ENH: add actions that can partition annotation artifacts from reads a…

…nd MAGs (#54)

Co-authored-by: Michal Ziemski <[email protected]>

q2_amr/card/partition.py

@@ -1,7 +1,11 @@
 import os
+import warnings
+from typing import Union
 
+import numpy as np
 from qiime2.util import duplicate
 
+from q2_amr.card.utils import copy_files
 from q2_amr.types import (
     CARDAlleleAnnotationDirectoryFormat,
     CARDAnnotationDirectoryFormat,
@@ -98,3 +102,92 @@ def _collate(partition_list):
                     duplicate(file, collated_partitions.path / sample.name / file.name)
 
     return collated_partitions
+
+
+def partition_mags_annotations(
+    annotations: CARDAnnotationDirectoryFormat, num_partitions: int = None
+) -> CARDAnnotationDirectoryFormat:
+    return _partition_annotations(annotations, num_partitions)
+
+
+def partition_reads_allele_annotations(
+    annotations: CARDAlleleAnnotationDirectoryFormat, num_partitions: int = None
+) -> CARDAlleleAnnotationDirectoryFormat:
+    return _partition_annotations(annotations, num_partitions)
+
+
+def partition_reads_gene_annotations(
+    annotations: CARDGeneAnnotationDirectoryFormat, num_partitions: int = None
+) -> CARDGeneAnnotationDirectoryFormat:
+    return _partition_annotations(annotations, num_partitions)
+
+
+def _partition_annotations(
+    annotations: Union[
+        CARDAnnotationDirectoryFormat,
+        CARDGeneAnnotationDirectoryFormat,
+        CARDAlleleAnnotationDirectoryFormat,
+    ],
+    num_partitions: int = None,
+):
+    partitioned_annotations = {}
+    annotations_all = []
+    # Add one tuples with sample ID, MAG ID and full paths to annotation files to
+    # annotations_all
+    if isinstance(annotations, CARDAnnotationDirectoryFormat):
+        for sample_id, mag in annotations.sample_dict().items():
+            for mag_id, file_paths in mag.items():
+                annotations_all.append((sample_id, mag_id, file_paths))
+
+    else:
+        for sample_id, file_paths in annotations.sample_dict().items():
+            annotations_all.append((sample_id, file_paths))
+
+    # Sort annotations_all for consistent splitting behaviour
+    annotations_all.sort()
+
+    # Retrieve the number of annotations
+    num_annotations = len(annotations_all)
+
+    # If no number of partitions is specified or the number is higher than the number
+    # of annotations, all annotations get partitioned by annotation
+    if num_partitions is None:
+        num_partitions = num_annotations
+    elif num_partitions > num_annotations:
+        warnings.warn(
+            "You have requested a number of partitions"
+            f" '{num_partitions}' that is greater than your number"
+            f" of annotations '{num_annotations}'. Your data will be"
+            f" partitioned by annotation into '{num_annotations}'"
+            " partitions."
+        )
+        num_partitions = num_annotations
+
+    # Splits annotations into the specified number of arrays
+    arrays = np.array_split(np.array(annotations_all, dtype=object), num_partitions)
+
+    for i, annotation_tuple in enumerate(arrays, 1):
+        # Creates directory with same format as input
+        partitioned_annotation = type(annotations)()
+
+        # Constructs paths to all annotation files and moves them to the new partition
+        # directories
+        if isinstance(annotations, CARDAnnotationDirectoryFormat):
+            for sample_id, mag_id, file_paths in annotation_tuple:
+                copy_files(file_paths, partitioned_annotation.path, sample_id, mag_id)
+
+        else:
+            mag_id = None
+            for sample_id, file_paths in annotation_tuple:
+                copy_files(file_paths, partitioned_annotation.path, sample_id)
+
+        # Set key for partitioned_annotations dict to mag_id or sample_id
+        partitioned_annotation_key = mag_id if mag_id else sample_id
+
+        # Add the partitioned object to the collection dict
+        if num_partitions == num_annotations:
+            partitioned_annotations[partitioned_annotation_key] = partitioned_annotation
+        else:
+            partitioned_annotations[i] = partitioned_annotation
+
+    return partitioned_annotations

q2_amr/card/tests/data/collated/card_allele_annotation/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

q2_amr/card/tests/data/collated/card_allele_annotation/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%)

q2_amr/card/tests/data/collated/card_allele_annotation/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

q2_amr/card/tests/data/collated/card_allele_annotation/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%)

q2_amr/card/tests/data/collated/card_annotation/sample1/e026af61-d911-4de3-a957-7e8bf837f30d/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

q2_amr/card/tests/data/collated/card_annotation/sample2/aa447c99-ecd9-4c4a-a53b-4df6999815dd/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

q2_amr/card/tests/data/collated/card_annotation/sample2/f5a16381-ea80-49f9-875e-620f333a9293/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

q2_amr/card/tests/data/collated/card_gene_annotation/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