombinationError,
+    change_names,
+    heatmap,
+    run_rgi_heatmap,
+)
+from q2_amr.types import CARDAnnotationDirectoryFormat
+
+
+class TestHeatmap(TestPluginBase):
+    package = "q2_amr.tests"
+
+    def test_heatmap(self):
+        amr_annotation = CARDAnnotationDirectoryFormat()
+
+        def mock_run_rgi_heatmap(tmp, json_files_dir, clus, cat, display, frequency):
+            file_types = [".png", ".eps", ".csv"]
+            for file_type in file_types:
+                with open(
+                    os.path.join(tmp, "results", f"heatmap-3.{file_type}"), "w"
+                ) as file:
+                    file.write(file_type)
+
+        with patch(
+            "q2_amr.card.heatmap.run_rgi_heatmap", side_effect=mock_run_rgi_heatmap
+        ), tempfile.TemporaryDirectory() as tmp:
+            os.makedirs(os.path.join(tmp, "results"))
+            heatmap(tmp, amr_annotation)
+            self.assertTrue(
+                os.path.exists(os.path.join(tmp, "rgi_data", "heatmap.png"))
+            )
+            self.assertTrue(
+                os.path.exists(os.path.join(tmp, "rgi_data", "heatmap.eps"))
+            )
+            self.assertTrue(
+                os.path.exists(os.path.join(tmp, "rgi_data", "heatmap.csv"))
+            )
+            self.assertTrue(os.path.exists(os.path.join(tmp, "index.html")))
+            self.assertTrue(os.path.exists(os.path.join(tmp, "q2templateassets")))
+
+    def test_run_rgi_heatmap(self):
+        with patch("q2_amr.card.heatmap.run_command") as mock_run_command:
+            run_rgi_heatmap(
+                "path_tmp", "json_files_dir_path", "samples", "drug_class", "fill", True
+            )
+            mock_run_command.assert_called_once_with(
+                [
+                    "rgi",
+                    "heatmap",
+                    "--input",
+                    "json_files_dir_path",
+                    "--output",
+                    "path_tmp/results/heatmap",
+                    "--display",
+                    "fill",
+                    "--clus",
+                    "samples",
+                    "--cat",
+                    "drug_class",
+                    "--frequency",
+                ],
+                "path_tmp",
+                verbose=True,
+            )
+
+    def test_change_names(self):
+        with patch(
+            "q2_amr.card.heatmap.os.listdir",
+            return_value=["heatmap-7.eps", "heatmap-7.png", "heatmap-7.csv"],
+        ), patch("q2_amr.card.heatmap.os.rename") as mock_rename:
+            results_dir = "/path/to/results"
+            change_names(results_dir)
+            expected_calls = [
+                ("/path/to/results/heatmap-7.eps", "/path/to/results/heatmap.eps"),
+                ("/path/to/results/heatmap-7.png", "/path/to/results/heatmap.png"),
+                ("/path/to/results/heatmap-7.csv", "/path/to/results/heatmap.csv"),
+            ]
+            actual_calls = [call[0] for call in mock_rename.call_args_list]
+            self.assertEqual(expected_calls, actual_calls)
+
+    def test_change_names_empty(self):
+        with patch("q2_amr.card.heatmap.os.listdir", return_value=[]), patch(
+            "q2_amr.card.heatmap.os.rename"
+        ) as mock_rename:
+            results_dir = "/path/to/results"
+            change_names(results_dir)
+            expected_calls = []
+            actual_calls = [call[0] for call in mock_rename.call_args_list]
+            self.assertEqual(expected_calls, actual_calls)
+
+    def test_invalid_combination_raises_error(self):
+        tmp = "path"
+        json_files_dir = "path"
+        clus = "both"
+        cat = "drug_class"
+        display = "text"
+        frequency = False
+
+        with self.assertRaises(InvalidParameterCombinationError) as cm:
+            run_rgi_heatmap(tmp, json_files_dir, clus, cat, display, frequency)
+
+        self.assertEqual(
+            str(cm.exception),
+            "If the parameter clus is set to genes"
+            " or both it is not possible to use "
+            "the cat parameter",
+        )
diff --git a/q2_amr/tests/card/test_mags.py b/q2_amr/tests/card/test_mags.py
index 912bf34..8573bda 100644
--- a/q2_amr/tests/card/test_mags.py
+++ b/q2_amr/tests/card/test_mags.py
@@ -1,8 +1,10 @@
 import os
 import shutil
 import subprocess
-from unittest.mock import patch
+from copy import deepcopy
+from unittest.mock import MagicMock, patch
 
+import pandas as pd
 from q2_types_genomics.per_sample_data import MultiMAGSequencesDirFmt
 from qiime2.plugin.testing import TestPluginBase
 
@@ -13,49 +15,77 @@
 class TestAnnotateMagsCard(TestPluginBase):
     package = "q2_amr.tests"
 
-    def test_annotate_mags_card(self):
+    table = pd.DataFrame(
+        {
+            "sample_id": ["sample1", "sample2"],
+            3000796: [1, 0],
+            3000815: [1, 1],
+            3000805: [1, 1],
+            3000026: [1, 2],
+            3000797: [0, 1],
+        }
+    )
+
+    def mock_run_rgi_main(
+        self,
+        tmp,
+        input_sequence,
+        alignment_tool,
+        split_prodigal_jobs,
+        include_loose,
+        include_nudge,
+        low_quality,
+        num_threads,
+    ):
         output_txt = self.get_data_path("rgi_output.txt")
         output_json = self.get_data_path("rgi_output.json")
+        shutil.copy(output_txt, f"{tmp}/output.txt")
+        shutil.copy(output_json, f"{tmp}/output.json")
+
+    def return_count_table(self, df_list):
+        count_table = deepcopy(self.table)
+        count_table.set_index("sample_id", inplace=True)
+        count_table = count_table.astype(float)
+        count_table.columns = count_table.columns.astype(float)
+        return count_table
+
+    def test_annotate_mags_card(self):
+
         manifest = self.get_data_path("MANIFEST_mags")
         mag = MultiMAGSequencesDirFmt()
         card_db = CARDDatabaseFormat()
         shutil.copy(manifest, os.path.join(str(mag), "MANIFEST"))
 
-        def mock_run_rgi_main(
-            tmp,
-            input_sequence,
-            alignment_tool,
-            input_type,
-            split_prodigal_jobs,
-            include_loose,
-            include_nudge,
-            low_quality,
-            num_threads,
-        ):
-            shutil.copy(output_txt, f"{tmp}/output.txt")
-            shutil.copy(output_json, f"{tmp}/output.json")
-
+        mock_create_count_table = MagicMock(side_effect=self.return_count_table)
+        mock_read_in_txt = MagicMock()
         with patch(
-            "q2_amr.card.mags.run_rgi_main", side_effect=mock_run_rgi_main
-        ), patch("q2_amr.card.mags.load_preprocess_card_db"):
+            "q2_amr.card.mags.run_rgi_main", side_effect=self.mock_run_rgi_main
+        ), patch("q2_amr.card.mags.load_preprocess_card_db"), patch(
+            "q2_amr.card.mags.read_in_txt", mock_read_in_txt
+        ), patch(
+            "q2_amr.card.mags.create_count_table", mock_create_count_table
+        ):
             result = annotate_mags_card(mag, card_db)
-            self.assertIsInstance(result, CARDAnnotationDirectoryFormat)
+            self.assertIsInstance(result[0], CARDAnnotationDirectoryFormat)
+            self.assertIsInstance(result[1], pd.DataFrame)
             self.assertTrue(
                 os.path.exists(
-                    os.path.join(str(result), "sample1", "bin1", "amr_annotation.txt")
+                    os.path.join(
+                        str(result[0]), "sample1", "bin1", "amr_annotation.txt"
+                    )
                 )
             )
             self.assertTrue(
                 os.path.exists(
-                    os.path.join(str(result), "sample1", "bin1", "amr_annotation.json")
+                    os.path.join(
+                        str(result[0]), "sample1", "bin1", "amr_annotation.json"
+                    )
                 )
             )
 
     def test_run_rgi_main(self):
         with patch("q2_amr.card.mags.run_command") as mock_run_command:
-            run_rgi_main(
-                "path_tmp", "path_input", "DIAMOND", "contig", True, True, True, True, 8
-            )
+            run_rgi_main("path_tmp", "path_input", "DIAMOND", True, True, True, True, 8)
             mock_run_command.assert_called_once_with(
                 [
                     "rgi",
@@ -80,15 +110,15 @@ def test_run_rgi_main(self):
                 verbose=True,
             )
 
-    @patch("q2_amr.card.mags.run_command")
-    def test_exception_raised(self, mock_run_command):
-        mock_run_command.side_effect = subprocess.CalledProcessError(1, "cmd")
-        tmp = "path/to/tmp"
-        input_sequence = "path/to/input_sequence.fasta"
+    def test_exception_raised(self):
         expected_message = (
             "An error was encountered while running rgi, "
             "(return code 1), please inspect stdout and stderr to learn more."
         )
-        with self.assertRaises(Exception) as cm:
-            run_rgi_main(tmp, input_sequence)
-        self.assertEqual(str(cm.exception), expected_message)
+        tmp = "path/to/tmp"
+        input_sequence = "path/to/input_sequence.fasta"
+        with patch("q2_amr.card.mags.run_command") as mock_run_command:
+            mock_run_command.side_effect = subprocess.CalledProcessError(1, "cmd")
+            with self.assertRaises(Exception) as cm:
+                run_rgi_main(tmp, input_sequence)
+            self.assertEqual(str(cm.exception), expected_message)
diff --git a/q2_amr/tests/card/test_reads.py b/q2_amr/tests/card/test_reads.py
index 25ff97a..1685454 100644
--- a/q2_amr/tests/card/test_reads.py
+++ b/q2_amr/tests/card/test_reads.py
@@ -2,7 +2,6 @@
 import shutil
 import subprocess
 import tempfile
-from copy import deepcopy
 from unittest.mock import ANY, MagicMock, call, patch
 
 import pandas as pd
@@ -11,14 +10,13 @@
     SingleLanePerSampleSingleEndFastqDirFmt,
 )
 from qiime2.plugin.testing import TestPluginBase
+from test_mags import TestAnnotateMagsCard
 
 from q2_amr.card.reads import (
     annotate_reads_card,
-    create_count_table,
     extract_sample_stats,
     move_files,
     plot_sample_stats,
-    read_in_txt,
     run_rgi_bwt,
     visualize_annotation_stats,
 )
@@ -38,38 +36,31 @@ def test_annotate_reads_card_single(self):
     def test_annotate_reads_card_paired(self):
         self.annotate_reads_card_test_body("paired")
 
+    def copy_needed_files(self, cwd, samp, **kwargs):
+        output_allele = self.get_data_path("output.allele_mapping_data.txt")
+        output_gene = self.get_data_path("output.gene_mapping_data.txt")
+        output_stats = self.get_data_path("output.overall_mapping_stats.txt")
+        samp_dir = os.path.join(cwd, samp)
+        shutil.copy(output_allele, samp_dir)
+        shutil.copy(output_gene, samp_dir)
+        shutil.copy(output_stats, samp_dir)
+
     def annotate_reads_card_test_body(self, read_type):
         manifest = self.get_data_path(f"MANIFEST_reads_{read_type}")
         if read_type == "single":
             reads = SingleLanePerSampleSingleEndFastqDirFmt()
             shutil.copy(manifest, os.path.join(str(reads), "MANIFEST"))
-
         else:
             reads = SingleLanePerSamplePairedEndFastqDirFmt()
             shutil.copy(manifest, os.path.join(str(reads), "MANIFEST"))
-
-        output_allele = self.get_data_path("output.allele_mapping_data.txt")
-        output_gene = self.get_data_path("output.gene_mapping_data.txt")
-        output_stats = self.get_data_path("output.overall_mapping_stats.txt")
         card_db = CARDDatabaseFormat()
-
-        def copy_needed_files(cwd, samp, **kwargs):
-            samp_dir = os.path.join(cwd, samp)
-            shutil.copy(output_allele, samp_dir)
-            shutil.copy(output_gene, samp_dir)
-            shutil.copy(output_stats, samp_dir)
-
-        def return_count_table(df_list):
-            count_table = deepcopy(self.table)
-            count_table.set_index("sample_id", inplace=True)
-            count_table = count_table.astype(float)
-            count_table.columns = count_table.columns.astype(float)
-            return count_table
-
-        mock_run_rgi_bwt = MagicMock(side_effect=copy_needed_files)
+        mock_run_rgi_bwt = MagicMock(side_effect=self.copy_needed_files)
         mock_run_rgi_load = MagicMock()
         mock_read_in_txt = MagicMock()
-        mock_create_count_table = MagicMock(side_effect=return_count_table)
+        mag_test_class = TestAnnotateMagsCard()
+        mock_create_count_table = MagicMock(
+            side_effect=mag_test_class.return_count_table
+        )
         with patch("q2_amr.card.reads.run_rgi_bwt", mock_run_rgi_bwt), patch(
             "q2_amr.card.reads.load_preprocess_card_db", mock_run_rgi_load
         ), patch("q2_amr.card.reads.read_in_txt", mock_read_in_txt), patch(
@@ -87,10 +78,6 @@ def return_count_table(df_list):
                         aligner="kma",
                         rev=None,
                         threads=1,
-                        include_baits=False,
-                        mapq=None,
-                        mapped=None,
-                        coverage=None,
                     ),
                     call(
                         cwd=tmp_dir,
@@ -99,10 +86,6 @@ def return_count_table(df_list):
                         aligner="kma",
                         rev=None,
                         threads=1,
-                        include_baits=False,
-                        mapq=None,
-                        mapped=None,
-                        coverage=None,
                     ),
                 ]
             else:
@@ -114,10 +97,6 @@ def return_count_table(df_list):
                         rev=f"{reads}/sample1_00_L001_R2_001.fastq.gz",
                         aligner="kma",
                         threads=1,
-                        include_baits=False,
-                        mapq=None,
-                        mapped=None,
-                        coverage=None,
                     ),
                     call(
                         cwd=tmp_dir,
@@ -126,10 +105,6 @@ def return_count_table(df_list):
                         rev=f"{reads}/sample2_00_L001_R2_001.fastq.gz",
                         aligner="kma",
                         threads=1,
-                        include_baits=False,
-                        mapq=None,
-                        mapped=None,
-                        coverage=None,
                     ),
                 ]
             exp_calls_mock_load = [
@@ -138,10 +113,26 @@ def return_count_table(df_list):
                 call(tmp_dir, ANY, "load_fasta"),
             ]
             exp_calls_mock_read = [
-                call(f"{tmp_dir}/sample1", "allele"),
-                call(f"{tmp_dir}/sample1", "gene"),
-                call(f"{tmp_dir}/sample2", "allele"),
-                call(f"{tmp_dir}/sample2", "gene"),
+                call(
+                    path=f"{tmp_dir}/sample1/output.allele_mapping_data.txt",
+                    col_name="ARO Accession",
+                    samp_bin_name="sample1",
+                ),
+                call(
+                    path=f"{tmp_dir}/sample1/output.gene_mapping_data.txt",
+                    col_name="ARO Accession",
+                    samp_bin_name="sample1",
+                ),
+                call(
+                    path=f"{tmp_dir}/sample2/output.allele_mapping_data.txt",
+                    col_name="ARO Accession",
+                    samp_bin_name="sample2",
+                ),
+                call(
+                    path=f"{tmp_dir}/sample2/output.gene_mapping_data.txt",
+                    col_name="ARO Accession",
+                    samp_bin_name="sample2",
+                ),
             ]
             exp_calls_mock_count = [call([ANY, ANY]), call([ANY, ANY])]
             mock_run_rgi_bwt.assert_has_calls(exp_calls_mock_run)
@@ -172,10 +163,6 @@ def test_run_rgi_bwt(self):
                 "path_rev",
                 "bowtie2",
                 8,
-                True,
-                3,
-                5,
-                3.2,
             )
             mock_run_command.assert_called_once_with(
                 [
@@ -193,26 +180,21 @@ def test_run_rgi_bwt(self):
                     "bowtie2",
                     "--read_two",
                     "path_rev",
-                    "--include_baits",
-                    "--mapq",
-                    "3",
-                    "--mapped",
-                    "5",
-                    "--coverage",
-                    "3.2",
                 ],
                 "path_tmp",
                 verbose=True,
             )
 
-    @patch("q2_amr.card.reads.run_command")
-    def test_exception_raised(self, mock_run_command):
-        mock_run_command.side_effect = subprocess.CalledProcessError(1, "cmd")
+    def test_exception_raised(self):
         expected_message = (
             "An error was encountered while running rgi, "
             "(return code 1), please inspect stdout and stderr to learn more."
         )
-        with self.assertRaises(Exception) as cm:
+
+        with patch(
+            "q2_amr.card.reads.run_command"
+        ) as mock_run_command, self.assertRaises(Exception) as cm:
+            mock_run_command.side_effect = subprocess.CalledProcessError(1, "cmd")
             run_rgi_bwt(
                 cwd="path/cwd",
                 samp="sample1",
@@ -220,12 +202,8 @@ def test_exception_raised(self, mock_run_command):
                 rev="path/rev",
                 aligner="bwa",
                 threads=1,
-                include_baits=True,
-                mapq=0.3,
-                mapped=0.3,
-                coverage=0.3,
             )
-        self.assertEqual(str(cm.exception), expected_message)
+            self.assertEqual(str(cm.exception), expected_message)
 
     def test_move_files_allele(self):
         self.move_files_test_body("allele")
@@ -312,54 +290,3 @@ def mock_plot_sample_stats(sample_stats, output_dir):
             self.assertTrue(os.path.exists(os.path.join(tmp, "sample_stats_plot.html")))
             self.assertTrue(os.path.exists(os.path.join(tmp, "index.html")))
             self.assertTrue(os.path.exists(os.path.join(tmp, "q2templateassets")))
-
-    mapping_data_sample1 = pd.DataFrame(
-        {
-            "ARO Accession": [3000796, 3000815, 3000805, 3000026],
-            "sample1": [1, 1, 1, 1],
-        }
-    )
-
-    mapping_data_sample2 = pd.DataFrame(
-        {
-            "ARO Accession": [3000797, 3000815, 3000805, 3000026],
-            "sample2": [1, 1, 1, 2],
-        }
-    )
-
-    table = pd.DataFrame(
-        {
-            "sample_id": ["sample1", "sample2"],
-            3000796: [1, 0],
-            3000815: [1, 1],
-            3000805: [1, 1],
-            3000026: [1, 2],
-            3000797: [0, 1],
-        }
-    )
-
-    def test_read_in_txt_allele(self):
-        self.read_in_txt_test_body("allele", self.mapping_data_sample1)
-
-    def test_read_in_txt_gene(self):
-        self.read_in_txt_test_body("gene", self.mapping_data_sample1)
-
-    def read_in_txt_test_body(self, map_type, mapping_data):
-        mapping_file = self.get_data_path(f"output.{map_type}_mapping_data.txt")
-        exp = mapping_data
-        with tempfile.TemporaryDirectory() as tmp:
-            samp_dir = os.path.join(tmp, "sample1")
-            os.mkdir(samp_dir)
-            shutil.copy(mapping_file, samp_dir)
-            obs = read_in_txt(samp_dir, map_type)
-            obs["ARO Accession"] = obs["ARO Accession"].astype(int)
-            pd.testing.assert_frame_equal(exp, obs)
-
-    def test_create_count_table(self):
-        df_list = [self.mapping_data_sample1, self.mapping_data_sample2]
-        obs = create_count_table(df_list)
-        exp = self.table
-        exp.set_index("sample_id", inplace=True)
-        exp = exp.astype(float)
-        exp.columns = exp.columns.astype(float)
-        pd.testing.assert_frame_equal(exp, obs)
diff --git a/q2_amr/tests/card/test_utils.py b/q2_amr/tests/card/test_utils.py
index 4fc49a8..10d3bc4 100644
--- a/q2_amr/tests/card/test_utils.py
+++ b/q2_amr/tests/card/test_utils.py
@@ -1,15 +1,38 @@
 import subprocess
 from unittest.mock import patch
 
+import pandas as pd
 from qiime2.plugin.testing import TestPluginBase
+from test_mags import TestAnnotateMagsCard
 
-from q2_amr.card.utils import load_preprocess_card_db
+from q2_amr.card.utils import create_count_table, load_preprocess_card_db, read_in_txt
 from q2_amr.types import CARDDatabaseFormat
 
 
 class TestAnnotateReadsCARD(TestPluginBase):
     package = "q2_amr.tests"
 
+    mapping_data_sample1 = pd.DataFrame(
+        {
+            "ARO Accession": [3000796, 3000815, 3000805, 3000026],
+            "sample1": [1, 1, 1, 1],
+        }
+    )
+
+    mags_mapping_data_sample1 = pd.DataFrame(
+        {
+            "ARO": [3000796, 3000815, 3000805, 3000026],
+            "sample1": [1, 1, 1, 1],
+        }
+    )
+
+    mapping_data_sample2 = pd.DataFrame(
+        {
+            "ARO Accession": [3000797, 3000815, 3000805, 3000026],
+            "sample2": [1, 1, 1, 2],
+        }
+    )
+
     def test_load_card_db(self):
         card_db = CARDDatabaseFormat()
         with patch("q2_amr.card.utils.run_command") as mock_run_command:
@@ -46,9 +69,7 @@ def test_load_card_db_fasta(self):
                 verbose=True,
             )
 
-    @patch("q2_amr.card.utils.run_command")
-    def test_exception_raised(self, mock_run_command):
-        mock_run_command.side_effect = subprocess.CalledProcessError(1, "cmd")
+    def test_exception_raised(self):
         tmp = "path/to/tmp"
         card_db = "path/to/card_db.json"
         expected_message = (
@@ -56,6 +77,45 @@ def test_exception_raised(self, mock_run_command):
             "(return code 1), please inspect stdout and stderr to learn more."
         )
         operation = "load"
-        with self.assertRaises(Exception) as cm:
+        with patch(
+            "q2_amr.card.utils.run_command"
+        ) as mock_run_command, self.assertRaises(Exception) as cm:
+            mock_run_command.side_effect = subprocess.CalledProcessError(1, "cmd")
             load_preprocess_card_db(tmp, card_db, operation)
-        self.assertEqual(str(cm.exception), expected_message)
+            self.assertEqual(str(cm.exception), expected_message)
+
+    def test_read_in_txt_mags(self):
+        path = self.get_data_path("output.mags.txt")
+        self.read_in_txt_test_body(
+            path, "ARO", "sample1", self.mags_mapping_data_sample1
+        )
+
+    def test_read_in_txt_allele(self):
+        path = self.get_data_path("output.allele_mapping_data.txt")
+        self.read_in_txt_test_body(
+            path, "ARO Accession", "sample1", self.mapping_data_sample1
+        )
+
+    def test_read_in_txt_gene(self):
+        path = self.get_data_path("output.gene_mapping_data.txt")
+        self.read_in_txt_test_body(
+            path, "ARO Accession", "sample1", self.mapping_data_sample1
+        )
+
+    def read_in_txt_test_body(self, path, col_name, samp_bin_name, mapping_data):
+        exp = mapping_data
+        obs = read_in_txt(path, col_name, samp_bin_name)
+        obs[col_name] = obs[col_name].astype(int)
+        pd.testing.assert_frame_equal(exp, obs)
+
+    def test_create_count_table(self):
+        df_list = [self.mapping_data_sample1, self.mapping_data_sample2]
+        obs = create_count_table(df_list)
+        mag_test_class = TestAnnotateMagsCard()
+        exp = mag_test_class.table
+        exp.set_index("sample_id", inplace=True)
+        exp = exp.astype(float)
+        exp.columns = exp.columns.astype(float)
+        pd.testing.assert_frame_equal(exp, obs)
+        df_list_empty = []
+        self.assertRaises(ValueError, create_count_table, df_list_empty)
diff --git a/q2_amr/tests/data/output.mags.txt b/q2_amr/tests/data/output.mags.txt
new file mode 100644
index 0000000..7d9fc51
--- /dev/null
+++ b/q2_amr/tests/data/output.mags.txt
@@ -0,0 +1,5 @@
+ORF_ID	Contig	Start	Stop	Orientation	Cut_Off	Pass_Bitscore	Best_Hit_Bitscore	Best_Hit_ARO	Best_Identities	ARO	Model_type	SNPs_in_Best_Hit_ARO	Other_SNPs	Drug Class	Resistance Mechanism	AMR Gene Family	Predicted_DNA	Predicted_Protein	CARD_Protein_Sequence	Percentage Length of Reference Sequence	ID	Model_ID	Nudged	Note
+NC_000962.3_689 # 759789 # 763325 # 1 # ID=1_689;partial=00;start_type=GTG;rbs_motif=None;rbs_spacer=None;gc_cont=0.643	NC_000962.3_689 	759789	763325	+	Strict	2300	2394.77	Mycobacterium tuberculosis rpoB mutants conferring resistance to rifampicin	99.91	3000796	protein variant model	D516G, H526T, L511R	n/a	rifamycin antibiotic	antibiotic target alteration; antibiotic target replacement	rifamycin-resistant beta-subunit of RNA polymerase (rpoB)	GTGCTGGAAGGATGCATCTTGGCAGATTCCCGCCAGAGCAAAACAGCCGCTAGTCCTAGTCCGAGTCGCCCGCAAAGTTCCTCGAATAACTCCGTACCCGGAGCGCCAAACCGGGTCTCCTTCGCTAAGCTGCGCGAACCACTTGAGGTTCCGGGACTCCTTGACGTCCAGACCGATTCGTTCGAGTGGCTGATCGGTTCGCCGCGCTGGCGCGAATCCGCCGCCGAGCGGGGTGATGTCAACCCAGTGGGTGGCCTGGAAGAGGTGCTCTACGAGCTGTCTCCGATCGAGGACTTCTCCGGGTCGATGTCGTTGTCGTTCTCTGACCCTCGTTTCGACGATGTCAAGGCACCCGTCGACGAGTGCAAAGACAAGGACATGACGTACGCGGCTCCACTGTTCGTCACCGCCGAGTTCATCAACAACAACACCGGTGAGATCAAGAGTCAGACGGTGTTCATGGGTGACTTCCCGATGATGACCGAGAAGGGCACGTTCATCATCAACGGGACCGAGCGTGTGGTGGTCAGCCAGCTGGTGCGGTCGCCCGGGGTGTACTTCGACGAGACCATTGACAAGTCCACCGACAAGACGCTGCACAGCGTCAAGGTGATCCCGAGCCGCGGCGCGTGGCTCGAGTTTGACGTCGACAAGCGCGACACCGTCGGCGTGCGCATCGACCGCAAACGCCGGCAACCGGTCACCGTGCTGCTCAAGGCGCTGGGCTGGACCAGCGAGCAGATTGTCGAGCGGTTCGGGTTCTCCGAGATCATGCGATCGACGCTGGAGAAGGACAACACCGTCGGCACCGACGAGGCGCTGTTGGACATCTACCGCAAGCTGCGTCCGGGCGAGCCCCCGACCAAAGAGTCAGCGCAGACGCTGTTGGAAAACTTGTTCTTCAAGGAGAAGCGCTACGACCTGGCCCGCGTCGGTCGCTATAAGGTCAACAAGAAGCTCGGGCTGCATGTCGGCGAGCCCATCACGTCGTCGACGCTGACCGAAGAAGACGTCGTGGCCACCATCGAATATCTGGTCCGCTTGCACGAGGGTCAGACCACGATGACCGTTCCGGGCGGCGTCGAGGTGCCGGTGGAAACCGACGACATCGACCACTTCGGCAACCGCCGCCTGCGTACGGTCGGCGAGCTGATCCAAAACCAGATCCGGGTCGGCATGTCGCGGATGGAGCGGGTGGTCCGGGAGCGGATGACCACCCAGGACGTGGAGGCGATCACACCGCAGACGTTGATCAACATCCGGCCGGTGGTCGCCGCGATCAAGGAGTTCTTCGGCACCAGCCAGCTGAGCCAATTCATGGACCAGAACAACCCGCTGTCGGGGTTGACCCACAAGCGCCGACTGTCGGCGCTGGGGCCCGGCGGTCTGTCACGTGAGCGTGCCGGGCTGGAGGTCCGCGACGTGCACCCGTCGCACTACGGCCGGATGTGCCCGATCGAAACCCCTGAGGGGCCCAACATCGGTCTGATCGGCTCGCTGTCGGTGTACGCGCGGGTCAACCCGTTCGGGTTCATCGAAACGCCGTACCGCAAGGTGGTCGACGGCGTGGTTAGCGACGAGATCGTGTACCTGACCGCCGACGAGGAGGACCGCCACGTGGTGGCACAGGCCAATTCGCCGATCGATGCGGACGGTCGCTTCGTCGAGCCGCGCGTGCTGGTCCGCCGCAAGGCGGGCGAGGTGGAGTACGTGCCCTCGTCTGAGGTGGACTACATGGACGTCTCGCCCCGCCAGATGGTGTCGGTGGCCACCGCGATGATTCCCTTCCTGGAGCACGACGACGCCAACCGTGCCCTCATGGGGGCAAACATGCAGCGCCAGGCGGTGCCGCTGGTCCGTAGCGAGGCCCCGCTGGTGGGCACCGGGATGGAGCTGCGCGCGGCGATCGACGCCGGCGACGTCGTCGTCGCCGAAGAAAGCGGCGTCATCGAGGAGGTGTCGGCCGACTACATCACTGTGATGCACGACAACGGCACCCGGCGTACCTACCGGATGCGCAAGTTTGCCCGGTCCAACCACGGCACTTGCGCCAACCAGTGCCCCATCGTGGACGCGGGCGACCGAGTCGAGGCCGGTCAGGTGATCGCCGACGGTCCCTGTACTGACGACGGCGAGATGGCGCTGGGCAAGAACCTGCTGGTGGCCATCATGCCGTGGGAGGGCCACAACTACGAGGACGCGATCATCCTGTCCAACCGCCTGGTCGAAGAGGACGTGCTCACCTCGATCCACATCGAGGAGCATGAGATCGATGCTCGCGACACCAAGCTGGGTGCGGAGGAGATCACCCGCGACATCCCGAACATCTCCGACGAGGTGCTCGCCGACCTGGATGAGCGGGGCATCGTGCGCATCGGTGCCGAGGTTCGCGACGGGGACATCCTGGTCGGCAAGGTCACCCCGAAGGGTGAGACCGAGCTGACGCCGGAGGAGCGGCTGCTGCGTGCCATCTTCGGTGAGAAGGCCCGCGAGGTGCGCGACACTTCGCTGAAGGTGCCGCACGGCGAATCCGGCAAGGTGATCGGCATTCGGGTGTTTTCCCGCGAGGACGAGGACGAGTTGCCGGCCGGTGTCAACGAGCTGGTGCGTGTGTATGTGGCTCAGAAACGCAAGATCTCCGACGGTGACAAGCTGGCCGGCCGGCACGGCAACAAGGGCGTGATCGGCAAGATCCTGCCGGTTGAGGACATGCCGTTCCTTGCCGACGGCACCCCGGTGGACATTATTTTGAACACCCACGGCGTGCCGCGACGGATGAACATCGGCCAGATTTTGGAGACCCACCTGGGTTGGTGTGCCCACAGCGGCTGGAAGGTCGACGCCGCCAAGGGGGTTCCGGACTGGGCCGCCAGGCTGCCCGACGAACTGCTCGAGGCGCAGCCGAACGCCATTGTGTCGACGCCGGTGTTCGACGGCGCCCAGGAGGCCGAGCTGCAGGGCCTGTTGTCGTGCACGCTGCCCAACCGCGACGGTGACGTGCTGGTCGACGCCGACGGCAAGGCCATGCTCTTCGACGGGCGCAGCGGCGAGCCGTTCCCGTACCCGGTCACGGTTGGCTACATGTACATCATGAAGCTGCACCACCTGGTGGACGACAAGATCCACGCCCGCTCCACCGGGCCGTACTCGATGATCACCCAGCAGCCGCTGGGCGGTAAGGCGCAGTTCGGTGGCCAGCGGTTCGGGGAGATGGAGTGCTGGGCCATGCAGGCCTACGGTGCTGCCTACACCCTGCAGGAGCTGTTGACCATCAAGTCCGATGACACCGTCGGCCGCGTCAAGGTGTACGAGGCGATCGTCAAGGGTGAGAACATCCCGGAGCCGGGCATCCCCGAGTCGTTCAAGGTGCTGCTCAAAGAACTGCAGTCGCTGTGCCTCAACGTCGAGGTGCTATCGAGTGACGGTGCGGCGATCGAACTGCGCGAAGGTGAGGACGAGGACCTGGAGCGGGCCGCGGCCAACCTGGGAATCAATCTGTCCCGCAACGAATCCGCAAGTGTCGAGGATCTTGCGTAA	MLEGCILADSRQSKTAASPSPSRPQSSSNNSVPGAPNRVSFAKLREPLEVPGLLDVQTDSFEWLIGSPRWRESAAERGDVNPVGGLEEVLYELSPIEDFSGSMSLSFSDPRFDDVKAPVDECKDKDMTYAAPLFVTAEFINNNTGEIKSQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDKSTDKTLHSVKVIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQIVERFGFSEIMRSTLEKDNTVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHVGEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRKAGEVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVAEESGVIEEVSADYITVMHDNGTRRTYRMRKFARSNHGTCANQCPIVDAGDRVEAGQVIADGPCTDDGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDEDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLADGTPVDIILNTHGVPRRMNIGQILETHLGWCAHSGWKVDAAKGVPDWAARLPDELLEAQPNAIVSTPVFDGAQEAELQGLLSCTLPNRDGDVLVDADGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLCLNVEVLSSDGAAIELREGEDEDLERAAANLGINLSRNESASVEDLA	MADSRQSKTAASPSPSRPQSSSNNSVPGAPNRVSFAKLREPLEVPGLLDVQTDSFEWLIGSPRWRESAAERGDVNPVGGLEEVLYELSPIEDFSGSMSLSFSDPRFDDVKAPVDECKDKDMTYAAPLFVTAEFINNNTGEIKSQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDKSTDKTLHSVKVIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQIVERFGFSEIMRSTLEKDNTVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHVGEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRKAGEVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVAEESGVIEEVSADYITVMHDNGTRRTYRMRKFARSNHGTCANQCPIVDAGDRVEAGQVIADGPCTDDGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDEDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLADGTPVDIILNTHGVPRRMNIGQILETHLGWCAHSGWKVDAAKGVPDWAARLPDELLEAQPNAIVSTPVFDGAQEAELQGLLSCTLPNRDGDVLVDADGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLCLNVEVLSSDGAAIELREGEDEDLERAAANLGINLSRNESASVEDLA	100.51	gnl|BL_ORD_ID|2005|hsp_num:0	1237
+NC_000962.3_689 # 759789 # 763325 # 1 # ID=1_689;partial=00;start_type=GTG;rbs_motif=None;rbs_spacer=None;gc_cont=0.643	NC_000962.3_689 	759789	763325	+	Strict	2300	2394.77	Mycobacterium tuberculosis rpoB mutants conferring resistance to rifampicin	99.91	3000815	protein variant model	D516G, H526T, L511R	n/a	rifamycin antibiotic	antibiotic target alteration; antibiotic target replacement	rifamycin-resistant beta-subunit of RNA polymerase (rpoB)	GTGCTGGAAGGATGCATCTTGGCAGATTCCCGCCAGAGCAAAACAGCCGCTAGTCCTAGTCCGAGTCGCCCGCAAAGTTCCTCGAATAACTCCGTACCCGGAGCGCCAAACCGGGTCTCCTTCGCTAAGCTGCGCGAACCACTTGAGGTTCCGGGACTCCTTGACGTCCAGACCGATTCGTTCGAGTGGCTGATCGGTTCGCCGCGCTGGCGCGAATCCGCCGCCGAGCGGGGTGATGTCAACCCAGTGGGTGGCCTGGAAGAGGTGCTCTACGAGCTGTCTCCGATCGAGGACTTCTCCGGGTCGATGTCGTTGTCGTTCTCTGACCCTCGTTTCGACGATGTCAAGGCACCCGTCGACGAGTGCAAAGACAAGGACATGACGTACGCGGCTCCACTGTTCGTCACCGCCGAGTTCATCAACAACAACACCGGTGAGATCAAGAGTCAGACGGTGTTCATGGGTGACTTCCCGATGATGACCGAGAAGGGCACGTTCATCATCAACGGGACCGAGCGTGTGGTGGTCAGCCAGCTGGTGCGGTCGCCCGGGGTGTACTTCGACGAGACCATTGACAAGTCCACCGACAAGACGCTGCACAGCGTCAAGGTGATCCCGAGCCGCGGCGCGTGGCTCGAGTTTGACGTCGACAAGCGCGACACCGTCGGCGTGCGCATCGACCGCAAACGCCGGCAACCGGTCACCGTGCTGCTCAAGGCGCTGGGCTGGACCAGCGAGCAGATTGTCGAGCGGTTCGGGTTCTCCGAGATCATGCGATCGACGCTGGAGAAGGACAACACCGTCGGCACCGACGAGGCGCTGTTGGACATCTACCGCAAGCTGCGTCCGGGCGAGCCCCCGACCAAAGAGTCAGCGCAGACGCTGTTGGAAAACTTGTTCTTCAAGGAGAAGCGCTACGACCTGGCCCGCGTCGGTCGCTATAAGGTCAACAAGAAGCTCGGGCTGCATGTCGGCGAGCCCATCACGTCGTCGACGCTGACCGAAGAAGACGTCGTGGCCACCATCGAATATCTGGTCCGCTTGCACGAGGGTCAGACCACGATGACCGTTCCGGGCGGCGTCGAGGTGCCGGTGGAAACCGACGACATCGACCACTTCGGCAACCGCCGCCTGCGTACGGTCGGCGAGCTGATCCAAAACCAGATCCGGGTCGGCATGTCGCGGATGGAGCGGGTGGTCCGGGAGCGGATGACCACCCAGGACGTGGAGGCGATCACACCGCAGACGTTGATCAACATCCGGCCGGTGGTCGCCGCGATCAAGGAGTTCTTCGGCACCAGCCAGCTGAGCCAATTCATGGACCAGAACAACCCGCTGTCGGGGTTGACCCACAAGCGCCGACTGTCGGCGCTGGGGCCCGGCGGTCTGTCACGTGAGCGTGCCGGGCTGGAGGTCCGCGACGTGCACCCGTCGCACTACGGCCGGATGTGCCCGATCGAAACCCCTGAGGGGCCCAACATCGGTCTGATCGGCTCGCTGTCGGTGTACGCGCGGGTCAACCCGTTCGGGTTCATCGAAACGCCGTACCGCAAGGTGGTCGACGGCGTGGTTAGCGACGAGATCGTGTACCTGACCGCCGACGAGGAGGACCGCCACGTGGTGGCACAGGCCAATTCGCCGATCGATGCGGACGGTCGCTTCGTCGAGCCGCGCGTGCTGGTCCGCCGCAAGGCGGGCGAGGTGGAGTACGTGCCCTCGTCTGAGGTGGACTACATGGACGTCTCGCCCCGCCAGATGGTGTCGGTGGCCACCGCGATGATTCCCTTCCTGGAGCACGACGACGCCAACCGTGCCCTCATGGGGGCAAACATGCAGCGCCAGGCGGTGCCGCTGGTCCGTAGCGAGGCCCCGCTGGTGGGCACCGGGATGGAGCTGCGCGCGGCGATCGACGCCGGCGACGTCGTCGTCGCCGAAGAAAGCGGCGTCATCGAGGAGGTGTCGGCCGACTACATCACTGTGATGCACGACAACGGCACCCGGCGTACCTACCGGATGCGCAAGTTTGCCCGGTCCAACCACGGCACTTGCGCCAACCAGTGCCCCATCGTGGACGCGGGCGACCGAGTCGAGGCCGGTCAGGTGATCGCCGACGGTCCCTGTACTGACGACGGCGAGATGGCGCTGGGCAAGAACCTGCTGGTGGCCATCATGCCGTGGGAGGGCCACAACTACGAGGACGCGATCATCCTGTCCAACCGCCTGGTCGAAGAGGACGTGCTCACCTCGATCCACATCGAGGAGCATGAGATCGATGCTCGCGACACCAAGCTGGGTGCGGAGGAGATCACCCGCGACATCCCGAACATCTCCGACGAGGTGCTCGCCGACCTGGATGAGCGGGGCATCGTGCGCATCGGTGCCGAGGTTCGCGACGGGGACATCCTGGTCGGCAAGGTCACCCCGAAGGGTGAGACCGAGCTGACGCCGGAGGAGCGGCTGCTGCGTGCCATCTTCGGTGAGAAGGCCCGCGAGGTGCGCGACACTTCGCTGAAGGTGCCGCACGGCGAATCCGGCAAGGTGATCGGCATTCGGGTGTTTTCCCGCGAGGACGAGGACGAGTTGCCGGCCGGTGTCAACGAGCTGGTGCGTGTGTATGTGGCTCAGAAACGCAAGATCTCCGACGGTGACAAGCTGGCCGGCCGGCACGGCAACAAGGGCGTGATCGGCAAGATCCTGCCGGTTGAGGACATGCCGTTCCTTGCCGACGGCACCCCGGTGGACATTATTTTGAACACCCACGGCGTGCCGCGACGGATGAACATCGGCCAGATTTTGGAGACCCACCTGGGTTGGTGTGCCCACAGCGGCTGGAAGGTCGACGCCGCCAAGGGGGTTCCGGACTGGGCCGCCAGGCTGCCCGACGAACTGCTCGAGGCGCAGCCGAACGCCATTGTGTCGACGCCGGTGTTCGACGGCGCCCAGGAGGCCGAGCTGCAGGGCCTGTTGTCGTGCACGCTGCCCAACCGCGACGGTGACGTGCTGGTCGACGCCGACGGCAAGGCCATGCTCTTCGACGGGCGCAGCGGCGAGCCGTTCCCGTACCCGGTCACGGTTGGCTACATGTACATCATGAAGCTGCACCACCTGGTGGACGACAAGATCCACGCCCGCTCCACCGGGCCGTACTCGATGATCACCCAGCAGCCGCTGGGCGGTAAGGCGCAGTTCGGTGGCCAGCGGTTCGGGGAGATGGAGTGCTGGGCCATGCAGGCCTACGGTGCTGCCTACACCCTGCAGGAGCTGTTGACCATCAAGTCCGATGACACCGTCGGCCGCGTCAAGGTGTACGAGGCGATCGTCAAGGGTGAGAACATCCCGGAGCCGGGCATCCCCGAGTCGTTCAAGGTGCTGCTCAAAGAACTGCAGTCGCTGTGCCTCAACGTCGAGGTGCTATCGAGTGACGGTGCGGCGATCGAACTGCGCGAAGGTGAGGACGAGGACCTGGAGCGGGCCGCGGCCAACCTGGGAATCAATCTGTCCCGCAACGAATCCGCAAGTGTCGAGGATCTTGCGTAA	MLEGCILADSRQSKTAASPSPSRPQSSSNNSVPGAPNRVSFAKLREPLEVPGLLDVQTDSFEWLIGSPRWRESAAERGDVNPVGGLEEVLYELSPIEDFSGSMSLSFSDPRFDDVKAPVDECKDKDMTYAAPLFVTAEFINNNTGEIKSQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDKSTDKTLHSVKVIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQIVERFGFSEIMRSTLEKDNTVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHVGEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRKAGEVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVAEESGVIEEVSADYITVMHDNGTRRTYRMRKFARSNHGTCANQCPIVDAGDRVEAGQVIADGPCTDDGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDEDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLADGTPVDIILNTHGVPRRMNIGQILETHLGWCAHSGWKVDAAKGVPDWAARLPDELLEAQPNAIVSTPVFDGAQEAELQGLLSCTLPNRDGDVLVDADGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLCLNVEVLSSDGAAIELREGEDEDLERAAANLGINLSRNESASVEDLA	MADSRQSKTAASPSPSRPQSSSNNSVPGAPNRVSFAKLREPLEVPGLLDVQTDSFEWLIGSPRWRESAAERGDVNPVGGLEEVLYELSPIEDFSGSMSLSFSDPRFDDVKAPVDECKDKDMTYAAPLFVTAEFINNNTGEIKSQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDKSTDKTLHSVKVIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQIVERFGFSEIMRSTLEKDNTVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHVGEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRKAGEVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVAEESGVIEEVSADYITVMHDNGTRRTYRMRKFARSNHGTCANQCPIVDAGDRVEAGQVIADGPCTDDGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDEDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLADGTPVDIILNTHGVPRRMNIGQILETHLGWCAHSGWKVDAAKGVPDWAARLPDELLEAQPNAIVSTPVFDGAQEAELQGLLSCTLPNRDGDVLVDADGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLCLNVEVLSSDGAAIELREGEDEDLERAAANLGINLSRNESASVEDLA	100.51	gnl|BL_ORD_ID|2005|hsp_num:0	1237
+NC_000962.3_689 # 759789 # 763325 # 1 # ID=1_689;partial=00;start_type=GTG;rbs_motif=None;rbs_spacer=None;gc_cont=0.643	NC_000962.3_689 	759789	763325	+	Strict	2300	2394.77	Mycobacterium tuberculosis rpoB mutants conferring resistance to rifampicin	99.91	3000805	protein variant model	D516G, H526T, L511R	n/a	rifamycin antibiotic	antibiotic target alteration; antibiotic target replacement	rifamycin-resistant beta-subunit of RNA polymerase (rpoB)	GTGCTGGAAGGATGCATCTTGGCAGATTCCCGCCAGAGCAAAACAGCCGCTAGTCCTAGTCCGAGTCGCCCGCAAAGTTCCTCGAATAACTCCGTACCCGGAGCGCCAAACCGGGTCTCCTTCGCTAAGCTGCGCGAACCACTTGAGGTTCCGGGACTCCTTGACGTCCAGACCGATTCGTTCGAGTGGCTGATCGGTTCGCCGCGCTGGCGCGAATCCGCCGCCGAGCGGGGTGATGTCAACCCAGTGGGTGGCCTGGAAGAGGTGCTCTACGAGCTGTCTCCGATCGAGGACTTCTCCGGGTCGATGTCGTTGTCGTTCTCTGACCCTCGTTTCGACGATGTCAAGGCACCCGTCGACGAGTGCAAAGACAAGGACATGACGTACGCGGCTCCACTGTTCGTCACCGCCGAGTTCATCAACAACAACACCGGTGAGATCAAGAGTCAGACGGTGTTCATGGGTGACTTCCCGATGATGACCGAGAAGGGCACGTTCATCATCAACGGGACCGAGCGTGTGGTGGTCAGCCAGCTGGTGCGGTCGCCCGGGGTGTACTTCGACGAGACCATTGACAAGTCCACCGACAAGACGCTGCACAGCGTCAAGGTGATCCCGAGCCGCGGCGCGTGGCTCGAGTTTGACGTCGACAAGCGCGACACCGTCGGCGTGCGCATCGACCGCAAACGCCGGCAACCGGTCACCGTGCTGCTCAAGGCGCTGGGCTGGACCAGCGAGCAGATTGTCGAGCGGTTCGGGTTCTCCGAGATCATGCGATCGACGCTGGAGAAGGACAACACCGTCGGCACCGACGAGGCGCTGTTGGACATCTACCGCAAGCTGCGTCCGGGCGAGCCCCCGACCAAAGAGTCAGCGCAGACGCTGTTGGAAAACTTGTTCTTCAAGGAGAAGCGCTACGACCTGGCCCGCGTCGGTCGCTATAAGGTCAACAAGAAGCTCGGGCTGCATGTCGGCGAGCCCATCACGTCGTCGACGCTGACCGAAGAAGACGTCGTGGCCACCATCGAATATCTGGTCCGCTTGCACGAGGGTCAGACCACGATGACCGTTCCGGGCGGCGTCGAGGTGCCGGTGGAAACCGACGACATCGACCACTTCGGCAACCGCCGCCTGCGTACGGTCGGCGAGCTGATCCAAAACCAGATCCGGGTCGGCATGTCGCGGATGGAGCGGGTGGTCCGGGAGCGGATGACCACCCAGGACGTGGAGGCGATCACACCGCAGACGTTGATCAACATCCGGCCGGTGGTCGCCGCGATCAAGGAGTTCTTCGGCACCAGCCAGCTGAGCCAATTCATGGACCAGAACAACCCGCTGTCGGGGTTGACCCACAAGCGCCGACTGTCGGCGCTGGGGCCCGGCGGTCTGTCACGTGAGCGTGCCGGGCTGGAGGTCCGCGACGTGCACCCGTCGCACTACGGCCGGATGTGCCCGATCGAAACCCCTGAGGGGCCCAACATCGGTCTGATCGGCTCGCTGTCGGTGTACGCGCGGGTCAACCCGTTCGGGTTCATCGAAACGCCGTACCGCAAGGTGGTCGACGGCGTGGTTAGCGACGAGATCGTGTACCTGACCGCCGACGAGGAGGACCGCCACGTGGTGGCACAGGCCAATTCGCCGATCGATGCGGACGGTCGCTTCGTCGAGCCGCGCGTGCTGGTCCGCCGCAAGGCGGGCGAGGTGGAGTACGTGCCCTCGTCTGAGGTGGACTACATGGACGTCTCGCCCCGCCAGATGGTGTCGGTGGCCACCGCGATGATTCCCTTCCTGGAGCACGACGACGCCAACCGTGCCCTCATGGGGGCAAACATGCAGCGCCAGGCGGTGCCGCTGGTCCGTAGCGAGGCCCCGCTGGTGGGCACCGGGATGGAGCTGCGCGCGGCGATCGACGCCGGCGACGTCGTCGTCGCCGAAGAAAGCGGCGTCATCGAGGAGGTGTCGGCCGACTACATCACTGTGATGCACGACAACGGCACCCGGCGTACCTACCGGATGCGCAAGTTTGCCCGGTCCAACCACGGCACTTGCGCCAACCAGTGCCCCATCGTGGACGCGGGCGACCGAGTCGAGGCCGGTCAGGTGATCGCCGACGGTCCCTGTACTGACGACGGCGAGATGGCGCTGGGCAAGAACCTGCTGGTGGCCATCATGCCGTGGGAGGGCCACAACTACGAGGACGCGATCATCCTGTCCAACCGCCTGGTCGAAGAGGACGTGCTCACCTCGATCCACATCGAGGAGCATGAGATCGATGCTCGCGACACCAAGCTGGGTGCGGAGGAGATCACCCGCGACATCCCGAACATCTCCGACGAGGTGCTCGCCGACCTGGATGAGCGGGGCATCGTGCGCATCGGTGCCGAGGTTCGCGACGGGGACATCCTGGTCGGCAAGGTCACCCCGAAGGGTGAGACCGAGCTGACGCCGGAGGAGCGGCTGCTGCGTGCCATCTTCGGTGAGAAGGCCCGCGAGGTGCGCGACACTTCGCTGAAGGTGCCGCACGGCGAATCCGGCAAGGTGATCGGCATTCGGGTGTTTTCCCGCGAGGACGAGGACGAGTTGCCGGCCGGTGTCAACGAGCTGGTGCGTGTGTATGTGGCTCAGAAACGCAAGATCTCCGACGGTGACAAGCTGGCCGGCCGGCACGGCAACAAGGGCGTGATCGGCAAGATCCTGCCGGTTGAGGACATGCCGTTCCTTGCCGACGGCACCCCGGTGGACATTATTTTGAACACCCACGGCGTGCCGCGACGGATGAACATCGGCCAGATTTTGGAGACCCACCTGGGTTGGTGTGCCCACAGCGGCTGGAAGGTCGACGCCGCCAAGGGGGTTCCGGACTGGGCCGCCAGGCTGCCCGACGAACTGCTCGAGGCGCAGCCGAACGCCATTGTGTCGACGCCGGTGTTCGACGGCGCCCAGGAGGCCGAGCTGCAGGGCCTGTTGTCGTGCACGCTGCCCAACCGCGACGGTGACGTGCTGGTCGACGCCGACGGCAAGGCCATGCTCTTCGACGGGCGCAGCGGCGAGCCGTTCCCGTACCCGGTCACGGTTGGCTACATGTACATCATGAAGCTGCACCACCTGGTGGACGACAAGATCCACGCCCGCTCCACCGGGCCGTACTCGATGATCACCCAGCAGCCGCTGGGCGGTAAGGCGCAGTTCGGTGGCCAGCGGTTCGGGGAGATGGAGTGCTGGGCCATGCAGGCCTACGGTGCTGCCTACACCCTGCAGGAGCTGTTGACCATCAAGTCCGATGACACCGTCGGCCGCGTCAAGGTGTACGAGGCGATCGTCAAGGGTGAGAACATCCCGGAGCCGGGCATCCCCGAGTCGTTCAAGGTGCTGCTCAAAGAACTGCAGTCGCTGTGCCTCAACGTCGAGGTGCTATCGAGTGACGGTGCGGCGATCGAACTGCGCGAAGGTGAGGACGAGGACCTGGAGCGGGCCGCGGCCAACCTGGGAATCAATCTGTCCCGCAACGAATCCGCAAGTGTCGAGGATCTTGCGTAA	MLEGCILADSRQSKTAASPSPSRPQSSSNNSVPGAPNRVSFAKLREPLEVPGLLDVQTDSFEWLIGSPRWRESAAERGDVNPVGGLEEVLYELSPIEDFSGSMSLSFSDPRFDDVKAPVDECKDKDMTYAAPLFVTAEFINNNTGEIKSQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDKSTDKTLHSVKVIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQIVERFGFSEIMRSTLEKDNTVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHVGEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRKAGEVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVAEESGVIEEVSADYITVMHDNGTRRTYRMRKFARSNHGTCANQCPIVDAGDRVEAGQVIADGPCTDDGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDEDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLADGTPVDIILNTHGVPRRMNIGQILETHLGWCAHSGWKVDAAKGVPDWAARLPDELLEAQPNAIVSTPVFDGAQEAELQGLLSCTLPNRDGDVLVDADGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLCLNVEVLSSDGAAIELREGEDEDLERAAANLGINLSRNESASVEDLA	MADSRQSKTAASPSPSRPQSSSNNSVPGAPNRVSFAKLREPLEVPGLLDVQTDSFEWLIGSPRWRESAAERGDVNPVGGLEEVLYELSPIEDFSGSMSLSFSDPRFDDVKAPVDECKDKDMTYAAPLFVTAEFINNNTGEIKSQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDKSTDKTLHSVKVIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQIVERFGFSEIMRSTLEKDNTVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHVGEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRKAGEVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVAEESGVIEEVSADYITVMHDNGTRRTYRMRKFARSNHGTCANQCPIVDAGDRVEAGQVIADGPCTDDGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDEDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLADGTPVDIILNTHGVPRRMNIGQILETHLGWCAHSGWKVDAAKGVPDWAARLPDELLEAQPNAIVSTPVFDGAQEAELQGLLSCTLPNRDGDVLVDADGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLCLNVEVLSSDGAAIELREGEDEDLERAAANLGINLSRNESASVEDLA	100.51	gnl|BL_ORD_ID|2005|hsp_num:0	1237
+NC_000962.3_689 # 759789 # 763325 # 1 # ID=1_689;partial=00;start_type=GTG;rbs_motif=None;rbs_spacer=None;gc_cont=0.643	NC_000962.3_689 	759789	763325	+	Strict	2300	2394.77	Mycobacterium tuberculosis rpoB mutants conferring resistance to rifampicin	99.91	3000026	protein variant model	D516G, H526T, L511R	n/a	rifamycin antibiotic	antibiotic target alteration; antibiotic target replacement	rifamycin-resistant beta-subunit of RNA polymerase (rpoB)	GTGCTGGAAGGATGCATCTTGGCAGATTCCCGCCAGAGCAAAACAGCCGCTAGTCCTAGTCCGAGTCGCCCGCAAAGTTCCTCGAATAACTCCGTACCCGGAGCGCCAAACCGGGTCTCCTTCGCTAAGCTGCGCGAACCACTTGAGGTTCCGGGACTCCTTGACGTCCAGACCGATTCGTTCGAGTGGCTGATCGGTTCGCCGCGCTGGCGCGAATCCGCCGCCGAGCGGGGTGATGTCAACCCAGTGGGTGGCCTGGAAGAGGTGCTCTACGAGCTGTCTCCGATCGAGGACTTCTCCGGGTCGATGTCGTTGTCGTTCTCTGACCCTCGTTTCGACGATGTCAAGGCACCCGTCGACGAGTGCAAAGACAAGGACATGACGTACGCGGCTCCACTGTTCGTCACCGCCGAGTTCATCAACAACAACACCGGTGAGATCAAGAGTCAGACGGTGTTCATGGGTGACTTCCCGATGATGACCGAGAAGGGCACGTTCATCATCAACGGGACCGAGCGTGTGGTGGTCAGCCAGCTGGTGCGGTCGCCCGGGGTGTACTTCGACGAGACCATTGACAAGTCCACCGACAAGACGCTGCACAGCGTCAAGGTGATCCCGAGCCGCGGCGCGTGGCTCGAGTTTGACGTCGACAAGCGCGACACCGTCGGCGTGCGCATCGACCGCAAACGCCGGCAACCGGTCACCGTGCTGCTCAAGGCGCTGGGCTGGACCAGCGAGCAGATTGTCGAGCGGTTCGGGTTCTCCGAGATCATGCGATCGACGCTGGAGAAGGACAACACCGTCGGCACCGACGAGGCGCTGTTGGACATCTACCGCAAGCTGCGTCCGGGCGAGCCCCCGACCAAAGAGTCAGCGCAGACGCTGTTGGAAAACTTGTTCTTCAAGGAGAAGCGCTACGACCTGGCCCGCGTCGGTCGCTATAAGGTCAACAAGAAGCTCGGGCTGCATGTCGGCGAGCCCATCACGTCGTCGACGCTGACCGAAGAAGACGTCGTGGCCACCATCGAATATCTGGTCCGCTTGCACGAGGGTCAGACCACGATGACCGTTCCGGGCGGCGTCGAGGTGCCGGTGGAAACCGACGACATCGACCACTTCGGCAACCGCCGCCTGCGTACGGTCGGCGAGCTGATCCAAAACCAGATCCGGGTCGGCATGTCGCGGATGGAGCGGGTGGTCCGGGAGCGGATGACCACCCAGGACGTGGAGGCGATCACACCGCAGACGTTGATCAACATCCGGCCGGTGGTCGCCGCGATCAAGGAGTTCTTCGGCACCAGCCAGCTGAGCCAATTCATGGACCAGAACAACCCGCTGTCGGGGTTGACCCACAAGCGCCGACTGTCGGCGCTGGGGCCCGGCGGTCTGTCACGTGAGCGTGCCGGGCTGGAGGTCCGCGACGTGCACCCGTCGCACTACGGCCGGATGTGCCCGATCGAAACCCCTGAGGGGCCCAACATCGGTCTGATCGGCTCGCTGTCGGTGTACGCGCGGGTCAACCCGTTCGGGTTCATCGAAACGCCGTACCGCAAGGTGGTCGACGGCGTGGTTAGCGACGAGATCGTGTACCTGACCGCCGACGAGGAGGACCGCCACGTGGTGGCACAGGCCAATTCGCCGATCGATGCGGACGGTCGCTTCGTCGAGCCGCGCGTGCTGGTCCGCCGCAAGGCGGGCGAGGTGGAGTACGTGCCCTCGTCTGAGGTGGACTACATGGACGTCTCGCCCCGCCAGATGGTGTCGGTGGCCACCGCGATGATTCCCTTCCTGGAGCACGACGACGCCAACCGTGCCCTCATGGGGGCAAACATGCAGCGCCAGGCGGTGCCGCTGGTCCGTAGCGAGGCCCCGCTGGTGGGCACCGGGATGGAGCTGCGCGCGGCGATCGACGCCGGCGACGTCGTCGTCGCCGAAGAAAGCGGCGTCATCGAGGAGGTGTCGGCCGACTACATCACTGTGATGCACGACAACGGCACCCGGCGTACCTACCGGATGCGCAAGTTTGCCCGGTCCAACCACGGCACTTGCGCCAACCAGTGCCCCATCGTGGACGCGGGCGACCGAGTCGAGGCCGGTCAGGTGATCGCCGACGGTCCCTGTACTGACGACGGCGAGATGGCGCTGGGCAAGAACCTGCTGGTGGCCATCATGCCGTGGGAGGGCCACAACTACGAGGACGCGATCATCCTGTCCAACCGCCTGGTCGAAGAGGACGTGCTCACCTCGATCCACATCGAGGAGCATGAGATCGATGCTCGCGACACCAAGCTGGGTGCGGAGGAGATCACCCGCGACATCCCGAACATCTCCGACGAGGTGCTCGCCGACCTGGATGAGCGGGGCATCGTGCGCATCGGTGCCGAGGTTCGCGACGGGGACATCCTGGTCGGCAAGGTCACCCCGAAGGGTGAGACCGAGCTGACGCCGGAGGAGCGGCTGCTGCGTGCCATCTTCGGTGAGAAGGCCCGCGAGGTGCGCGACACTTCGCTGAAGGTGCCGCACGGCGAATCCGGCAAGGTGATCGGCATTCGGGTGTTTTCCCGCGAGGACGAGGACGAGTTGCCGGCCGGTGTCAACGAGCTGGTGCGTGTGTATGTGGCTCAGAAACGCAAGATCTCCGACGGTGACAAGCTGGCCGGCCGGCACGGCAACAAGGGCGTGATCGGCAAGATCCTGCCGGTTGAGGACATGCCGTTCCTTGCCGACGGCACCCCGGTGGACATTATTTTGAACACCCACGGCGTGCCGCGACGGATGAACATCGGCCAGATTTTGGAGACCCACCTGGGTTGGTGTGCCCACAGCGGCTGGAAGGTCGACGCCGCCAAGGGGGTTCCGGACTGGGCCGCCAGGCTGCCCGACGAACTGCTCGAGGCGCAGCCGAACGCCATTGTGTCGACGCCGGTGTTCGACGGCGCCCAGGAGGCCGAGCTGCAGGGCCTGTTGTCGTGCACGCTGCCCAACCGCGACGGTGACGTGCTGGTCGACGCCGACGGCAAGGCCATGCTCTTCGACGGGCGCAGCGGCGAGCCGTTCCCGTACCCGGTCACGGTTGGCTACATGTACATCATGAAGCTGCACCACCTGGTGGACGACAAGATCCACGCCCGCTCCACCGGGCCGTACTCGATGATCACCCAGCAGCCGCTGGGCGGTAAGGCGCAGTTCGGTGGCCAGCGGTTCGGGGAGATGGAGTGCTGGGCCATGCAGGCCTACGGTGCTGCCTACACCCTGCAGGAGCTGTTGACCATCAAGTCCGATGACACCGTCGGCCGCGTCAAGGTGTACGAGGCGATCGTCAAGGGTGAGAACATCCCGGAGCCGGGCATCCCCGAGTCGTTCAAGGTGCTGCTCAAAGAACTGCAGTCGCTGTGCCTCAACGTCGAGGTGCTATCGAGTGACGGTGCGGCGATCGAACTGCGCGAAGGTGAGGACGAGGACCTGGAGCGGGCCGCGGCCAACCTGGGAATCAATCTGTCCCGCAACGAATCCGCAAGTGTCGAGGATCTTGCGTAA	MLEGCILADSRQSKTAASPSPSRPQSSSNNSVPGAPNRVSFAKLREPLEVPGLLDVQTDSFEWLIGSPRWRESAAERGDVNPVGGLEEVLYELSPIEDFSGSMSLSFSDPRFDDVKAPVDECKDKDMTYAAPLFVTAEFINNNTGEIKSQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDKSTDKTLHSVKVIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQIVERFGFSEIMRSTLEKDNTVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHVGEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRKAGEVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVAEESGVIEEVSADYITVMHDNGTRRTYRMRKFARSNHGTCANQCPIVDAGDRVEAGQVIADGPCTDDGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDEDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLADGTPVDIILNTHGVPRRMNIGQILETHLGWCAHSGWKVDAAKGVPDWAARLPDELLEAQPNAIVSTPVFDGAQEAELQGLLSCTLPNRDGDVLVDADGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLCLNVEVLSSDGAAIELREGEDEDLERAAANLGINLSRNESASVEDLA	MADSRQSKTAASPSPSRPQSSSNNSVPGAPNRVSFAKLREPLEVPGLLDVQTDSFEWLIGSPRWRESAAERGDVNPVGGLEEVLYELSPIEDFSGSMSLSFSDPRFDDVKAPVDECKDKDMTYAAPLFVTAEFINNNTGEIKSQTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDKSTDKTLHSVKVIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQIVERFGFSEIMRSTLEKDNTVGTDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHVGEPITSSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGELIQNQIRVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGLTHKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPFGFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRKAGEVEYVPSSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTGMELRAAIDAGDVVVAEESGVIEEVSADYITVMHDNGTRRTYRMRKFARSNHGTCANQCPIVDAGDRVEAGQVIADGPCTDDGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVLTSIHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVRDGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDEDELPAGVNELVRVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLADGTPVDIILNTHGVPRRMNIGQILETHLGWCAHSGWKVDAAKGVPDWAARLPDELLEAQPNAIVSTPVFDGAQEAELQGLLSCTLPNRDGDVLVDADGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLCLNVEVLSSDGAAIELREGEDEDLERAAANLGINLSRNESASVEDLA	100.51	gnl|BL_ORD_ID|2005|hsp_num:0	1237
diff --git a/q2_amr/types/_transformer.py b/q2_amr/types/_transformer.py
index 163740a..0700715 100644
--- a/q2_amr/types/_transformer.py
+++ b/q2_amr/types/_transformer.py
@@ -175,8 +175,7 @@ def _11(data: CARDAnnotationDirectoryFormat) -> ProteinsDirectoryFormat:
     return proteins_directory
 
 
-def create_dir_structure(data, seq_type, genes_protein_directory):
-    annotation_dir = str(data)
+def create_dir_structure(annotation_dir, seq_type, genes_protein_directory):
     for sample in os.listdir(annotation_dir):
         for bin in os.listdir(os.path.join(annotation_dir, sample)):
             for file in os.listdir(os.path.join(annotation_dir, sample, bin)):
@@ -233,9 +232,41 @@ def read_mapping_data(data_path, variant):
 
 @plugin.register_transformer
 def _12(data: CARDAlleleAnnotationDirectoryFormat) -> qiime2.Metadata:
-    return read_mapping_data(data, "allele")
+    return tabulate_data(data, "allele")
 
 
 @plugin.register_transformer
 def _13(data: CARDGeneAnnotationDirectoryFormat) -> qiime2.Metadata:
-    return read_mapping_data(data, "gene")
+    return tabulate_data(data, "gene")
+
+
+@plugin.register_transformer
+def _14(data: CARDAnnotationDirectoryFormat) -> qiime2.Metadata:
+    return tabulate_data(data, "mags")
+
+
+def tabulate_data(data_path, data_type):
+    df_list = []
+    for samp in os.listdir(str(data_path)):
+        if data_type == "mags":
+            for bin in os.listdir(os.path.join(str(data_path), samp)):
+                file_path = os.path.join(
+                    str(data_path), samp, bin, "amr_annotation.txt"
+                )
+                df = pd.read_csv(file_path, sep="\t")
+                df.insert(0, "Sample Name", f"{samp}/{bin}")
+                df["Nudged"] = df["Nudged"].astype(str)
+        elif data_type == "gene" or "allele":
+            file_path = os.path.join(
+                str(data_path), samp, f"{data_type}_mapping_data.txt"
+            )
+            df = pd.read_csv(file_path, sep="\t")
+            df.insert(0, "Sample Name", samp)
+        df_list.append(df)
+    df_combined = pd.concat(df_list, axis=0)
+    df_combined.reset_index(inplace=True, drop=True)
+    df_combined.index.name = "id"
+    df_combined.index = df_combined.index.astype(str)
+    if data_type == "mags":
+        df_combined.rename(columns={"ID": "HSP_Identifier"}, inplace=True)
+    return qiime2.Metadata(df_combined)
diff --git a/q2_amr/types/_type.py b/q2_amr/types/_type.py
index 6e74527..c281c4e 100644
--- a/q2_amr/types/_type.py
+++ b/q2_amr/types/_type.py
@@ -10,5 +10,9 @@
 
 CARDDatabase = SemanticType("CARDDatabase")
 CARDAnnotation = SemanticType("CARDAnnotation", variant_of=SampleData.field["type"])
-CARDAlleleAnnotation = SemanticType("CARDAlleleAnnotation")
-CARDGeneAnnotation = SemanticType("CARDGeneAnnotation")
+CARDAlleleAnnotation = SemanticType(
+    "CARDAlleleAnnotation", variant_of=SampleData.field["type"]
+)
+CARDGeneAnnotation = SemanticType(
+    "CARDGeneAnnotation", variant_of=SampleData.field["type"]
+)
diff --git a/q2_amr/types/tests/data/annotate_mags_output/sample1/bin1/sample1_bin1_amr_annotation.json b/q2_amr/types/tests/data/annotate_mags_output/sample1/bin1/amr_annotation.json
similarity index 100%
rename from q2_amr/types/tests/data/annotate_mags_output/sample1/bin1/sample1_bin1_amr_annotation.json
rename to q2_amr/types/tests/data/annotate_mags_output/sample1/bin1/amr_annotation.json
diff --git a/q2_amr/types/tests/data/annotate_mags_output/sample1/bin1/sample1_bin1_amr_annotation.txt b/q2_amr/types/tests/data/annotate_mags_output/sample1/bin1/amr_annotation.txt
similarity index 100%
rename from q2_amr/types/tests/data/annotate_mags_output/sample1/bin1/sample1_bin1_amr_annotation.txt
rename to q2_amr/types/tests/data/annotate_mags_output/sample1/bin1/amr_annotation.txt
diff --git a/q2_amr/types/tests/data/annotate_mags_output/sample2/bin1/sample2_bin1_amr_annotation.json b/q2_amr/types/tests/data/annotate_mags_output/sample2/bin1/amr_annotation.json
similarity index 100%
rename from q2_amr/types/tests/data/annotate_mags_output/sample2/bin1/sample2_bin1_amr_annotation.json
rename to q2_amr/types/tests/data/annotate_mags_output/sample2/bin1/amr_annotation.json
diff --git a/q2_amr/types/tests/data/annotate_mags_output/sample2/bin1/sample2_bin1_amr_annotation.txt b/q2_amr/types/tests/data/annotate_mags_output/sample2/bin1/amr_annotation.txt
similarity index 96%
rename from q2_amr/types/tests/data/annotate_mags_output/sample2/bin1/sample2_bin1_amr_annotation.txt
rename to q2_amr/types/tests/data/annotate_mags_output/sample2/bin1/amr_annotation.txt
index 1f16da6..dbf3c40 100644
--- a/q2_amr/types/tests/data/annotate_mags_output/sample2/bin1/sample2_bin1_amr_annotation.txt
+++ b/q2_amr/types/tests/data/annotate_mags_output/sample2/bin1/amr_annotation.txt
@@ -1,3 +1,3 @@
 ORF_ID	Contig	Start	Stop	Orientation	Cut_Off	Pass_Bitscore	Best_Hit_Bitscore	Best_Hit_ARO	Best_Identities	ARO	Model_type	SNPs_in_Best_Hit_ARO	Other_SNPs	Drug Class	Resistance Mechanism	AMR Gene Family	Predicted_DNA	Predicted_Protein	CARD_Protein_Sequence	Percentage Length of Reference Sequence	ID	Model_ID	Nudged	Note
-k141_1197_2 # 683 # 1345 # 1 # ID=49_2;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.588	k141_1197_2	683	1345	+	Strict	200	326.635	vanX gene in vanO cluster	75.25	3002954	protein homolog model	n/a	n/a	glycopeptide antibiotic	antibiotic target alteration	vanX; glycopeptide resistance gene cluster	ATGAAGGGTGACTTCGTTTTCGTTGATGAGTGTGTTCCAGGAGTCCGCTGGGATGCCAAATACGCCACATCGGACAACTTCACCGGCAAACCGGTGGAGGGATATCTGGCCAACCGGATTGTCGGGACCAGGGCTTTGTGCTCAGCGCTGGAAAGCGTGCGGCAACGGGCTGCATCCCGCGGTTTCGGGTTGCTGCTGTGGGACGGCTACCGCCCGCAGCGCGCCGTGGATTCGTTCCTGCACTGGGCGAAACAACCAGAGGACGGCGCAACTAAACGCCGCCACTATCCAAATATTTCCCGAGCGGAAATGTTCGAAAGAGGATACGTAGCCTCCAAGTCCGGCCACAGCCGGGGCAGCACCGTCGATTTGACCCTGTATGACCTGGTTACCGGTGACCTCGTTCCCATGGGCGGCGGCCACGACTTGATGGATGAAATTTCGCATCACGGAGCGCCCGGCATCACCCGGGCCGAGACCGGCAACCGCCACACGCTGCGTTCGCTCATGGAGGCCTGCGGTTTCAGTTCCTACGATTCTGAGTGGTGGCATTACACCCTGAAGAACGAACCCTATCCGGACACTTATTTCGATTTTCCCGTTACGGATCCGCTTCCATCAGACGCCGCAACGGCCAGGGACCTTGTCTTCCAGAATGCATAG	MKGDFVFVDECVPGVRWDAKYATSDNFTGKPVEGYLANRIVGTRALCSALESVRQRAASRGFGLLLWDGYRPQRAVDSFLHWAKQPEDGATKRRHYPNISRAEMFERGYVASKSGHSRGSTVDLTLYDLVTGDLVPMGGGHDLMDEISHHGAPGITRAETGNRHTLRSLMEACGFSSYDSEWWHYTLKNEPYPDTYFDFPVTDPLPSDAATARDLVFQNA	MNDDFVYVDDWVPGVRWDAKYATWDNFTGKPVDGYLANRIVGTRALCAALEQAREKAASLGFGLLLWDGYRPRRAVDSFLRWSEQPEDGQTKQRHYPNIDRPEMLEKGYVATQSGHSRGGAVDLTLYHLATGELAPMGGDHDLMDPISHHRARGIKPIESKNRELLRSIMEDCGFDRYDCEWWHYTLKREPYPDVYFDFPIT	108.91	gnl|BL_ORD_ID|1672|hsp_num:0	1699
-k141_10683_1 # 1 # 453 # 1 # ID=423_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.658	k141_10683_1	1	453	+	Strict	50	90.8929	vanY gene in vanM cluster	38.62	3002961	protein homolog model	n/a	n/a	glycopeptide antibiotic	antibiotic target alteration	vanY; glycopeptide resistance gene cluster	GAGGCTGCAGGGGCCTACCGGCAAATGGCCGCGGAAGCGGGCGCCGCCGGAGTTCCCATGTCCGCGGTGAGCGGCTTTCGGACCGGAGCAGAGCAGGACCAGCTGTACGTCTCCTACACGGAGAACTTTGGGCCGGAGGCAGCCGACGCCATTTCGGCCCGTCCCGGGTACAGCGAGCATCAGACGGGGCTGGCCATCGACATCGCCAACCCGGACGGAACCTGCGCCCTGGAATCCTGCTTCGCCGAAACCTTGGCGGGTTCGTGGGCGGCCGCCAATGCCCAGCACTACGGCTTCATCATCCGTTATCCGGCAGGAGCCGAGCACATCACCGGGTACGCCCATGAACCGTGGCATCTGCGGTACGTGGGGACGGAACATGCCCGGACAATGCACGACGCCGGCACCACCTTGGAAGAATATCTGGGACTTCCTGCCGCGCCGGGTTACTGA	EAAGAYRQMAAEAGAAGVPMSAVSGFRTGAEQDQLYVSYTENFGPEAADAISARPGYSEHQTGLAIDIANPDGTCALESCFAETLAGSWAAANAQHYGFIIRYPAGAEHITGYAHEPWHLRYVGTEHARTMHDAGTTLEEYLGLPAAPGY	MVFQGNLLLVNNEYPVLEESIKTDVVNLFKHDELTKGYELLNREIYLSEKVAREFSEMVDAAEKEGVRHFSINSGFRNFDEQNALYQEMGSDYALPAGYSEHNLGLALDIGSTQMEMSEAPEGKWLEDNAWEYGFILRYPMDKTAITGIQYEPWHFRYVGLPHSAIIEEKNFALEEYLDFLKEQKSISGTIHGENYEISYYPITEKTDIEMPANLHYEISGNNMDGVIVTVYR	64.38	gnl|BL_ORD_ID|1673|hsp_num:0	1713
+k141_1197_2 # 683 # 1345 # 1 # ID=49_2;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.588	k141_1197_2	683	1345	+	Strict	200	326.635	vanX gene in vanO cluster	75.25	3002954	protein homolog model	n/a	n/a	glycopeptide antibiotic	antibiotic target alteration	vanX; glycopeptide resistance gene cluster	ATGAAGGGTGACTTCGTTTTCGTTGATGAGTGTGTTCCAGGAGTCCGCTGGGATGCCAAATACGCCACATCGGACAACTTCACCGGCAAACCGGTGGAGGGATATCTGGCCAACCGGATTGTCGGGACCAGGGCTTTGTGCTCAGCGCTGGAAAGCGTGCGGCAACGGGCTGCATCCCGCGGTTTCGGGTTGCTGCTGTGGGACGGCTACCGCCCGCAGCGCGCCGTGGATTCGTTCCTGCACTGGGCGAAACAACCAGAGGACGGCGCAACTAAACGCCGCCACTATCCAAATATTTCCCGAGCGGAAATGTTCGAAAGAGGATACGTAGCCTCCAAGTCCGGCCACAGCCGGGGCAGCACCGTCGATTTGACCCTGTATGACCTGGTTACCGGTGACCTCGTTCCCATGGGCGGCGGCCACGACTTGATGGATGAAATTTCGCATCACGGAGCGCCCGGCATCACCCGGGCCGAGACCGGCAACCGCCACACGCTGCGTTCGCTCATGGAGGCCTGCGGTTTCAGTTCCTACGATTCTGAGTGGTGGCATTACACCCTGAAGAACGAACCCTATCCGGACACTTATTTCGATTTTCCCGTTACGGATCCGCTTCCATCAGACGCCGCAACGGCCAGGGACCTTGTCTTCCAGAATGCATAG	MKGDFVFVDECVPGVRWDAKYATSDNFTGKPVEGYLANRIVGTRALCSALESVRQRAASRGFGLLLWDGYRPQRAVDSFLHWAKQPEDGATKRRHYPNISRAEMFERGYVASKSGHSRGSTVDLTLYDLVTGDLVPMGGGHDLMDEISHHGAPGITRAETGNRHTLRSLMEACGFSSYDSEWWHYTLKNEPYPDTYFDFPVTDPLPSDAATARDLVFQNA	MNDDFVYVDDWVPGVRWDAKYATWDNFTGKPVDGYLANRIVGTRALCAALEQAREKAASLGFGLLLWDGYRPRRAVDSFLRWSEQPEDGQTKQRHYPNIDRPEMLEKGYVATQSGHSRGGAVDLTLYHLATGELAPMGGDHDLMDPISHHRARGIKPIESKNRELLRSIMEDCGFDRYDCEWWHYTLKREPYPDVYFDFPIT	108.91	gnl|BL_ORD_ID|1674|hsp_num:0	1699
+k141_10683_1 # 1 # 453 # 1 # ID=423_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.658	k141_10683_1	1	453	+	Strict	50	90.8929	vanY gene in vanM cluster	38.62	3002961	protein homolog model	n/a	n/a	glycopeptide antibiotic	antibiotic target alteration	vanY; glycopeptide resistance gene cluster	GAGGCTGCAGGGGCCTACCGGCAAATGGCCGCGGAAGCGGGCGCCGCCGGAGTTCCCATGTCCGCGGTGAGCGGCTTTCGGACCGGAGCAGAGCAGGACCAGCTGTACGTCTCCTACACGGAGAACTTTGGGCCGGAGGCAGCCGACGCCATTTCGGCCCGTCCCGGGTACAGCGAGCATCAGACGGGGCTGGCCATCGACATCGCCAACCCGGACGGAACCTGCGCCCTGGAATCCTGCTTCGCCGAAACCTTGGCGGGTTCGTGGGCGGCCGCCAATGCCCAGCACTACGGCTTCATCATCCGTTATCCGGCAGGAGCCGAGCACATCACCGGGTACGCCCATGAACCGTGGCATCTGCGGTACGTGGGGACGGAACATGCCCGGACAATGCACGACGCCGGCACCACCTTGGAAGAATATCTGGGACTTCCTGCCGCGCCGGGTTACTGA	EAAGAYRQMAAEAGAAGVPMSAVSGFRTGAEQDQLYVSYTENFGPEAADAISARPGYSEHQTGLAIDIANPDGTCALESCFAETLAGSWAAANAQHYGFIIRYPAGAEHITGYAHEPWHLRYVGTEHARTMHDAGTTLEEYLGLPAAPGY	MVFQGNLLLVNNEYPVLEESIKTDVVNLFKHDELTKGYELLNREIYLSEKVAREFSEMVDAAEKEGVRHFSINSGFRNFDEQNALYQEMGSDYALPAGYSEHNLGLALDIGSTQMEMSEAPEGKWLEDNAWEYGFILRYPMDKTAITGIQYEPWHFRYVGLPHSAIIEEKNFALEEYLDFLKEQKSISGTIHGENYEISYYPITEKTDIEMPANLHYEISGNNMDGVIVTVYR	64.38	gnl|BL_ORD_ID|1675|hsp_num:0	1713
diff --git a/q2_amr/types/tests/data/annotate_reads_output/sample1/sample1.allele_mapping_data.txt b/q2_amr/types/tests/data/annotate_reads_output/sample1/allele_mapping_data.txt
similarity index 100%
rename from q2_amr/types/tests/data/annotate_reads_output/sample1/sample1.allele_mapping_data.txt
rename to q2_amr/types/tests/data/annotate_reads_output/sample1/allele_mapping_data.txt
diff --git a/q2_amr/types/tests/data/annotate_reads_output/sample1/sample1.gene_mapping_data.txt b/q2_amr/types/tests/data/annotate_reads_output/sample1/gene_mapping_data.txt
similarity index 100%
rename from q2_amr/types/tests/data/annotate_reads_output/sample1/sample1.gene_mapping_data.txt
rename to q2_amr/types/tests/data/annotate_reads_output/sample1/gene_mapping_data.txt
diff --git a/q2_amr/types/tests/data/annotate_reads_output/sample1/sample1.overall_mapping_stats.txt b/q2_amr/types/tests/data/annotate_reads_output/sample1/overall_mapping_stats.txt
similarity index 100%
rename from q2_amr/types/tests/data/annotate_reads_output/sample1/sample1.overall_mapping_stats.txt
rename to q2_amr/types/tests/data/annotate_reads_output/sample1/overall_mapping_stats.txt
diff --git a/q2_amr/types/tests/data/annotate_reads_output/sample2/sample2.allele_mapping_data.txt b/q2_amr/types/tests/data/annotate_reads_output/sample2/allele_mapping_data.txt
similarity index 100%
rename from q2_amr/types/tests/data/annotate_reads_output/sample2/sample2.allele_mapping_data.txt
rename to q2_amr/types/tests/data/annotate_reads_output/sample2/allele_mapping_data.txt
diff --git a/q2_amr/types/tests/data/annotate_reads_output/sample2/sample2.gene_mapping_data.txt b/q2_amr/types/tests/data/annotate_reads_output/sample2/gene_mapping_data.txt
similarity index 100%
rename from q2_amr/types/tests/data/annotate_reads_output/sample2/sample2.gene_mapping_data.txt
rename to q2_amr/types/tests/data/annotate_reads_output/sample2/gene_mapping_data.txt
diff --git a/q2_amr/types/tests/data/annotate_reads_output/sample2/sample2.overall_mapping_stats.txt b/q2_amr/types/tests/data/annotate_reads_output/sample2/overall_mapping_stats.txt
similarity index 100%
rename from q2_amr/types/tests/data/annotate_reads_output/sample2/sample2.overall_mapping_stats.txt
rename to q2_amr/types/tests/data/annotate_reads_output/sample2/overall_mapping_stats.txt
diff --git a/q2_amr/types/tests/test_types_formats_transformers.py b/q2_amr/types/tests/test_types_formats_transformers.py
index 363b67d..db5414b 100644
--- a/q2_amr/types/tests/test_types_formats_transformers.py
+++ b/q2_amr/types/tests/test_types_formats_transformers.py
@@ -224,6 +224,16 @@ def test_CARDAnnotationDirectoryFormat_to_ProteinsDirectoryFormat_transformer(se
             os.path.exists(os.path.join(str(obs), "sample2", "bin1_proteins.fasta"))
         )
 
+    def test_CARDAnnotationDirectoryFormat_to_qiime2_Metadata_transformer(self):
+        transformer = self.get_transformer(
+            CARDAnnotationDirectoryFormat, qiime2.Metadata
+        )
+        annotation = CARDAnnotationDirectoryFormat(
+            self.get_data_path("annotate_mags_output"), "r"
+        )
+        metadata_obt = transformer(annotation)
+        self.assertIsInstance(metadata_obt, qiime2.Metadata)
+
 
 class TestCARDReadsAnnotationTypesAndFormats(AMRTypesTestPluginBase):
     def test_CARDGeneAnnotationDirectoryFormat_to_qiime2_Metadata_transformer(self):