Merge pull request #101 from zwets/update-rgi-parser

Update RGI parser

.github/workflows/test_package.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.10.15, 3.12.8]
+        python-version: [3.10.16, 3.12.8]
 
     steps:
     - uses: actions/checkout@v2

hAMRonization/RgiIO.py

@@ -36,8 +36,7 @@ def __init__(self, source, metadata):
                     "Reference Model Type": "genetic_variation_type",
                     "Reference DB": "reference_database_name",
                     "Alleles with Mapped Reads": None,
-                    "Reference Allele(s) Identity "
-                    "to CARD Reference Protein (%)": "sequence_identity",
+                    "Reference Allele(s) Identity to CARD Reference Protein (%)": "sequence_identity",
                     "Resistomes & Variants: Observed in Genome(s)": None,
                     "Resistomes & Variants: Observed in Plasmid(s)": None,
                     "Resistomes & Variants: Observed Pathogen(s)": None,
@@ -50,11 +49,9 @@ def __init__(self, source, metadata):
                     "Number of Mapped Baits": None,
                     "Number of Mapped Baits with Reads": None,
                     "Average Number of reads per Bait": None,
-                    "Number of reads per Bait " "Coefficient of Variation (%)": None,
-                    "Number of reads mapping to baits "
-                    "and mapping to complete gene": None,
-                    "Number of reads mapping to baits and "
-                    "mapping to complete gene (%)": None,
+                    "Number of reads per Bait Coefficient of Variation (%)": None,
+                    "Number of reads mapping to baits and mapping to complete gene": None,
+                    "Number of reads mapping to baits and mapping to complete gene (%)": None,
                     "Mate Pair Linkage (# reads)": None,
                     "Reference Length": "reference_gene_length",
                     "AMR Gene Family": "gene_name",
@@ -91,6 +88,9 @@ def __init__(self, source, metadata):
                     "Model_ID": None,
                     "Nudged": None,
                     "Note": None,
+                    "Hit_Start": "reference_gene_start",
+                    "Hit_End": "reference_gene_stop",
+                    "Antibiotic": "antimicrobial_agent",
                 }
                 # if RGI is run on ORFs then Contig should be None
                 # and input_sequence_id should the ORF_ID i.e., reverse of
@@ -114,16 +114,14 @@ def parse(self, handle):
         # skip any manually specified fields for later
         reader = csv.DictReader(handle, delimiter="\t")
         for result in reader:
+            result["_nucleotide_mutation"] = None
+            result["_amino_acid_mutation"] = None
+
             # rgi-bwt mode doesn't support variant mutations
             if "Model_type" not in result:
-                result["_nucleotide_mutation"] = None
-                result["_amino_acid_mutation"] = None
                 result["Reference Model Type"] = GENE_PRESENCE
             # normal RGI model
             else:
-                result["_nucleotide_mutation"] = None
-                result["_amino_acid_mutation"] = None
-
                 if result["SNPs_in_Best_Hit_ARO"] == "n/a":
                     result["SNPs_in_Best_Hit_ARO"] = None
 

schema/csv2json.py

@@ -7,15 +7,17 @@
 from datetime import datetime
 from ast import literal_eval
 
-FIELDNAMES = ['Interface Label','Required/Optional','Definition','Ontology','Value Type','Example','Guidance','Values']
+FIELDNAMES = ['Interface Label', 'Required/Optional', 'Definition', 'Ontology', 'Value Type', 'Example', 'Guidance', 'Values']
 SEPARATOR = ','
 QUOTE = '"'
 
+
 def string_list_to_list(string):
     to_list = literal_eval(string)
     to_list = [n.strip() for n in to_list]
     return to_list
 
+
 def interface_label_to_property_key(interface_label):
     property_key = re.sub(r'[^\w {}]', '_', interface_label).replace(' ', '_').replace('__', '_').lower()
     property_key = re.sub(r'_$', '', property_key)
@@ -35,7 +37,7 @@ def parse_properties_table(path_to_properties_table):
         "SRA_ID": "string",
         "Genbank_ID": "string",
         "GISAID_ID": "string",
-        "Enums":{
+        "Enums": {
                 "type": "string",
                 "enum": "",
             },
@@ -74,8 +76,8 @@ def parse_properties_table(path_to_properties_table):
         "Bioproject_ID": "^PRJ(N|E|D)([a-zA-Z]?)[0-9]+*",
         "Biosample_ID": "^SAM(D|N|E([AG]?))[0-9]+",
         "SRA_ID": "^(SRR|ERR|DRR)[0-9]+",
-        "Genbank_ID": "^([a-zA-Z]{2})\d*.\d{1}",
-        "GISAID_ID": "^EPI_ISL_\d*",
+        "Genbank_ID": "^([a-zA-Z]{2})\\d*.\\d{1}",
+        "GISAID_ID": "^EPI_ISL_\\d*",
         "Integer_or_Range": None,
         "Enums": None
     }
@@ -112,23 +114,22 @@ def parse_properties_table(path_to_properties_table):
                 for i in range(len(examples)):
                     if '-' not in examples[i]:
                         examples[i] = int(examples[i])
-            
+
             # Special case: enumns
             if row['Value Type'] == "Enums":
                 type = datatype_map[row['Value Type']]
                 properties[property_key]['type'] = "string"
                 properties[property_key]['Enums'] = string_list_to_list(row['Values'])
-
-            properties[property_key]['examples'] = examples
 
+            properties[property_key]['examples'] = examples
 
     return properties
 
 
 def get_required_fields(path_to_properties_table):
     required_fields = set()
     with open(path_to_properties_table) as f:
-        reader = csv.DictReader(f, delimiter=SEPARATOR,quotechar=QUOTE)
+        reader = csv.DictReader(f, delimiter=SEPARATOR, quotechar=QUOTE)
         for row in reader:
             property_key = interface_label_to_property_key(row['Interface Label'])
             if row['Required/Optional'] == 'Required':
@@ -138,19 +139,18 @@ def get_required_fields(path_to_properties_table):
 
 
 def main(args):
-    
+
     schema = {
         "$schema": "http://json-schema.org/draft/2019-09/schema#",
         "version": datetime.now().isoformat(),
         "type": "object",
         "properties": {},
         "required": [],
     }
-    
+
     schema["properties"] = parse_properties_table(args.input)
     schema["required"] = get_required_fields(args.input)
-
-    #print(json.dumps(schema))
+
     with open(args.input.replace("csv", "json"), "w") as fh:
         fh.write(json.dumps(schema))
 
@@ -160,4 +160,4 @@ def main(args):
     parser.add_argument('input', help='Input schema attributes table')
 
     args = parser.parse_args()
-    main(args)
+    main(args)

setup.py

@@ -1,4 +1,3 @@
-import setuptools
 import re
 from distutils.core import setup
 
@@ -7,7 +6,7 @@
 
 with open('hAMRonization/__init__.py') as fh:
     info = fh.read()
-    version = re.search('^__version__\s*=\s*"(.*)"',
+    version = re.search('^__version__\\s*=\\s*"(.*)"',
                         info, re.M).group(1)
 
 setup(

test/data/dummy/rgi/rgi.txt

@@ -1,2 +1,2 @@
-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
-NZ_LR792628.1_1289 # 1333608 # 1334783 # -1 # ID=1_1289;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.599	NZ_LR792628.1_1289	1333608	1334783	-	Strict	670	792.727	oqxA	99.49	3003922	protein homolog model	n/a	n/a	fluoroquinolone antibiotic; glycylcycline; tetracycline antibiotic; diaminopyrimidine antibiotic; nitrofuran antibiotic	antibiotic efflux	resistance-nodulation-cell division (RND) antibiotic efflux pump	ATGAGCCTGCAAAAAACCTGGGGAAACATTCACCTGACCGCGCTCGGCGCGATGATGCTCTCCTTTCTGCTCGTCGACTGCGACGACAGCGTCGCGCAGAATGCTGCGCCTCCCGCCCCGACAGTCAGCGCCGCTAAGGTGCTGGTGAAGTCGATCAGTCAGTGGGATAGTTTTAACGGTCGCATTGAAGCGGTGGAGAGCGTTCAGCTTCGCCCTCGCGTCTCGGGATACATTGATAAAGTGAATTACACCGACGGCCAGGAGGTGAAAAAGGGCCAGGTGCTGTTCACGATAGATGACAGAACCTATCGCGCCGCGCTGGAGCAGGCGCAGGCGGCGTTGGCAAGAGCCAAAACGCAGGCCAGCCTCGCGCAAAGCGAGGCGAACCGCACCGATAAATTAGTCCATACCAACCTCGTCTCCCGTGAAGAGTGGGAGCAGCGCCGGTCAGCCGCGGTTCAGGCGCAGGCCGACATTCGCGCCGCGCAGGCGGCGGTGGATGCCGCGCAGCTTAACCTCGACCTCACCAAAGTGACCGCCCCTATTGACGGCCGCGCCAGCCGGGCGCTGATCACCAGCGGTAACCTGGTCACCGCGGGCGACACCGCCAGCGTGCTCACCACCCTGGTCTCGCAAAAGACGGTGTACGTCTACTTTGACGTCGACGAGTCAACCTACCTCCACTATCAAAACCTCGCCCGCCGCGGGCAAGGCGCGTCCAGCGATAATCAGGCGCTCCCGGTGGAGATTGGCCTGGTGGGCGAGGAGGGTTACCCCCACCAGGGCAAAGTGGATTTTCTCGATAATCAGTTAACGCCGAGTACCGGCACCATCCGCATGCGTGCGCTGCTGGATAACTCGCAGCGTCTGTTCACGCCGGGGCTGTTTGCCCGCGTGCGTCTGCCGGGCAGCGCAGAGTTCAAAGCCACGCTGATCGACGACAAAGCGGTACTGACCGATCAGGATCGTAAATACGTCTATATCGTTGATAAAGATGGTAAAGCACAGCGCCGCGACATTACCCCAGGGCGGCTGGCAGACGGTTTACGCATCGTTCAGAAGGGGTTGAATCCTGGGGATAGCGTCATCGTCGACGGCTTACAAAAAGTGTTTATGCCGGGTATGCCGGTTAACGCCAAAACCGTTGCCATGACCTCCAGCGCCACCCTTAACTGA	MSLQKTWGNIHLTALGAMMLSFLLVDCDDSVAQNAAPPAPTVSAAKVLVKSISQWDSFNGRIEAVESVQLRPRVSGYIDKVNYTDGQEVKKGQVLFTIDDRTYRAALEQAQAALARAKTQASLAQSEANRTDKLVHTNLVSREEWEQRRSAAVQAQADIRAAQAAVDAAQLNLDLTKVTAPIDGRASRALITSGNLVTAGDTASVLTTLVSQKTVYVYFDVDESTYLHYQNLARRGQGASSDNQALPVEIGLVGEEGYPHQGKVDFLDNQLTPSTGTIRMRALLDNSQRLFTPGLFARVRLPGSAEFKATLIDDKAVLTDQDRKYVYIVDKDGKAQRRDITPGRLADGLRIVQKGLNPGDSVIVDGLQKVFMPGMPVNAKTVAMTSSATLN	MSLQKTWGNIHLTALGAMMLSFLLVGCDDSVAQNAAPPAPTVSAAKVLVKSISQWDSFNGRIEAVESVQLRPRVSGYIDKVNYTDGQEVKKGQVLFTIDDRTYRAALEQAQAALARAKTQASLAQSEANRTDKLVHTNLVSREEWEQRRSAAVQAQADIRAAQAAVDAAQLNLDFTKVTAPIDGRASRALITSGNLVTAGDTASVLTTLVSQKTVYVYFDVDESTYLHYQNLARRGQGASSDNQALPVEIGLVGEEGYPHQGKVDFLDNQLTPSTGTIRMRALLDNSQRLFTPGLFARVRLPGSAEFKATLIDDKAVLTDQDRKYVYIVDKDGKAQRRDITPGRLADGLRIVQKGLNPGDSVIVDGLQKVFMPGMPVNAKTVAMTSSATLN	100.00	gnl|BL_ORD_ID|2216|hsp_num:0	2399		
+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	Hit_Start	Hit_End	Antibiotic
+NZ_LR792628.1_1289 # 1333608 # 1334783 # -1 # ID=1_1289;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.599	NZ_LR792628.1_1289	1333608	1334783	-	Strict	670	792.727	oqxA	99.49	3003922	protein homolog model	n/a	n/a	fluoroquinolone antibiotic; glycylcycline; tetracycline antibiotic; diaminopyrimidine antibiotic; nitrofuran antibiotic	antibiotic efflux	resistance-nodulation-cell division (RND) antibiotic efflux pump	ATGAGCCTGCAAAAAACCTGGGGAAACATTCACCTGACCGCGCTCGGCGCGATGATGCTCTCCTTTCTGCTCGTCGACTGCGACGACAGCGTCGCGCAGAATGCTGCGCCTCCCGCCCCGACAGTCAGCGCCGCTAAGGTGCTGGTGAAGTCGATCAGTCAGTGGGATAGTTTTAACGGTCGCATTGAAGCGGTGGAGAGCGTTCAGCTTCGCCCTCGCGTCTCGGGATACATTGATAAAGTGAATTACACCGACGGCCAGGAGGTGAAAAAGGGCCAGGTGCTGTTCACGATAGATGACAGAACCTATCGCGCCGCGCTGGAGCAGGCGCAGGCGGCGTTGGCAAGAGCCAAAACGCAGGCCAGCCTCGCGCAAAGCGAGGCGAACCGCACCGATAAATTAGTCCATACCAACCTCGTCTCCCGTGAAGAGTGGGAGCAGCGCCGGTCAGCCGCGGTTCAGGCGCAGGCCGACATTCGCGCCGCGCAGGCGGCGGTGGATGCCGCGCAGCTTAACCTCGACCTCACCAAAGTGACCGCCCCTATTGACGGCCGCGCCAGCCGGGCGCTGATCACCAGCGGTAACCTGGTCACCGCGGGCGACACCGCCAGCGTGCTCACCACCCTGGTCTCGCAAAAGACGGTGTACGTCTACTTTGACGTCGACGAGTCAACCTACCTCCACTATCAAAACCTCGCCCGCCGCGGGCAAGGCGCGTCCAGCGATAATCAGGCGCTCCCGGTGGAGATTGGCCTGGTGGGCGAGGAGGGTTACCCCCACCAGGGCAAAGTGGATTTTCTCGATAATCAGTTAACGCCGAGTACCGGCACCATCCGCATGCGTGCGCTGCTGGATAACTCGCAGCGTCTGTTCACGCCGGGGCTGTTTGCCCGCGTGCGTCTGCCGGGCAGCGCAGAGTTCAAAGCCACGCTGATCGACGACAAAGCGGTACTGACCGATCAGGATCGTAAATACGTCTATATCGTTGATAAAGATGGTAAAGCACAGCGCCGCGACATTACCCCAGGGCGGCTGGCAGACGGTTTACGCATCGTTCAGAAGGGGTTGAATCCTGGGGATAGCGTCATCGTCGACGGCTTACAAAAAGTGTTTATGCCGGGTATGCCGGTTAACGCCAAAACCGTTGCCATGACCTCCAGCGCCACCCTTAACTGA	MSLQKTWGNIHLTALGAMMLSFLLVDCDDSVAQNAAPPAPTVSAAKVLVKSISQWDSFNGRIEAVESVQLRPRVSGYIDKVNYTDGQEVKKGQVLFTIDDRTYRAALEQAQAALARAKTQASLAQSEANRTDKLVHTNLVSREEWEQRRSAAVQAQADIRAAQAAVDAAQLNLDLTKVTAPIDGRASRALITSGNLVTAGDTASVLTTLVSQKTVYVYFDVDESTYLHYQNLARRGQGASSDNQALPVEIGLVGEEGYPHQGKVDFLDNQLTPSTGTIRMRALLDNSQRLFTPGLFARVRLPGSAEFKATLIDDKAVLTDQDRKYVYIVDKDGKAQRRDITPGRLADGLRIVQKGLNPGDSVIVDGLQKVFMPGMPVNAKTVAMTSSATLN	MSLQKTWGNIHLTALGAMMLSFLLVGCDDSVAQNAAPPAPTVSAAKVLVKSISQWDSFNGRIEAVESVQLRPRVSGYIDKVNYTDGQEVKKGQVLFTIDDRTYRAALEQAQAALARAKTQASLAQSEANRTDKLVHTNLVSREEWEQRRSAAVQAQADIRAAQAAVDAAQLNLDFTKVTAPIDGRASRALITSGNLVTAGDTASVLTTLVSQKTVYVYFDVDESTYLHYQNLARRGQGASSDNQALPVEIGLVGEEGYPHQGKVDFLDNQLTPSTGTIRMRALLDNSQRLFTPGLFARVRLPGSAEFKATLIDDKAVLTDQDRKYVYIVDKDGKAQRRDITPGRLADGLRIVQKGLNPGDSVIVDGLQKVFMPGMPVNAKTVAMTSSATLN	100.00	gnl|BL_ORD_ID|2147|hsp_num:0	2399			0	1173	tigecycline; ciprofloxacin; nitrofurantoin; trimethoprim

test/data/dummy/rgi/rgi_orf.txt

@@ -1,2 +1,2 @@
-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
-gb|AEN03071.1|+|NDM-5 [Escherichia coli]					Perfect	500	555.444	NDM-5	100.0	3000467	protein homolog model	n/a	n/a	carbapenem; cephalosporin; cephamycin; penam	antibiotic inactivation	NDM beta-lactamase		MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLLVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR	MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLLVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGLVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR	100.00	gnl|BL_ORD_ID|1015|hsp_num:0	1106		
+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	Hit_Start	Hit_End	Antibiotic
+ndm-1_1 # 1 # 813 # 1 # ID=1_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.615	ndm-1_1	1	813	+	Perfect	500	555.829	NDM-1	100.0	3000589	protein homolog model	n/a	n/a	carbapenem; cephalosporin; penicillin beta-lactam	antibiotic inactivation	NDM beta-lactamase	ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA	MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR	MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR	100.00	gnl|BL_ORD_ID|711|hsp_num:0	783			0	810	ertapenem; meropenem; imipenem

test/data/dummy/rgi/rgi_var.txt

@@ -1,2 +1,2 @@
-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
-BAE77595.1 DNA gyrase, subunit B [Escherichia coli str. K-12 substr. W3110]					Strict	1600	1664.05	Escherichia coli gyrB conferring resistance to aminocoumarin	99.88	3003303	protein variant model	R136L		aminocoumarin antibiotic	antibiotic target alteration	aminocoumarin resistant gyrB		MSNSYDSSSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQLEGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHYEGGIKAFVEYLNKNKTPIHPNIFYFSTEKDGIGVEVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLIAVVSVKVPDPKFSSQTKDKLVSSEVKSAVEQQMNELLAEYLLENPTDAKIVVGKIIDAARAREAARRAREMTRRKGALDLAGLPGKLADCQERDPALSELYLVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMLSSQEVATLITALGCGIGRDEYNPDKLRYHSIIIMTDADVDGSHIRTLLLTFFYRQMPEIVERGHVYIAQPPLYKVKKGKQEQYIKDDEAMDQYQISIALDGATLHTNASAPALAGEALEKLVSEYNATQKMINRMERRYPKAMLKELIYQPTLTEADLSDEQTVTRWVNALVSELNDKEQHGSQWKFDVHTNAEQNLFEPIVRVRTHGVDTDYPLDHEFITGGEYRRICTLGEKLRGLLEEDAFIERGERRQPVASFEQALDWLVKESRRGLSIQRYKGLGEMNPEQLWETTMDPESRRMLRVTVKDAIAADQLFTTLMGDAVEPRRAFIEENALKAANIDI	MSNSYDSSSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHYEGGIKAFVEYLNKNKTPIHPNIFYFSTEKDGIGVEVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLIAVVSVKVPDPKFSSQTKDKLVSSEVKSAVEQQMNELLAEYLLENPTDAKIVVGKIIDAARAREAARRAREMTRRKGALDLAGLPGKLADCQERDPALSELYLVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMLSSQEVATLITALGCGIGRDEYNPDKLRYHSIIIMTDADVDGSHIRTLLLTFFYRQMPEIVERGHVYIAQPPLYKVKKGKQEQYIKDDEAMDQYQISIALDGATLHTNASAPALAGEALEKLVSEYNATQKMINRMERRYPKAMLKELIYQPTLTEADLSDEQTVTRWVNALVSELNDKEQHGSQWKFDVHTNAEQNLFEPIVRVRTHGVDTDYPLDHEFITGGEYRRICTLGEKLRGLLEEDAFIERGERRQPVASFEQALDWLVKESRRGLSIQRYKGLGEMNPEQLWETTMDPESRRMLRVTVKDAIAADQLFTTLMGDAVEPRRAFIEENALKAANIDI	100.00	gnl|BL_ORD_ID|1933|hsp_num:0	111		
+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	Hit_Start	Hit_End	Antibiotic
+BAE77595.1 DNA gyrase, subunit B [Escherichia coli str. K-12 substr. W3110]					Strict	1600	1664.05	Escherichia coli gyrB conferring resistance to aminocoumarin	99.88	3003303	protein variant model	R136L		aminocoumarin antibiotic	antibiotic target alteration	aminocoumarin resistant gyrB		MSNSYDSSSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQLEGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHYEGGIKAFVEYLNKNKTPIHPNIFYFSTEKDGIGVEVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLIAVVSVKVPDPKFSSQTKDKLVSSEVKSAVEQQMNELLAEYLLENPTDAKIVVGKIIDAARAREAARRAREMTRRKGALDLAGLPGKLADCQERDPALSELYLVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMLSSQEVATLITALGCGIGRDEYNPDKLRYHSIIIMTDADVDGSHIRTLLLTFFYRQMPEIVERGHVYIAQPPLYKVKKGKQEQYIKDDEAMDQYQISIALDGATLHTNASAPALAGEALEKLVSEYNATQKMINRMERRYPKAMLKELIYQPTLTEADLSDEQTVTRWVNALVSELNDKEQHGSQWKFDVHTNAEQNLFEPIVRVRTHGVDTDYPLDHEFITGGEYRRICTLGEKLRGLLEEDAFIERGERRQPVASFEQALDWLVKESRRGLSIQRYKGLGEMNPEQLWETTMDPESRRMLRVTVKDAIAADQLFTTLMGDAVEPRRAFIEENALKAANIDI	MSNSYDSSSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHYEGGIKAFVEYLNKNKTPIHPNIFYFSTEKDGIGVEVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLIAVVSVKVPDPKFSSQTKDKLVSSEVKSAVEQQMNELLAEYLLENPTDAKIVVGKIIDAARAREAARRAREMTRRKGALDLAGLPGKLADCQERDPALSELYLVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMLSSQEVATLITALGCGIGRDEYNPDKLRYHSIIIMTDADVDGSHIRTLLLTFFYRQMPEIVERGHVYIAQPPLYKVKKGKQEQYIKDDEAMDQYQISIALDGATLHTNASAPALAGEALEKLVSEYNATQKMINRMERRYPKAMLKELIYQPTLTEADLSDEQTVTRWVNALVSELNDKEQHGSQWKFDVHTNAEQNLFEPIVRVRTHGVDTDYPLDHEFITGGEYRRICTLGEKLRGLLEEDAFIERGERRQPVASFEQALDWLVKESRRGLSIQRYKGLGEMNPEQLWETTMDPESRRMLRVTVKDAIAADQLFTTLMGDAVEPRRAFIEENALKAANIDI	100.00	gnl|BL_ORD_ID|1933|hsp_num:0	111