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bokulich-lab · Apr 9, 2024 · d9cb04a · d9cb04a
2 parents 753e572 + 6cb68a5
commit d9cb04a
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diff --git a/q2_amr/card/partition.py b/q2_amr/card/partition.py
@@ -9,9 +9,100 @@
     CARDAlleleAnnotationDirectoryFormat,
     CARDAnnotationDirectoryFormat,
     CARDGeneAnnotationDirectoryFormat,
+    CARDMAGsKmerAnalysisDirectoryFormat,
+    CARDReadsAlleleKmerAnalysisDirectoryFormat,
+    CARDReadsGeneKmerAnalysisDirectoryFormat,
 )
 
 
+def collate_mags_annotations(
+    annotations: CARDAnnotationDirectoryFormat,
+) -> CARDAnnotationDirectoryFormat:
+    return _collate(annotations)
+
+
+def collate_reads_allele_annotations(
+    annotations: CARDAlleleAnnotationDirectoryFormat,
+) -> CARDAlleleAnnotationDirectoryFormat:
+    return _collate(annotations)
+
+
+def collate_reads_gene_annotations(
+    annotations: CARDGeneAnnotationDirectoryFormat,
+) -> CARDGeneAnnotationDirectoryFormat:
+    return _collate(annotations)
+
+
+def collate_mags_kmer_analyses(
+    kmer_analyses: CARDMAGsKmerAnalysisDirectoryFormat,
+) -> CARDMAGsKmerAnalysisDirectoryFormat:
+    return _collate(kmer_analyses)
+
+
+def collate_reads_allele_kmer_analyses(
+    kmer_analyses: CARDReadsAlleleKmerAnalysisDirectoryFormat,
+) -> CARDReadsAlleleKmerAnalysisDirectoryFormat:
+    return _collate(kmer_analyses)
+
+
+def collate_reads_gene_kmer_analyses(
+    kmer_analyses: CARDReadsGeneKmerAnalysisDirectoryFormat,
+) -> CARDReadsGeneKmerAnalysisDirectoryFormat:
+    return _collate(kmer_analyses)
+
+
+def _collate(partition_list):
+    collated_partitions = type(partition_list[0])()
+    # For every partition
+    for partition in partition_list:
+        # For every sample
+        for sample in partition.path.iterdir():
+            # If artifacts are annotations or kmer analyses from MAGs
+            if isinstance(
+                partition_list[0],
+                (CARDAnnotationDirectoryFormat, CARDMAGsKmerAnalysisDirectoryFormat),
+            ):
+                # For every MAG
+                for mag in sample.iterdir():
+                    # Create directories in collate. If dir already exists raise error
+                    try:
+                        os.makedirs(collated_partitions.path / sample.name / mag.name)
+                    except FileExistsError as e:
+                        raise FileExistsError(
+                            f"The directory already exists: {e.filename}. MAG IDs must"
+                            f" be unique across all artifacts. Each artifact in the"
+                            f" list must be unique and cannot be repeated."
+                        )
+
+                    # Copy every file in the MAG directory to the collated directory
+                    for file in mag.iterdir():
+                        duplicate(
+                            file,
+                            collated_partitions.path
+                            / sample.name
+                            / mag.name
+                            / file.name,
+                        )
+
+            # If artifacts are annotations or kmer analyses are from reads
+            else:
+                # Create directories in collate. If dir already exists raise error
+                try:
+                    os.makedirs(collated_partitions.path / sample.name)
+                except FileExistsError as e:
+                    raise FileExistsError(
+                        f"The directory already exists: {e.filename}. Sample IDs must"
+                        f" be unique across all artifacts. Each artifact in the"
+                        f" list must be unique and cannot be repeated."
+                    )
+
+                # Copy every file in the sample directory to the collated directory
+                for file in sample.iterdir():
+                    duplicate(file, collated_partitions.path / sample.name / file.name)
+
+    return collated_partitions
+
+
 def partition_mags_annotations(
     annotations: CARDAnnotationDirectoryFormat, num_partitions: int = None
 ) -> CARDAnnotationDirectoryFormat:

diff --git a/q2_amr/card/tests/data/partitioned/annotate_mags_output_1/sample1/bin1/amr_annotation.json b/q2_amr/card/tests/data/partitioned/annotate_mags_output_1/sample1/bin1/amr_annotation.json
diff --git a/q2_amr/card/tests/data/partitioned/annotate_mags_output_1/sample1/bin1/amr_annotation.txt b/q2_amr/card/tests/data/partitioned/annotate_mags_output_1/sample1/bin1/amr_annotation.txt
@@ -0,0 +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
diff --git a/q2_amr/card/tests/data/partitioned/annotate_mags_output_2/sample2/bin2/amr_annotation.json b/q2_amr/card/tests/data/partitioned/annotate_mags_output_2/sample2/bin2/amr_annotation.json
diff --git a/q2_amr/card/tests/data/partitioned/annotate_mags_output_2/sample2/bin2/amr_annotation.txt b/q2_amr/card/tests/data/partitioned/annotate_mags_output_2/sample2/bin2/amr_annotation.txt
@@ -0,0 +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|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/...ard/tests/data/partitioned/annotate_reads_allele_output_1/sample1/allele_mapping_data.txt b/...ard/tests/data/partitioned/annotate_reads_allele_output_1/sample1/allele_mapping_data.txt
@@ -0,0 +1,5 @@
+Reference Sequence	ARO Term	ARO Accession	Reference Model Type	Reference DB	Reference Allele Source	Resistomes & Variants: Observed in Genome(s)	Resistomes & Variants: Observed in Plasmid(s)	Resistomes & Variants: Observed Pathogen(s)	Completely Mapped Reads	Mapped Reads with Flanking Sequence	All Mapped Reads	Percent Coverage	Length Coverage (bp)	Average MAPQ (Completely Mapped Reads)	Mate Pair Linkage	Reference Length	AMR Gene Family	Drug Class	Resistance Mechanism
+ARO:3000796|ID:121|Name:mdtF|NCBI:U00096.1	mdtF	3000796	protein homolog model	CARD	CARD curation	no data	no data	Escherichia coli	2	0	2	8.09	252	193.00	*	3114	resistance-nodulation-cell division (RND) antibiotic efflux pump	macrolide antibiotic; fluoroquinolone antibiotic; penam	antibiotic efflux
+ARO:3000815|ID:154|Name:mgrA|NCBI:BA000018.3	mgrA	3000815	protein homolog model	CARD	CARD curation	no data	no data	Staphylococcus aureus	1	0	1	19.59	87	172.00	*	444	ATP-binding cassette (ABC) antibiotic efflux pump; major facilitator superfamily (MFS) antibiotic efflux pump	fluoroquinolone antibiotic; cephalosporin; penam; tetracycline antibiotic; peptide antibiotic; disinfecting agents and antiseptics	antibiotic efflux
+ARO:3000805|ID:172|Name:OprN|NCBI:AE004091.2	OprN	3000805	protein homolog model	CARD	CARD curation	no data	no data	Pseudomonas aeruginosa	2	0	2	17.76	252	193.00	*	1419	resistance-nodulation-cell division (RND) antibiotic efflux pump	fluoroquinolone antibiotic; diaminopyrimidine antibiotic; phenicol antibiotic	antibiotic efflux
+ARO:3000026|ID:377|Name:mepA|NCBI:AY661734.1	mepA	3000026	protein homolog model	CARD	CARD curation	no data	no data	Staphylococcus aureus	2	0	2	17.70	240	190.50	*	1356	multidrug and toxic compound extrusion (MATE) transporter	glycylcycline; tetracycline antibiotic	antibiotic efflux
diff --git a/...d/tests/data/partitioned/annotate_reads_allele_output_1/sample1/overall_mapping_stats.txt b/...d/tests/data/partitioned/annotate_reads_allele_output_1/sample1/overall_mapping_stats.txt
@@ -0,0 +1,17 @@
+
+**********************************************
+Stats for BAM file(s):
+**********************************************
+
+Total reads:       5000
+Mapped reads:      59	(1.18%)
+Forward strand:    685	(13.7%)
+Reverse strand:    4315	(86.3%)
+Failed QC:         0	(0%)
+Duplicates:        0	(0%)
+Paired-end reads:  5000	(100%)
+'Proper-pairs':    42	(0.84%)
+Both pairs mapped: 49	(0.98%)
+Read 1:            2500
+Read 2:            2500
+Singletons:        10	(0.2%)
diff --git a/.../card/tests/data/partitioned/annotate_reads_allele_output_1/sample1/sorted.length_100.bam b/.../card/tests/data/partitioned/annotate_reads_allele_output_1/sample1/sorted.length_100.bam
diff --git a/...ard/tests/data/partitioned/annotate_reads_allele_output_2/sample2/allele_mapping_data.txt b/...ard/tests/data/partitioned/annotate_reads_allele_output_2/sample2/allele_mapping_data.txt
@@ -0,0 +1,5 @@
+Reference Sequence	ARO Term	ARO Accession	Reference Model Type	Reference DB	Reference Allele Source	Resistomes & Variants: Observed in Genome(s)	Resistomes & Variants: Observed in Plasmid(s)	Resistomes & Variants: Observed Pathogen(s)	Completely Mapped Reads	Mapped Reads with Flanking Sequence	All Mapped Reads	Percent Coverage	Length Coverage (bp)	Average MAPQ (Completely Mapped Reads)	Mate Pair Linkage	Reference Length	AMR Gene Family	Drug Class	Resistance Mechanism
+ARO:3000796|ID:121|Name:mdtF|NCBI:U00096.1	mdtF	3000796	protein homolog model	CARD	CARD curation	no data	no data	Escherichia coli	2	0	2	8.09	252	193.00	*	3114	resistance-nodulation-cell division (RND) antibiotic efflux pump	macrolide antibiotic; fluoroquinolone antibiotic; penam	antibiotic efflux
+ARO:3000815|ID:154|Name:mgrA|NCBI:BA000018.3	mgrA	3000815	protein homolog model	CARD	CARD curation	no data	no data	Staphylococcus aureus	1	0	1	19.59	87	172.00	*	444	ATP-binding cassette (ABC) antibiotic efflux pump; major facilitator superfamily (MFS) antibiotic efflux pump	fluoroquinolone antibiotic; cephalosporin; penam; tetracycline antibiotic; peptide antibiotic; disinfecting agents and antiseptics	antibiotic efflux
+ARO:3000805|ID:172|Name:OprN|NCBI:AE004091.2	OprN	3000805	protein homolog model	CARD	CARD curation	no data	no data	Pseudomonas aeruginosa	2	0	2	17.76	252	193.00	*	1419	resistance-nodulation-cell division (RND) antibiotic efflux pump	fluoroquinolone antibiotic; diaminopyrimidine antibiotic; phenicol antibiotic	antibiotic efflux
+ARO:3000026|ID:377|Name:mepA|NCBI:AY661734.1	mepA	3000026	protein homolog model	CARD	CARD curation	no data	no data	Staphylococcus aureus	2	0	2	17.70	240	190.50	*	1356	multidrug and toxic compound extrusion (MATE) transporter	glycylcycline; tetracycline antibiotic	antibiotic efflux
diff --git a/...d/tests/data/partitioned/annotate_reads_allele_output_2/sample2/overall_mapping_stats.txt b/...d/tests/data/partitioned/annotate_reads_allele_output_2/sample2/overall_mapping_stats.txt
@@ -0,0 +1,17 @@
+
+**********************************************
+Stats for BAM file(s):
+**********************************************
+
+Total reads:       5000
+Mapped reads:      59	(1.18%)
+Forward strand:    685	(13.7%)
+Reverse strand:    4315	(86.3%)
+Failed QC:         0	(0%)
+Duplicates:        0	(0%)
+Paired-end reads:  5000	(100%)
+'Proper-pairs':    42	(0.84%)
+Both pairs mapped: 49	(0.98%)
+Read 1:            2500
+Read 2:            2500
+Singletons:        10	(0.2%)
diff --git a/.../card/tests/data/partitioned/annotate_reads_allele_output_2/sample2/sorted.length_100.bam b/.../card/tests/data/partitioned/annotate_reads_allele_output_2/sample2/sorted.length_100.bam
diff --git a/...mr/card/tests/data/partitioned/annotate_reads_gene_output_1/sample1/gene_mapping_data.txt b/...mr/card/tests/data/partitioned/annotate_reads_gene_output_1/sample1/gene_mapping_data.txt
@@ -0,0 +1,5 @@
+ARO Term	ARO Accession	Reference Model Type	Reference DB	Alleles with Mapped Reads	Reference Allele(s) Identity to CARD Reference Protein (%)	Resistomes & Variants: Observed in Genome(s)	Resistomes & Variants: Observed in Plasmid(s)	Resistomes & Variants: Observed Pathogen(s)	Completely Mapped Reads	Mapped Reads with Flanking Sequence	All Mapped Reads	Average Percent Coverage	Average Length Coverage (bp)	Average MAPQ (Completely Mapped Reads)	Number of Mapped Baits	Number of Mapped Baits with Reads	Average Number of reads per Bait	Number of reads per Bait Coefficient of Variation (%)	Number of reads mapping to baits and mapping to complete gene	Number of reads mapping to baits and mapping to complete gene (%)	Mate Pair Linkage (# reads)	Reference Length	AMR Gene Family	Drug Class	Resistance Mechanism
+mdtF	3000796	protein homolog model	CARD	1	100.0	no data	no data	Escherichia coli	2.00	0.00	2.00	8.09	252.00	193.00	0	0	0	0	N/A	N/A		3114	resistance-nodulation-cell division (RND) antibiotic efflux pump	macrolide antibiotic; fluoroquinolone antibiotic; penam	antibiotic efflux
+mgrA	3000815	protein homolog model	CARD	1	100.0	no data	no data	Staphylococcus aureus	1.00	0.00	1.00	19.59	87.00	172.00	0	0	0	0	N/A	N/A		444	ATP-binding cassette (ABC) antibiotic efflux pump; major facilitator superfamily (MFS) antibiotic efflux pump	fluoroquinolone antibiotic; cephalosporin; penam; tetracycline antibiotic; peptide antibiotic; disinfecting agents and antiseptics	antibiotic efflux
+OprN	3000805	protein homolog model	CARD	1	100.0	no data	no data	Pseudomonas aeruginosa	2.00	0.00	2.00	17.76	252.00	193.00	0	0	0	0	N/A	N/A		1419	resistance-nodulation-cell division (RND) antibiotic efflux pump	fluoroquinolone antibiotic; diaminopyrimidine antibiotic; phenicol antibiotic	antibiotic efflux
+mepA	3000026	protein homolog model	CARD	1	100.0	no data	no data	Staphylococcus aureus	2.00	0.00	2.00	17.70	240.00	190.50	0	0	0	0	N/A	N/A		1356	multidrug and toxic compound extrusion (MATE) transporter	glycylcycline; tetracycline antibiotic	antibiotic efflux
diff --git a/...mr/card/tests/data/partitioned/annotate_reads_gene_output_2/sample2/gene_mapping_data.txt b/...mr/card/tests/data/partitioned/annotate_reads_gene_output_2/sample2/gene_mapping_data.txt
@@ -0,0 +1,5 @@
+ARO Term	ARO Accession	Reference Model Type	Reference DB	Alleles with Mapped Reads	Reference Allele(s) Identity to CARD Reference Protein (%)	Resistomes & Variants: Observed in Genome(s)	Resistomes & Variants: Observed in Plasmid(s)	Resistomes & Variants: Observed Pathogen(s)	Completely Mapped Reads	Mapped Reads with Flanking Sequence	All Mapped Reads	Average Percent Coverage	Average Length Coverage (bp)	Average MAPQ (Completely Mapped Reads)	Number of Mapped Baits	Number of Mapped Baits with Reads	Average Number of reads per Bait	Number of reads per Bait Coefficient of Variation (%)	Number of reads mapping to baits and mapping to complete gene	Number of reads mapping to baits and mapping to complete gene (%)	Mate Pair Linkage (# reads)	Reference Length	AMR Gene Family	Drug Class	Resistance Mechanism
+mdtF	3000796	protein homolog model	CARD	1	100.0	no data	no data	Escherichia coli	2.00	0.00	2.00	8.09	252.00	193.00	0	0	0	0	N/A	N/A		3114	resistance-nodulation-cell division (RND) antibiotic efflux pump	macrolide antibiotic; fluoroquinolone antibiotic; penam	antibiotic efflux
+mgrA	3000815	protein homolog model	CARD	1	100.0	no data	no data	Staphylococcus aureus	1.00	0.00	1.00	19.59	87.00	172.00	0	0	0	0	N/A	N/A		444	ATP-binding cassette (ABC) antibiotic efflux pump; major facilitator superfamily (MFS) antibiotic efflux pump	fluoroquinolone antibiotic; cephalosporin; penam; tetracycline antibiotic; peptide antibiotic; disinfecting agents and antiseptics	antibiotic efflux
+OprN	3000805	protein homolog model	CARD	1	100.0	no data	no data	Pseudomonas aeruginosa	2.00	0.00	2.00	17.76	252.00	193.00	0	0	0	0	N/A	N/A		1419	resistance-nodulation-cell division (RND) antibiotic efflux pump	fluoroquinolone antibiotic; diaminopyrimidine antibiotic; phenicol antibiotic	antibiotic efflux
+mepA	3000026	protein homolog model	CARD	1	100.0	no data	no data	Staphylococcus aureus	2.00	0.00	2.00	17.70	240.00	190.50	0	0	0	0	N/A	N/A		1356	multidrug and toxic compound extrusion (MATE) transporter	glycylcycline; tetracycline antibiotic	antibiotic efflux
diff --git a/q2_amr/card/tests/data/partitioned/kmer_analysis_mags_1/sample1/bin1/61mer_analysis.json b/q2_amr/card/tests/data/partitioned/kmer_analysis_mags_1/sample1/bin1/61mer_analysis.json
@@ -0,0 +1 @@
+{"k141_1617_82 # 105913 # 109473 # 1 # ID=42_82;partial=00;start_type=TTG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.630": {"ORF": "k141_1617_82 # 105913 # 109473 # 1 # ID=42_82;partial=00;start_type=TTG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.630", "contig": "k141_1617_82", "HSP": "gnl|BL_ORD_ID|4713|hsp_num:0", "ARO_model": "Bifidobacterium adolescentis rpoB mutants conferring resistance to rifampicin", "type_hit": "Perfect", "#_of_kmers_in_sequence": 3501, "#_of_AMR_kmers": 2274, "taxonomic_info": {"species": {"Bifidobacterium longum": 75, "Bifidobacterium dentium": 67, "Parascardovia denticolens": 3, "Bifidobacterium animalis": 7, "Bifidobacterium bifidum": 9}, "genus": {}}, "genomic_info": {"chr + plasmid": 0, "plasmid": 0, "chr": 234}}}
diff --git a/...d/tests/data/partitioned/kmer_analysis_mags_1/sample1/bin1/61mer_analysis_rgi_summary.txt b/...d/tests/data/partitioned/kmer_analysis_mags_1/sample1/bin1/61mer_analysis_rgi_summary.txt
@@ -0,0 +1,2 @@
+ORF_ID	Contig	Cut_Off	Best_Hit_ARO	CARD*kmer Prediction	Taxonomic kmers	Genomic kmers
+"NC_000962.3_273 # 314309 # 314854 # -1 # ID=1_273;partial=00;start_type=GTG;rbs_motif=AGG;rbs_spacer=4bp;gc_cont=0.679"	NC_000962.3_273	Perfect	AAC(2')-Ic	Mycobacterium tuberculosis (chromosome)	"Mycobacterium tuberculosis: 486; "	"chr + plasmid: 0; plasmid: 0; chr: 486; "
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		{"k141_1617_82 # 105913 # 109473 # 1 # ID=42_82;partial=00;start_type=TTG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.630": {"ORF": "k141_1617_82 # 105913 # 109473 # 1 # ID=42_82;partial=00;start_type=TTG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.630", "contig": "k141_1617_82", "HSP": "gnl\|BL_ORD_ID\|4713\|hsp_num:0", "ARO_model": "Bifidobacterium adolescentis rpoB mutants conferring resistance to rifampicin", "type_hit": "Perfect", "#_of_kmers_in_sequence": 3501, "#_of_AMR_kmers": 2274, "taxonomic_info": {"species": {"Bifidobacterium longum": 75, "Bifidobacterium dentium": 67, "Parascardovia denticolens": 3, "Bifidobacterium animalis": 7, "Bifidobacterium bifidum": 9}, "genus": {}}, "genomic_info": {"chr + plasmid": 0, "plasmid": 0, "chr": 234}}}
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		ORF_ID Contig Cut_Off Best_Hit_ARO CARD*kmer Prediction Taxonomic kmers Genomic kmers
		"NC_000962.3_273 # 314309 # 314854 # -1 # ID=1_273;partial=00;start_type=GTG;rbs_motif=AGG;rbs_spacer=4bp;gc_cont=0.679" NC_000962.3_273 Perfect AAC(2')-Ic Mycobacterium tuberculosis (chromosome) "Mycobacterium tuberculosis: 486; " "chr + plasmid: 0; plasmid: 0; chr: 486; "