From 2305306f6fb7b5b1733963cd79d66920515e803c Mon Sep 17 00:00:00 2001 From: Marco van Zwetselaar Date: Wed, 15 Jan 2025 03:04:31 +0300 Subject: [PATCH 1/3] Minor fixes and cheer up flake --- schema/csv2json.py | 26 +++++++++++++------------- setup.py | 3 +-- test/test_interfaces.py | 5 ----- 3 files changed, 14 insertions(+), 20 deletions(-) diff --git a/schema/csv2json.py b/schema/csv2json.py index 8c7f285..91b03ba 100644 --- a/schema/csv2json.py +++ b/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'_$', '', property_key) @@ -35,7 +37,7 @@ def parse_properties_table(path_to_properties_table): "SRA_ID": "string", "Genbank_ID": "string", "GISAID_ID": "string", - "Enums":{ + "Enums": { "type": "string", "enum": "", }, @@ -74,8 +76,8 @@ def parse_properties_table(path_to_properties_table): "Bioproject_ID": "^PRJ(N|E|D)([a-zA-Z]?)[0-9]+*", "Biosample_ID": "^SAM(D|N|E([AG]?))[0-9]+", "SRA_ID": "^(SRR|ERR|DRR)[0-9]+", - "Genbank_ID": "^([a-zA-Z]{2})\d*.\d{1}", - "GISAID_ID": "^EPI_ISL_\d*", + "Genbank_ID": "^([a-zA-Z]{2})\\d*.\\d{1}", + "GISAID_ID": "^EPI_ISL_\\d*", "Integer_or_Range": None, "Enums": None } @@ -112,15 +114,14 @@ def parse_properties_table(path_to_properties_table): for i in range(len(examples)): if '-' not in examples[i]: examples[i] = int(examples[i]) - + # Special case: enumns if row['Value Type'] == "Enums": type = datatype_map[row['Value Type']] properties[property_key]['type'] = "string" properties[property_key]['Enums'] = string_list_to_list(row['Values']) - - properties[property_key]['examples'] = examples + properties[property_key]['examples'] = examples return properties @@ -128,7 +129,7 @@ def parse_properties_table(path_to_properties_table): def get_required_fields(path_to_properties_table): required_fields = set() with open(path_to_properties_table) as f: - reader = csv.DictReader(f, delimiter=SEPARATOR,quotechar=QUOTE) + reader = csv.DictReader(f, delimiter=SEPARATOR, quotechar=QUOTE) for row in reader: property_key = interface_label_to_property_key(row['Interface Label']) if row['Required/Optional'] == 'Required': @@ -138,7 +139,7 @@ def get_required_fields(path_to_properties_table): def main(args): - + schema = { "$schema": "http://json-schema.org/draft/2019-09/schema#", "version": datetime.now().isoformat(), @@ -146,11 +147,10 @@ def main(args): "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) \ No newline at end of file + main(args) diff --git a/setup.py b/setup.py index c96ffe8..846452d 100644 --- a/setup.py +++ b/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( diff --git a/test/test_interfaces.py b/test/test_interfaces.py index 2084438..e3179fd 100644 --- a/test/test_interfaces.py +++ b/test/test_interfaces.py @@ -71,11 +71,6 @@ def test_summarize_empty_reports(): output_location="amrfinderplus_empty_summarize.json", output_format="json" ) - rgi_metadata = { - "analysis_software_version": "5.1.0", - "reference_database_version": "2019-Jul-28", - "input_file_name": "Non-empty report", - } rgi_parsed_report = hAMRonization.parse( "data/raw_outputs/rgi/rgi.txt", metadata, "rgi" ) From 39a6a673dde1abf3850e7b02233d60a613c8d7fc Mon Sep 17 00:00:00 2001 From: Marco van Zwetselaar Date: Wed, 15 Jan 2025 03:06:16 +0300 Subject: [PATCH 2/3] RGI: add mappings for antibiotics and hit positions - Closes https://github.com/pha4ge/hAMRonization/issues/100 --- hAMRonization/RgiIO.py | 22 +++++---- test/data/dummy/rgi/rgi.txt | 4 +- test/data/dummy/rgi/rgi_orf.txt | 4 +- test/data/dummy/rgi/rgi_var.txt | 4 +- test/data/raw_outputs/rgi/rgi.txt | 22 ++++----- test/test_parsing_validity.py | 75 +++++++++++++++++-------------- 6 files changed, 68 insertions(+), 63 deletions(-) diff --git a/hAMRonization/RgiIO.py b/hAMRonization/RgiIO.py index a53a5e5..7b3c54d 100644 --- a/hAMRonization/RgiIO.py +++ b/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 diff --git a/test/data/dummy/rgi/rgi.txt b/test/data/dummy/rgi/rgi.txt index 96fc8c6..6692833 100644 --- a/test/data/dummy/rgi/rgi.txt +++ b/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 diff --git a/test/data/dummy/rgi/rgi_orf.txt b/test/data/dummy/rgi/rgi_orf.txt index 72acb92..a1c81ab 100644 --- a/test/data/dummy/rgi/rgi_orf.txt +++ b/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 diff --git a/test/data/dummy/rgi/rgi_var.txt b/test/data/dummy/rgi/rgi_var.txt index 69da802..6680789 100644 --- a/test/data/dummy/rgi/rgi_var.txt +++ b/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 diff --git a/test/data/raw_outputs/rgi/rgi.txt b/test/data/raw_outputs/rgi/rgi.txt index 35eaa24..7bda2a8 100644 --- a/test/data/raw_outputs/rgi/rgi.txt +++ b/test/data/raw_outputs/rgi/rgi.txt @@ -1,11 +1,11 @@ -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_020818.1_7 # 7011 # 7790 # 1 # ID=3_7;partial=00;start_type=ATG;rbs_motif=TAA;rbs_spacer=12bp;gc_cont=0.336 NC_020818.1_7 7011 7790 + Perfect 500 526.554 APH(3')-VI 100.0 3003687 protein homolog model n/a n/a aminoglycoside antibiotic antibiotic inactivation APH(3') ATGGAATTGCCCAATATTATTCAACAATTTATTGGAAACAGCGTTTTAGAGCCAAATAAAATTGGTCAGTCGCCATCGGATGTTTATTCTTTTAATCGAAATAATGAAACTTTTTTTCTTAAGCGATCTAGCACTTTATATACAGAGACCACATACAGTGTCTCTCGCGAAGCGAAAATGTTGAGTTGGCTCTCTGAGAAATTAAAGGTGCCTGAACTCATCATGACTTTTCAGGATGAGCAGTTTGAATTAATGATCACTAAAGCGATCAATGCAAAACCAATTTCAGCGCTTTTTTTAACAGACCAAGAATTGCTTGCTATCTATAAGGAGGCACTCAATCTGTTAAATTCAGTTGCTATTATTGATTGTCCATTTATTTCAAACATTGATCATCGGTTAAAAGAGTCAAAATTTTTTATTGATAACCAACTCCTTGACGATATAGATCAAGATGATTTTGACGCTGAATTATGGGGAGACCATAGAACTTACCTAAGTCTATGGAATGAGTTAACTGAGACTCGTGTTGAAGAAAGATTGGTTTTTTCTCATGGCGATATCACGGATAGTAATATTTTTATAGATAAATTCAATGAAATTTACTTTTTAGATCTTGGCCGTGCTGGGTTAGCTGATGAATTTGTAGATATATCCTTTGTTGAACGTTGCCTAAGAGAGGATGCCTCGGAGGAAACTGCTAAAATATTTTTAAAGCATTTAAAAAATGATAGACCTGACAAAAGGAATTATTTTTTAAAACTTGATGAATTGAATTGA MELPNIIQQFIGNSVLEPNKIGQSPSDVYSFNRNNETFFLKRSSTLYTETTYSVSREAKMLSWLSEKLKVPELIMTFQDEQFELMITKAINAKPISALFLTDQELLAIYKEALNLLNSVAIIDCPFISNIDHRLKESKFFIDNQLLDDIDQDDFDAELWGDHRTYLSLWNELTETRVEERLVFSHGDITDSNIFIDKFNEIYFLDLGRAGLADEFVDISFVERCLREDASEETAKIFLKHLKNDRPDKRNYFLKLDELN MELPNIIQQFIGNSVLEPNKIGQSPSDVYSFNRNNETFFLKRSSTLYTETTYSVSREAKMLSWLSEKLKVPELIMTFQDEQFELMITKAINAKPISALFLTDQELLAIYKEALNLLNSVAIIDCPFISNIDHRLKESKFFIDNQLLDDIDQDDFDAELWGDHRTYLSLWNELTETRVEERLVFSHGDITDSNIFIDKFNEIYFLDLGRAGLADEFVDISFVERCLREDASEETAKIFLKHLKNDRPDKRNYFLKLDELN 100.00 gnl|BL_ORD_ID|2016|hsp_num:0 2200 -NC_020818.1_9 # 9068 # 9880 # 1 # ID=3_9;partial=00;start_type=ATG;rbs_motif=TAA;rbs_spacer=12bp;gc_cont=0.615 NC_020818.1_9 9068 9880 + Perfect 500 555.829 NDM-1 100.0 3000589 protein homolog model n/a n/a carbapenem; cephalosporin; cephamycin; penam antibiotic inactivation NDM beta-lactamase ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 100.00 gnl|BL_ORD_ID|713|hsp_num:0 783 -NC_020818.1_12 # 12051 # 12935 # -1 # ID=3_12;partial=00;start_type=ATG;rbs_motif=TAA;rbs_spacer=12bp;gc_cont=0.365 NC_020818.1_12 12051 12935 - Perfect 500 600.127 mphE 100.0 3003741 protein homolog model n/a n/a macrolide antibiotic antibiotic inactivation macrolide phosphotransferase (MPH) ATGACAATTCAAGATATTCAATCACTTGCTGAAGCACACGGCTTGTTGCTTACGGACAAAATGAATTTCAATGAAATGGGCATTGATTTTAAGGTCGTTTTTGCTCTTGATACAAAGGGGCAACAATGGTTGCTGCGTATTCCTCGTCGTGATGGCATGAGGGAACAAATCAAGAAAGAAAAACGCATTTTAGAATTGGTAAAAAAACATCTTTCTGTAGAGGTTCCTGATTGGAGAATTTCATCTACAGAATTAGTGGCTTATCCCATACTTAAAGATAATCCTGTTTTAAATTTGGATGCTGAAACCTATGAAATAATTTGGAATATGGACAAAGATAGCCCGAAATACATAACATCTTTGGCAAAAACCTTATTTGAAATCCATAGTATTCCTGAAAAAGAAGTTCGGGAAAATGATTTGAAAATTATGAAACCTTCAGATTTAAGACCTGAAATAGCAAACAATTTGCAGTTAGTAAAATCTGAAATTGGTATAAGTGAGCAATTGGAAACCCGCTACAGAAAATGGTTGGATAATGATGTTCTATGGGCAGATTTCACCCAATTTATACATGGCGATTTATATGCTGGGCATGTACTAGCTTCAAAGGATGGAGCTGTTTCAGGCGTTATTGATTGGTCAACAGCCCATATAGATGACCCAGCGATTGATTTTGCTGGGCATGTAACTTTGTTTGGAGAAGAAAGCCTCAAAACTCTAATCATCGAGTATGAAAAACTAGGGGGTAAAGTTTGGAATAAACTATATGAACAGACTTTAGAAAGAGCAGCGGCCTCTCCTTTGATGTATGGTTTATTTGCCTTAGAAACTCAAAATGAAAGCCTTATCGTTGGAGCAAAAGCTCAGTTGGGAGTTATATAA MTIQDIQSLAEAHGLLLTDKMNFNEMGIDFKVVFALDTKGQQWLLRIPRRDGMREQIKKEKRILELVKKHLSVEVPDWRISSTELVAYPILKDNPVLNLDAETYEIIWNMDKDSPKYITSLAKTLFEIHSIPEKEVRENDLKIMKPSDLRPEIANNLQLVKSEIGISEQLETRYRKWLDNDVLWADFTQFIHGDLYAGHVLASKDGAVSGVIDWSTAHIDDPAIDFAGHVTLFGEESLKTLIIEYEKLGGKVWNKLYEQTLERAAASPLMYGLFALETQNESLIVGAKAQLGVI MTIQDIQSLAEAHGLLLTDKMNFNEMGIDFKVVFALDTKGQQWLLRIPRRDGMREQIKKEKRILELVKKHLSVEVPDWRISSTELVAYPILKDNPVLNLDAETYEIIWNMDKDSPKYITSLAKTLFEIHSIPEKEVRENDLKIMKPSDLRPEIANNLQLVKSEIGISEQLETRYRKWLDNDVLWADFTQFIHGDLYAGHVLASKDGAVSGVIDWSTAHIDDPAIDFAGHVTLFGEESLKTLIIEYEKLGGKVWNKLYEQTLERAAASPLMYGLFALETQNESLIVGAKAQLGVI 100.00 gnl|BL_ORD_ID|2697|hsp_num:0 2614 -NC_020818.1_13 # 12991 # 14466 # -1 # ID=3_13;partial=00;start_type=ATG;rbs_motif=TAAA;rbs_spacer=5bp;gc_cont=0.399 NC_020818.1_13 12991 14466 - Perfect 950 1000.73 msrE 100.0 3003109 protein homolog model n/a n/a macrolide antibiotic; streptogramin antibiotic antibiotic target protection msr-type ABC-F protein ATGAGTTTAATTATTAAAGCGAGAAACATACGCTTGGATTATGCTGGGCGTGATGTTTTGGATATTGATGAATTGGAAATTCACTCTTATGACCGTATTGGTCTTGTGGGTGATAACGGAGCAGGAAAGAGTAGTTTACTCAAAGTACTTAATGGCGAAATTGTTTTAGCCGAAGCGACATTACAGCGTTTTGGTGATTTTGCACATATCAGCCAACTGGGCGGAATCGAAATAGAAACGGTCGAAGACCGGGCAATGTTATCTCGCCTTGGTGTTTCCAATGTACAAAACGACACAATGAGTGGCGGAGAGGAAACTCGTGCAAAAATTGCTGCCGCATTTTCCCAACAAGTACATGGCATTCTAGCGGATGAACCAACCAGCCACCTTGATCTCAATGGAATAGATCTACTTATTGGTCAACTTAAAGCATTTGATGGAGCATTACTTGTTATCAGTCATGACCGATATTTTCTTGATATGGTTGTAGACAAGATATGGGAGTTAAAAGACGGTAAAATTACGGAATATTGGGGTGGTTACTCGGATTACTTGCGTCAAAAAGAAGAAGAGCGACAACACCAAGCCGTAGAATATGAGCTGATGATGAAGGAACGGGAGCGATTAGAATCTGCTGTGCAAGAAAAACGCCAGCAAGCTAATCGATTAGACAATAAGAAAAAAGGAGAAAAATCCAAAAACTCTACCGAAAGTGCTGGACGACTTGGGCATGCAAAAATGACTGGCACCAAGCAAAGAAAACTGTATCAGGCAGCTAAGAGTATGGAAAAGCGTTTGGCTGCATTAGAAGATATTCAAGCACCAGAGCATTTGCGTTCTATTCGTTTTCGTCAAAGTTCAGCCCTAGAACTGCACAATAAGTTCCCGATTACGGCAGATGGTCTGAGCTTAAAATTTGGTAGCCGTACTATCTTTGATGACGCTAACTTTATAATACCGCTTGGCGCTAAAGTCGCTATAACTGGATCGAATGGAACAGGGAAAACGTCCTTGTTAAAAATGATATCAGAACGTGCTGATGGATTAACCATATCTCCAAAAGCTGAAATTGGCTACTTTACACAAACAGGATATAAATTTAACACGCATAAATCTGTGCTCTCCTTTATGCAGGAAGAGTGCGAGTACACAGTTGCGGAAATTCGTGCAGTATTGGCTTCAATGGGGATCGGAGCGAATGATATTCAAAAAAACTTATCCGACTTATCGGGAGGTGAAATCATCAAACTGCTTTTATCCAAAATGCTTTTAGGAAAATATAATATTTTGCTTATGGATGAACCAGGAAACTATCTTGACCTAAAAAGTATTGCCGCATTAGAAACAATGATGAAGTCCTATGCAGGAACTATTATCTTCGTATCTCATGACAAGCAATTGGTCGATAATATTGCTGACATTATCTACGAGATCAAAGACCACAAAATCATCAAGACTTTTGAGAGAGATTGTTAA MSLIIKARNIRLDYAGRDVLDIDELEIHSYDRIGLVGDNGAGKSSLLKVLNGEIVLAEATLQRFGDFAHISQLGGIEIETVEDRAMLSRLGVSNVQNDTMSGGEETRAKIAAAFSQQVHGILADEPTSHLDLNGIDLLIGQLKAFDGALLVISHDRYFLDMVVDKIWELKDGKITEYWGGYSDYLRQKEEERQHQAVEYELMMKERERLESAVQEKRQQANRLDNKKKGEKSKNSTESAGRLGHAKMTGTKQRKLYQAAKSMEKRLAALEDIQAPEHLRSIRFRQSSALELHNKFPITADGLSLKFGSRTIFDDANFIIPLGAKVAITGSNGTGKTSLLKMISERADGLTISPKAEIGYFTQTGYKFNTHKSVLSFMQEECEYTVAEIRAVLASMGIGANDIQKNLSDLSGGEIIKLLLSKMLLGKYNILLMDEPGNYLDLKSIAALETMMKSYAGTIIFVSHDKQLVDNIADIIYEIKDHKIIKTFERDC MSLIIKARNIRLDYAGRDVLDIDELEIHSYDRIGLVGDNGAGKSSLLKVLNGEIVLAEATLQRFGDFAHISQLGGIEIETVEDRAMLSRLGVSNVQNDTMSGGEETRAKIAAAFSQQVHGILADEPTSHLDLNGIDLLIGQLKAFDGALLVISHDRYFLDMVVDKIWELKDGKITEYWGGYSDYLRQKEEERQHQAVEYELMMKERERLESAVQEKRQQANRLDNKKKGEKSKNSTESAGRLGHAKMTGTKQRKLYQAAKSMEKRLAALEDIQAPEHLRSIRFRQSSALELHNKFPITADGLSLKFGSRTIFDDANFIIPLGAKVAITGSNGTGKTSLLKMISERADGLTISPKAEIGYFTQTGYKFNTHKSVLSFMQEECEYTVAEIRAVLASMGIGANDIQKNLSDLSGGEIIKLLLSKMLLGKYNILLMDEPGNYLDLKSIAALETMMKSYAGTIIFVSHDKQLVDNIADIIYEIKDHKIIKTFERDC 100.00 gnl|BL_ORD_ID|27|hsp_num:0 33 -2826_4171 | model_type_id: 40295 | pass_bit_score: 5000 | SNP: A2129C | Streptococcus pneumoniae 23S rRNA mutation conferring resistance to macrolides and streptogramins antibiotics | QUERY: 2826_4171 2826_4171 2 2905 + Strict 5000 5358.25 Streptococcus pneumoniae 23S rRNA mutation conferring resistance to macrolides and streptogramins antibiotics 99.97 3004181 rRNA gene variant model A2129C n/a macrolide antibiotic; streptogramin antibiotic; streptogramin A antibiotic; streptogramin B antibiotic antibiotic target alteration 23S rRNA with mutation conferring resistance to macrolide antibiotics; 23S rRNA with mutation conferring resistance to streptogramins antibiotics AAACCTATTCAGGAGCTCGATAATCATAATCAGGCGATGTACACAGCGGTGTGAAGGTGAAGATTGGATAGATGGACTAGTAGAGAGTCCCGAGAATGACTATATATTAGTACCCTTTAGAGTAGAACTCCACCCAAAGTGTGAATCTACGAAAGTCGCAAATAGGGAAGGGATGTATCGATGGGTCGCTACGGAAACCGTTCTGTTGACCATGTGGTCGCCATTCAGGTGAGACCAGGAGAGCATGATCCTCGTCTAGGAGAGTTTAAAGGATGCGGGCGCTGCCTATCCCTGGCTTGACAGAGTGCTGCAAGACTTGGGTCGAGCGCACGGCGAAATTACCCGCTTGTCGGGTTGGGAACCCTGGCTGATGTCGGGGTCCTACGCTGCTCGGCTGTAGCTCCACGGTTTGGAGGGGCAGCTACACTTGAGAACCCCCTCTATTCGGACAATAGGGGTCCCATCGAAAATAGGCAACTCGCTACCGGGAAGGTATGCCTTGGTGGCCTAGTGATTCGGGCTGAAAGCAGGGACGAGCTCAACATCGAGAGCGTCAGTTCGAGGGAATATGGAAATATGAGACGCTTACTAAAGGTTGGTAAGACTCCCTTGGAAACCCGCGGAGGCAATGGAAAATCCTCCGCTGGCGGGGTCAGTTTGACGGGCAGTCTGTGACAGAGGCTATCCCTAGTGGATAGACCCAATCTCACCGGTATTGTGTTCCCATCATAGGGTTGTCGCAGAGGAAGCTTTGACCGCAGGGCTAGAGAATCTGAGGATGGATAGGACATGTACACCATGTCTGTGAGTTATAGTTTGACGTCATTTCGAGGTACCCCAGAAAGGCAGGACAGCGCCCATTGGACGTAGAAGTGTCCATGATTTTAAAGTGGCTCAGAGAGCAACTCTGTCACGGGTTTAGTAATGCGGAAAGCACGCCCAGCCTTGAATGGGCTGTTCCTTAAAGCGATGGAATCCTGGCAATATCAATGCCGGCGGCAAATGACCCCGAAGTTAAGTATGGAAGCGAATGCGATTCGTGAGGAGAATTGGAAGGTCGTGGCCCGTCCGCAGTGGGGGATATGTAGTAGAATGCTAAATCGTCTCTCGACACAAAAACTATTTGTCAACGAACCCGGATAAGTGACGCCGACTGGATTTCAGTCGTGGGGAAGAGGGCTTCAATGCCCCAGTAAAACGGCTCAAGGAATTGCTCTCAAGAGAGCGAGTGGACTCCGATGAGCGGAGCTGATGGACACAGCCAAACGCCATGCCCATCTCATACAAATTTGCGATCTTCGAAAAGAACCGTCACACTGCAGTGATTGAAGCGATGATTTGAAGCGAGGGGTAGTGTCGAGTTACAATATCTTAATTCGTAAACTGAGTTAAGTGTGGAGTGACGAATCTGTCTGAGAAGGTTAGCAGACGAAATCAATCGGATGACGCAGGGAGGTAGTGATGTATGAGATCATGTCCTTATAGTTGGACAACAGGTAGCCTATGTGGAAAGCCAGAGAGGAATCCAGGGCTGATTGGGTCCCGCCTGCTCGGAAGGGGACCTTTGGAATCAGAATGCCACCTGTCCTAAGAGTGGACAGAAAGCGATGAGTATGGCCGTAAGAGTGAAGATACGCAAGGTCGTGAGGAGTGCCATATGGAAGTAGTGTGTATCTTGCGAGAGGATGGTATGGATATTTCCATAGGTGTCGAAGCCATTTAACAAAATCGGGGCCATGTAAAAGCCGCGTCCCAGTGAGCTGATCACTCGATAATGCGTGAGAAACTTACTTATCGACGAAGATTCGATTGTAGGATCAACAGACACGTTGGGGTGTAGGAAAAGGTGAATTGTTAATAAAACCCTGGAATCGACCACCAGACCCGACAAAGGGAAAGCTGATGCCTAGAATCGTGAGCGTCAGACTGACGGCTGGTATTAAGTAACCGTAAGCCTCAAATAGACTCTAACCATTAGGCCCTACCTGGGGAGTGGGTTTGTCACGAGATGGAGGTTCTTAGAGATTACAGCTGCGATCGGGATTTCGATAAAGCCTCTCTTGGTCGATAGAGGTTCAAGCAAACCTTAAAGAGGCGATGGGTGTTCAGTAGGTTCGTGAAAAGTTGCCCGGGACCAAGCCAGGAGGTCACGCAGAATGGCGTGGAAGTTGGACGAGTACCCATCCAGTGTACCAAAGCCCAGATGCAGTACTATGATTAAGCGGGACAAGTCTGAGCCAAAGGGATGCCGAGGCAGAGAAGTTGAATTGGAGCGTAGTATTGCATTGAGCGGCCAAGTAAGATGTTTTCCGTGCGAGAGTGGGTAATTGCCCGAGCTTGAACAACATCCGTGTGCCAAAGTCCAAGATAAAGTGAGGGGAGGGCCCCACGAAAAGTGGAAAGGGAGTGCCATGACCAAGTGATAGCCAGTGATCCCTCATAAATCCCAACCCTCTACCAGGAGGGTCTAAGGCTGCCCTAAAGTGCACAGGGCGGCATGAGTCCTATGACGATCCATGTTTCTGATAAAATTTATGCTCCGATAATGAGAGAAACCGACTAGAAGGGTTTAGTAAGAAGATATTAGAAACTCAGGTGTAACGTCAGGATGTTGGGGCTTCTCATTTGAGAAGCCAAACGGGAAGACGGCAAAGCGAGCGGCGATGATTCCGTTAGCGAAAACGAAAGAGAAGGACGTCGATGAATCTACAAAGTCAAGTGACGCAGAAGGAGGAGTGTAGGAATTGTCTACACCCATTGTCCATAATGGACAACCCAAGGGGGTAAGCCTTTAGGGACCTAGTAGCGAATGAATGTCGATGGGTTCCATATAGCAGCAAACAGTGCAGGAAGCAGCCGAGGATCACGGTTCCGTAGGTGGCACGCGGGAATAATTGAATTGGA 99.97 gnl|BL_ORD_ID|1|hsp_num:0 2826 -gb|NP_249116.1|+|testA-strict-s Strict 650 757.288 MexA 99.22 3000377 protein homolog model n/a n/a macrolide antibiotic; fluoroquinolone antibiotic; monobactam; carbapenem; cephalosporin; cephamycin; penam; tetracycline antibiotic; peptide antibiotic; aminocoumarin antibiotic; diaminopyrimidine antibiotic; sulfonamide antibiotic; phenicol antibiotic; penem antibiotic efflux resistance-nodulation-cell division (RND) antibiotic efflux pump MQRTPAMRVLVPALLVAISALSGCGKSEAPPPAQTPEVGIVTLEAQTVTLNTELPGRTNAFRIAEVRPQVNGIILKRLFKEGSDVKAGQQLYQIDPATYEADYQSAQANLASTQEQAQRYKLLVADQAVSKQQYADANAAYLQSKAAVEQARINLRYTKVLSPISGRIGRSAVTEGALVTNGQMATVQQLDPIYVDVTQPSTALLRLRRELASGQLERAGDNAAKVSLKLEDGSQYPLEGRLEFSEVSVDEGTGSVTIRAVFPNPNNELLPGMFVHAQLQEGVKQKAILAPQQGVTRDLKGQATALVVNAQNKVELRVIKADRVIGDKWLVTEGLNAGDKIITEGLQFVQPGVEVKTVPAKNVASAQKADAAPAKTDSKG MQRTPAMRVLVPALLVAISALSGCGKSEAPPPAQTPEVGIVTLEAQTVTLNTELPGRTNAFRIAEVRPQVNGIILKRLFKEGSDVKAGQQLYQIDPATYEADYQSAQANLASTQEQAQRYKLLVADQAVSKQQYADANAAYLQSKAAVEQARINLRYTKVLSPISGRIGRSAVTEGALVTNGQANAMATVQQLDPIYVDVTQPSTALLRLRRELASGQLERAGDNAAKVSLKLEDGSQYPLEGRLEFSEVSVDEGTGSVTIRAVFPNPNNELLPGMFVHAQLQEGVKQKAILAPQQGVTRDLKGQATALVVNAQNKVELRVIKADRVIGDKWLVTEGLNAGDKIITEGLQFVQPGVEVKTVPAKNVASAQKADAAPAKTDSKG 99.22 gnl|BL_ORD_ID|438|hsp_num:0 440 -gb|CAZ39946.1|-|NDM-1 [Klebsiella pneumoniae] Perfect 500 555.829 NDM-1 100.0 3000589 protein homolog model n/a n/a carbapenem; cephalosporin; cephamycin; penam antibiotic inactivation NDM beta-lactamase MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 100.00 gnl|BL_ORD_ID|713|hsp_num:0 783 -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 -gi|NP_252410.1|+|nalC [Pseudomonas aeruginosa PAO1] - no mutation Strict 400 432.95 nalC 100.0 3000818 protein overexpression model n/a n/a macrolide antibiotic; fluoroquinolone antibiotic; monobactam; carbapenem; cephalosporin; cephamycin; penam; tetracycline antibiotic; peptide antibiotic; aminocoumarin antibiotic; diaminopyrimidine antibiotic; sulfonamide antibiotic; phenicol antibiotic; penem antibiotic efflux resistance-nodulation-cell division (RND) antibiotic efflux pump MNDASPRLTERGRQRRRAMLDAATQAFLEHGFEGTTLDMVIERAGGSRGTLYSSFGGKEGLFAAVIAHMIEEIFDDSADQPRPAATLSATLEHFGRRFLTSLLDPRCQSLYRLVVAESPRFPAIGKSFYEQGPQQSYLLLSERLAAVAPHMDEETLYAVACQFLEMLKADLFLKALSVADFQPTMALLETRLKLSVDIIACYLEHLSQSPAQG MNDASPRLTERGRQRRRAMLDAATQAFLEHGFEGTTLDMVIERAGGSRGTLYSSFGGKEGLFAAVIAHMIGEIFDDSADQPRPAATLSATLEHFGRRFLTSLLDPRCQSLYRLVVAESPRFPAIGKSFYEQGPQQSYLLLSERLAAVAPHMDEETLYAVACQFLEMLKADLFLKALSVADFQPTMALLETRLKLSVDIIACYLEHLSQSPAQG 100.00 gnl|BL_ORD_ID|2132|hsp_num:0 1670 -gi|NP_252410.1|+|nalC [Pseudomonas aeruginosa PAO1] - with mutation G71E Strict 400 429.869 nalC 99.53 3000818 protein overexpression model G71E macrolide antibiotic; fluoroquinolone antibiotic; monobactam; carbapenem; cephalosporin; cephamycin; penam; tetracycline antibiotic; peptide antibiotic; aminocoumarin antibiotic; diaminopyrimidine antibiotic; sulfonamide antibiotic; phenicol antibiotic; penem antibiotic efflux resistance-nodulation-cell division (RND) antibiotic efflux pump MNDASPRLTERGRQRRRAMLDAATQAFLEHGFEGTTLDMVIERAGGSRGTLYSSFGGKEGLFAAVIAHMIEEIFDDSADQPRPAATLSATLEHFGRRFLTSLLDPRCQSLYRLVVAESPRFPAIGKSFYEQGPQQSYLLLSERLAAVAPHMDEETLYAVACQFLEMLKADLFLKALSVADFQPTMALLETRLKLSVDIIACYLEHLSQSPAQG MNDASPRLTERGRQRRRAMLDAATQAFLEHGFEGTTLDMVIERAGGSRGTLYSSFGGKEGLFAAVIAHMIGEIFDDSADQPRPAATLSATLEHFGRRFLTSLLDPRCQSLYRLVVAESPRFPAIGKSFYEQGPQQSYLLLSERLAAVAPHMDEETLYAVACQFLEMLKADLFLKALSVADFQPTMALLETRLKLSVDIIACYLEHLSQSPAQG 100.00 gnl|BL_ORD_ID|2132|hsp_num:0 1670 +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 +NC_020818.1_7 # 7011 # 7790 # 1 # ID=3_7;partial=00;start_type=ATG;rbs_motif=TAA;rbs_spacer=12bp;gc_cont=0.336 NC_020818.1_7 7011 7790 + Perfect 500 526.554 APH(3')-VI 100.0 3003687 protein homolog model n/a n/a aminoglycoside antibiotic antibiotic inactivation APH(3') ATGGAATTGCCCAATATTATTCAACAATTTATTGGAAACAGCGTTTTAGAGCCAAATAAAATTGGTCAGTCGCCATCGGATGTTTATTCTTTTAATCGAAATAATGAAACTTTTTTTCTTAAGCGATCTAGCACTTTATATACAGAGACCACATACAGTGTCTCTCGCGAAGCGAAAATGTTGAGTTGGCTCTCTGAGAAATTAAAGGTGCCTGAACTCATCATGACTTTTCAGGATGAGCAGTTTGAATTAATGATCACTAAAGCGATCAATGCAAAACCAATTTCAGCGCTTTTTTTAACAGACCAAGAATTGCTTGCTATCTATAAGGAGGCACTCAATCTGTTAAATTCAGTTGCTATTATTGATTGTCCATTTATTTCAAACATTGATCATCGGTTAAAAGAGTCAAAATTTTTTATTGATAACCAACTCCTTGACGATATAGATCAAGATGATTTTGACGCTGAATTATGGGGAGACCATAGAACTTACCTAAGTCTATGGAATGAGTTAACTGAGACTCGTGTTGAAGAAAGATTGGTTTTTTCTCATGGCGATATCACGGATAGTAATATTTTTATAGATAAATTCAATGAAATTTACTTTTTAGATCTTGGCCGTGCTGGGTTAGCTGATGAATTTGTAGATATATCCTTTGTTGAACGTTGCCTAAGAGAGGATGCCTCGGAGGAAACTGCTAAAATATTTTTAAAGCATTTAAAAAATGATAGACCTGACAAAAGGAATTATTTTTTAAAACTTGATGAATTGAATTGA MELPNIIQQFIGNSVLEPNKIGQSPSDVYSFNRNNETFFLKRSSTLYTETTYSVSREAKMLSWLSEKLKVPELIMTFQDEQFELMITKAINAKPISALFLTDQELLAIYKEALNLLNSVAIIDCPFISNIDHRLKESKFFIDNQLLDDIDQDDFDAELWGDHRTYLSLWNELTETRVEERLVFSHGDITDSNIFIDKFNEIYFLDLGRAGLADEFVDISFVERCLREDASEETAKIFLKHLKNDRPDKRNYFLKLDELN MELPNIIQQFIGNSVLEPNKIGQSPSDVYSFNRNNETFFLKRSSTLYTETTYSVSREAKMLSWLSEKLKVPELIMTFQDEQFELMITKAINAKPISALFLTDQELLAIYKEALNLLNSVAIIDCPFISNIDHRLKESKFFIDNQLLDDIDQDDFDAELWGDHRTYLSLWNELTETRVEERLVFSHGDITDSNIFIDKFNEIYFLDLGRAGLADEFVDISFVERCLREDASEETAKIFLKHLKNDRPDKRNYFLKLDELN 100.00 gnl|BL_ORD_ID|2016|hsp_num:0 2200 +NC_020818.1_9 # 9068 # 9880 # 1 # ID=3_9;partial=00;start_type=ATG;rbs_motif=TAA;rbs_spacer=12bp;gc_cont=0.615 NC_020818.1_9 9068 9880 + Perfect 500 555.829 NDM-1 100.0 3000589 protein homolog model n/a n/a carbapenem; cephalosporin; cephamycin; penam antibiotic inactivation NDM beta-lactamase ATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGGTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGATGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGA MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 100.00 gnl|BL_ORD_ID|713|hsp_num:0 783 +NC_020818.1_12 # 12051 # 12935 # -1 # ID=3_12;partial=00;start_type=ATG;rbs_motif=TAA;rbs_spacer=12bp;gc_cont=0.365 NC_020818.1_12 12051 12935 - Perfect 500 600.127 mphE 100.0 3003741 protein homolog model n/a n/a macrolide antibiotic antibiotic inactivation macrolide phosphotransferase (MPH) ATGACAATTCAAGATATTCAATCACTTGCTGAAGCACACGGCTTGTTGCTTACGGACAAAATGAATTTCAATGAAATGGGCATTGATTTTAAGGTCGTTTTTGCTCTTGATACAAAGGGGCAACAATGGTTGCTGCGTATTCCTCGTCGTGATGGCATGAGGGAACAAATCAAGAAAGAAAAACGCATTTTAGAATTGGTAAAAAAACATCTTTCTGTAGAGGTTCCTGATTGGAGAATTTCATCTACAGAATTAGTGGCTTATCCCATACTTAAAGATAATCCTGTTTTAAATTTGGATGCTGAAACCTATGAAATAATTTGGAATATGGACAAAGATAGCCCGAAATACATAACATCTTTGGCAAAAACCTTATTTGAAATCCATAGTATTCCTGAAAAAGAAGTTCGGGAAAATGATTTGAAAATTATGAAACCTTCAGATTTAAGACCTGAAATAGCAAACAATTTGCAGTTAGTAAAATCTGAAATTGGTATAAGTGAGCAATTGGAAACCCGCTACAGAAAATGGTTGGATAATGATGTTCTATGGGCAGATTTCACCCAATTTATACATGGCGATTTATATGCTGGGCATGTACTAGCTTCAAAGGATGGAGCTGTTTCAGGCGTTATTGATTGGTCAACAGCCCATATAGATGACCCAGCGATTGATTTTGCTGGGCATGTAACTTTGTTTGGAGAAGAAAGCCTCAAAACTCTAATCATCGAGTATGAAAAACTAGGGGGTAAAGTTTGGAATAAACTATATGAACAGACTTTAGAAAGAGCAGCGGCCTCTCCTTTGATGTATGGTTTATTTGCCTTAGAAACTCAAAATGAAAGCCTTATCGTTGGAGCAAAAGCTCAGTTGGGAGTTATATAA MTIQDIQSLAEAHGLLLTDKMNFNEMGIDFKVVFALDTKGQQWLLRIPRRDGMREQIKKEKRILELVKKHLSVEVPDWRISSTELVAYPILKDNPVLNLDAETYEIIWNMDKDSPKYITSLAKTLFEIHSIPEKEVRENDLKIMKPSDLRPEIANNLQLVKSEIGISEQLETRYRKWLDNDVLWADFTQFIHGDLYAGHVLASKDGAVSGVIDWSTAHIDDPAIDFAGHVTLFGEESLKTLIIEYEKLGGKVWNKLYEQTLERAAASPLMYGLFALETQNESLIVGAKAQLGVI MTIQDIQSLAEAHGLLLTDKMNFNEMGIDFKVVFALDTKGQQWLLRIPRRDGMREQIKKEKRILELVKKHLSVEVPDWRISSTELVAYPILKDNPVLNLDAETYEIIWNMDKDSPKYITSLAKTLFEIHSIPEKEVRENDLKIMKPSDLRPEIANNLQLVKSEIGISEQLETRYRKWLDNDVLWADFTQFIHGDLYAGHVLASKDGAVSGVIDWSTAHIDDPAIDFAGHVTLFGEESLKTLIIEYEKLGGKVWNKLYEQTLERAAASPLMYGLFALETQNESLIVGAKAQLGVI 100.00 gnl|BL_ORD_ID|2697|hsp_num:0 2614 +NC_020818.1_13 # 12991 # 14466 # -1 # ID=3_13;partial=00;start_type=ATG;rbs_motif=TAAA;rbs_spacer=5bp;gc_cont=0.399 NC_020818.1_13 12991 14466 - Perfect 950 1000.73 msrE 100.0 3003109 protein homolog model n/a n/a macrolide antibiotic; streptogramin antibiotic antibiotic target protection msr-type ABC-F protein ATGAGTTTAATTATTAAAGCGAGAAACATACGCTTGGATTATGCTGGGCGTGATGTTTTGGATATTGATGAATTGGAAATTCACTCTTATGACCGTATTGGTCTTGTGGGTGATAACGGAGCAGGAAAGAGTAGTTTACTCAAAGTACTTAATGGCGAAATTGTTTTAGCCGAAGCGACATTACAGCGTTTTGGTGATTTTGCACATATCAGCCAACTGGGCGGAATCGAAATAGAAACGGTCGAAGACCGGGCAATGTTATCTCGCCTTGGTGTTTCCAATGTACAAAACGACACAATGAGTGGCGGAGAGGAAACTCGTGCAAAAATTGCTGCCGCATTTTCCCAACAAGTACATGGCATTCTAGCGGATGAACCAACCAGCCACCTTGATCTCAATGGAATAGATCTACTTATTGGTCAACTTAAAGCATTTGATGGAGCATTACTTGTTATCAGTCATGACCGATATTTTCTTGATATGGTTGTAGACAAGATATGGGAGTTAAAAGACGGTAAAATTACGGAATATTGGGGTGGTTACTCGGATTACTTGCGTCAAAAAGAAGAAGAGCGACAACACCAAGCCGTAGAATATGAGCTGATGATGAAGGAACGGGAGCGATTAGAATCTGCTGTGCAAGAAAAACGCCAGCAAGCTAATCGATTAGACAATAAGAAAAAAGGAGAAAAATCCAAAAACTCTACCGAAAGTGCTGGACGACTTGGGCATGCAAAAATGACTGGCACCAAGCAAAGAAAACTGTATCAGGCAGCTAAGAGTATGGAAAAGCGTTTGGCTGCATTAGAAGATATTCAAGCACCAGAGCATTTGCGTTCTATTCGTTTTCGTCAAAGTTCAGCCCTAGAACTGCACAATAAGTTCCCGATTACGGCAGATGGTCTGAGCTTAAAATTTGGTAGCCGTACTATCTTTGATGACGCTAACTTTATAATACCGCTTGGCGCTAAAGTCGCTATAACTGGATCGAATGGAACAGGGAAAACGTCCTTGTTAAAAATGATATCAGAACGTGCTGATGGATTAACCATATCTCCAAAAGCTGAAATTGGCTACTTTACACAAACAGGATATAAATTTAACACGCATAAATCTGTGCTCTCCTTTATGCAGGAAGAGTGCGAGTACACAGTTGCGGAAATTCGTGCAGTATTGGCTTCAATGGGGATCGGAGCGAATGATATTCAAAAAAACTTATCCGACTTATCGGGAGGTGAAATCATCAAACTGCTTTTATCCAAAATGCTTTTAGGAAAATATAATATTTTGCTTATGGATGAACCAGGAAACTATCTTGACCTAAAAAGTATTGCCGCATTAGAAACAATGATGAAGTCCTATGCAGGAACTATTATCTTCGTATCTCATGACAAGCAATTGGTCGATAATATTGCTGACATTATCTACGAGATCAAAGACCACAAAATCATCAAGACTTTTGAGAGAGATTGTTAA MSLIIKARNIRLDYAGRDVLDIDELEIHSYDRIGLVGDNGAGKSSLLKVLNGEIVLAEATLQRFGDFAHISQLGGIEIETVEDRAMLSRLGVSNVQNDTMSGGEETRAKIAAAFSQQVHGILADEPTSHLDLNGIDLLIGQLKAFDGALLVISHDRYFLDMVVDKIWELKDGKITEYWGGYSDYLRQKEEERQHQAVEYELMMKERERLESAVQEKRQQANRLDNKKKGEKSKNSTESAGRLGHAKMTGTKQRKLYQAAKSMEKRLAALEDIQAPEHLRSIRFRQSSALELHNKFPITADGLSLKFGSRTIFDDANFIIPLGAKVAITGSNGTGKTSLLKMISERADGLTISPKAEIGYFTQTGYKFNTHKSVLSFMQEECEYTVAEIRAVLASMGIGANDIQKNLSDLSGGEIIKLLLSKMLLGKYNILLMDEPGNYLDLKSIAALETMMKSYAGTIIFVSHDKQLVDNIADIIYEIKDHKIIKTFERDC MSLIIKARNIRLDYAGRDVLDIDELEIHSYDRIGLVGDNGAGKSSLLKVLNGEIVLAEATLQRFGDFAHISQLGGIEIETVEDRAMLSRLGVSNVQNDTMSGGEETRAKIAAAFSQQVHGILADEPTSHLDLNGIDLLIGQLKAFDGALLVISHDRYFLDMVVDKIWELKDGKITEYWGGYSDYLRQKEEERQHQAVEYELMMKERERLESAVQEKRQQANRLDNKKKGEKSKNSTESAGRLGHAKMTGTKQRKLYQAAKSMEKRLAALEDIQAPEHLRSIRFRQSSALELHNKFPITADGLSLKFGSRTIFDDANFIIPLGAKVAITGSNGTGKTSLLKMISERADGLTISPKAEIGYFTQTGYKFNTHKSVLSFMQEECEYTVAEIRAVLASMGIGANDIQKNLSDLSGGEIIKLLLSKMLLGKYNILLMDEPGNYLDLKSIAALETMMKSYAGTIIFVSHDKQLVDNIADIIYEIKDHKIIKTFERDC 100.00 gnl|BL_ORD_ID|27|hsp_num:0 33 +2826_4171 | model_type_id: 40295 | pass_bit_score: 5000 | SNP: A2129C | Streptococcus pneumoniae 23S rRNA mutation conferring resistance to macrolides and streptogramins antibiotics | QUERY: 2826_4171 2826_4171 2 2905 + Strict 5000 5358.25 Streptococcus pneumoniae 23S rRNA mutation conferring resistance to macrolides and streptogramins antibiotics 99.97 3004181 rRNA gene variant model A2129C n/a macrolide antibiotic; streptogramin antibiotic; streptogramin A antibiotic; streptogramin B antibiotic antibiotic target alteration 23S rRNA with mutation conferring resistance to macrolide antibiotics; 23S rRNA with mutation conferring resistance to streptogramins antibiotics AAACCTATTCAGGAGCTCGATAATCATAATCAGGCGATGTACACAGCGGTGTGAAGGTGAAGATTGGATAGATGGACTAGTAGAGAGTCCCGAGAATGACTATATATTAGTACCCTTTAGAGTAGAACTCCACCCAAAGTGTGAATCTACGAAAGTCGCAAATAGGGAAGGGATGTATCGATGGGTCGCTACGGAAACCGTTCTGTTGACCATGTGGTCGCCATTCAGGTGAGACCAGGAGAGCATGATCCTCGTCTAGGAGAGTTTAAAGGATGCGGGCGCTGCCTATCCCTGGCTTGACAGAGTGCTGCAAGACTTGGGTCGAGCGCACGGCGAAATTACCCGCTTGTCGGGTTGGGAACCCTGGCTGATGTCGGGGTCCTACGCTGCTCGGCTGTAGCTCCACGGTTTGGAGGGGCAGCTACACTTGAGAACCCCCTCTATTCGGACAATAGGGGTCCCATCGAAAATAGGCAACTCGCTACCGGGAAGGTATGCCTTGGTGGCCTAGTGATTCGGGCTGAAAGCAGGGACGAGCTCAACATCGAGAGCGTCAGTTCGAGGGAATATGGAAATATGAGACGCTTACTAAAGGTTGGTAAGACTCCCTTGGAAACCCGCGGAGGCAATGGAAAATCCTCCGCTGGCGGGGTCAGTTTGACGGGCAGTCTGTGACAGAGGCTATCCCTAGTGGATAGACCCAATCTCACCGGTATTGTGTTCCCATCATAGGGTTGTCGCAGAGGAAGCTTTGACCGCAGGGCTAGAGAATCTGAGGATGGATAGGACATGTACACCATGTCTGTGAGTTATAGTTTGACGTCATTTCGAGGTACCCCAGAAAGGCAGGACAGCGCCCATTGGACGTAGAAGTGTCCATGATTTTAAAGTGGCTCAGAGAGCAACTCTGTCACGGGTTTAGTAATGCGGAAAGCACGCCCAGCCTTGAATGGGCTGTTCCTTAAAGCGATGGAATCCTGGCAATATCAATGCCGGCGGCAAATGACCCCGAAGTTAAGTATGGAAGCGAATGCGATTCGTGAGGAGAATTGGAAGGTCGTGGCCCGTCCGCAGTGGGGGATATGTAGTAGAATGCTAAATCGTCTCTCGACACAAAAACTATTTGTCAACGAACCCGGATAAGTGACGCCGACTGGATTTCAGTCGTGGGGAAGAGGGCTTCAATGCCCCAGTAAAACGGCTCAAGGAATTGCTCTCAAGAGAGCGAGTGGACTCCGATGAGCGGAGCTGATGGACACAGCCAAACGCCATGCCCATCTCATACAAATTTGCGATCTTCGAAAAGAACCGTCACACTGCAGTGATTGAAGCGATGATTTGAAGCGAGGGGTAGTGTCGAGTTACAATATCTTAATTCGTAAACTGAGTTAAGTGTGGAGTGACGAATCTGTCTGAGAAGGTTAGCAGACGAAATCAATCGGATGACGCAGGGAGGTAGTGATGTATGAGATCATGTCCTTATAGTTGGACAACAGGTAGCCTATGTGGAAAGCCAGAGAGGAATCCAGGGCTGATTGGGTCCCGCCTGCTCGGAAGGGGACCTTTGGAATCAGAATGCCACCTGTCCTAAGAGTGGACAGAAAGCGATGAGTATGGCCGTAAGAGTGAAGATACGCAAGGTCGTGAGGAGTGCCATATGGAAGTAGTGTGTATCTTGCGAGAGGATGGTATGGATATTTCCATAGGTGTCGAAGCCATTTAACAAAATCGGGGCCATGTAAAAGCCGCGTCCCAGTGAGCTGATCACTCGATAATGCGTGAGAAACTTACTTATCGACGAAGATTCGATTGTAGGATCAACAGACACGTTGGGGTGTAGGAAAAGGTGAATTGTTAATAAAACCCTGGAATCGACCACCAGACCCGACAAAGGGAAAGCTGATGCCTAGAATCGTGAGCGTCAGACTGACGGCTGGTATTAAGTAACCGTAAGCCTCAAATAGACTCTAACCATTAGGCCCTACCTGGGGAGTGGGTTTGTCACGAGATGGAGGTTCTTAGAGATTACAGCTGCGATCGGGATTTCGATAAAGCCTCTCTTGGTCGATAGAGGTTCAAGCAAACCTTAAAGAGGCGATGGGTGTTCAGTAGGTTCGTGAAAAGTTGCCCGGGACCAAGCCAGGAGGTCACGCAGAATGGCGTGGAAGTTGGACGAGTACCCATCCAGTGTACCAAAGCCCAGATGCAGTACTATGATTAAGCGGGACAAGTCTGAGCCAAAGGGATGCCGAGGCAGAGAAGTTGAATTGGAGCGTAGTATTGCATTGAGCGGCCAAGTAAGATGTTTTCCGTGCGAGAGTGGGTAATTGCCCGAGCTTGAACAACATCCGTGTGCCAAAGTCCAAGATAAAGTGAGGGGAGGGCCCCACGAAAAGTGGAAAGGGAGTGCCATGACCAAGTGATAGCCAGTGATCCCTCATAAATCCCAACCCTCTACCAGGAGGGTCTAAGGCTGCCCTAAAGTGCACAGGGCGGCATGAGTCCTATGACGATCCATGTTTCTGATAAAATTTATGCTCCGATAATGAGAGAAACCGACTAGAAGGGTTTAGTAAGAAGATATTAGAAACTCAGGTGTAACGTCAGGATGTTGGGGCTTCTCATTTGAGAAGCCAAACGGGAAGACGGCAAAGCGAGCGGCGATGATTCCGTTAGCGAAAACGAAAGAGAAGGACGTCGATGAATCTACAAAGTCAAGTGACGCAGAAGGAGGAGTGTAGGAATTGTCTACACCCATTGTCCATAATGGACAACCCAAGGGGGTAAGCCTTTAGGGACCTAGTAGCGAATGAATGTCGATGGGTTCCATATAGCAGCAAACAGTGCAGGAAGCAGCCGAGGATCACGGTTCCGTAGGTGGCACGCGGGAATAATTGAATTGGA 99.97 gnl|BL_ORD_ID|1|hsp_num:0 2826 +gb|NP_249116.1|+|testA-strict-s Strict 650 757.288 MexA 99.22 3000377 protein homolog model n/a n/a macrolide antibiotic; fluoroquinolone antibiotic; monobactam; carbapenem; cephalosporin; cephamycin; penam; tetracycline antibiotic; peptide antibiotic; aminocoumarin antibiotic; diaminopyrimidine antibiotic; sulfonamide antibiotic; phenicol antibiotic; penem antibiotic efflux resistance-nodulation-cell division (RND) antibiotic efflux pump MQRTPAMRVLVPALLVAISALSGCGKSEAPPPAQTPEVGIVTLEAQTVTLNTELPGRTNAFRIAEVRPQVNGIILKRLFKEGSDVKAGQQLYQIDPATYEADYQSAQANLASTQEQAQRYKLLVADQAVSKQQYADANAAYLQSKAAVEQARINLRYTKVLSPISGRIGRSAVTEGALVTNGQMATVQQLDPIYVDVTQPSTALLRLRRELASGQLERAGDNAAKVSLKLEDGSQYPLEGRLEFSEVSVDEGTGSVTIRAVFPNPNNELLPGMFVHAQLQEGVKQKAILAPQQGVTRDLKGQATALVVNAQNKVELRVIKADRVIGDKWLVTEGLNAGDKIITEGLQFVQPGVEVKTVPAKNVASAQKADAAPAKTDSKG MQRTPAMRVLVPALLVAISALSGCGKSEAPPPAQTPEVGIVTLEAQTVTLNTELPGRTNAFRIAEVRPQVNGIILKRLFKEGSDVKAGQQLYQIDPATYEADYQSAQANLASTQEQAQRYKLLVADQAVSKQQYADANAAYLQSKAAVEQARINLRYTKVLSPISGRIGRSAVTEGALVTNGQANAMATVQQLDPIYVDVTQPSTALLRLRRELASGQLERAGDNAAKVSLKLEDGSQYPLEGRLEFSEVSVDEGTGSVTIRAVFPNPNNELLPGMFVHAQLQEGVKQKAILAPQQGVTRDLKGQATALVVNAQNKVELRVIKADRVIGDKWLVTEGLNAGDKIITEGLQFVQPGVEVKTVPAKNVASAQKADAAPAKTDSKG 99.22 gnl|BL_ORD_ID|438|hsp_num:0 440 +gb|CAZ39946.1|-|NDM-1 [Klebsiella pneumoniae] Perfect 500 555.829 NDM-1 100.0 3000589 protein homolog model n/a n/a carbapenem; cephalosporin; cephamycin; penam antibiotic inactivation NDM beta-lactamase MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR MELPNIMHPVAKLSTALAAALMLSGCMPGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 100.00 gnl|BL_ORD_ID|713|hsp_num:0 783 +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 +gi|NP_252410.1|+|nalC [Pseudomonas aeruginosa PAO1] - no mutation Strict 400 432.95 nalC 100.0 3000818 protein overexpression model n/a n/a macrolide antibiotic; fluoroquinolone antibiotic; monobactam; carbapenem; cephalosporin; cephamycin; penam; tetracycline antibiotic; peptide antibiotic; aminocoumarin antibiotic; diaminopyrimidine antibiotic; sulfonamide antibiotic; phenicol antibiotic; penem antibiotic efflux resistance-nodulation-cell division (RND) antibiotic efflux pump MNDASPRLTERGRQRRRAMLDAATQAFLEHGFEGTTLDMVIERAGGSRGTLYSSFGGKEGLFAAVIAHMIEEIFDDSADQPRPAATLSATLEHFGRRFLTSLLDPRCQSLYRLVVAESPRFPAIGKSFYEQGPQQSYLLLSERLAAVAPHMDEETLYAVACQFLEMLKADLFLKALSVADFQPTMALLETRLKLSVDIIACYLEHLSQSPAQG MNDASPRLTERGRQRRRAMLDAATQAFLEHGFEGTTLDMVIERAGGSRGTLYSSFGGKEGLFAAVIAHMIGEIFDDSADQPRPAATLSATLEHFGRRFLTSLLDPRCQSLYRLVVAESPRFPAIGKSFYEQGPQQSYLLLSERLAAVAPHMDEETLYAVACQFLEMLKADLFLKALSVADFQPTMALLETRLKLSVDIIACYLEHLSQSPAQG 100.00 gnl|BL_ORD_ID|2132|hsp_num:0 1670 +gi|NP_252410.1|+|nalC [Pseudomonas aeruginosa PAO1] - with mutation G71E Strict 400 429.869 nalC 99.53 3000818 protein overexpression model G71E macrolide antibiotic; fluoroquinolone antibiotic; monobactam; carbapenem; cephalosporin; cephamycin; penam; tetracycline antibiotic; peptide antibiotic; aminocoumarin antibiotic; diaminopyrimidine antibiotic; sulfonamide antibiotic; phenicol antibiotic; penem antibiotic efflux resistance-nodulation-cell division (RND) antibiotic efflux pump MNDASPRLTERGRQRRRAMLDAATQAFLEHGFEGTTLDMVIERAGGSRGTLYSSFGGKEGLFAAVIAHMIEEIFDDSADQPRPAATLSATLEHFGRRFLTSLLDPRCQSLYRLVVAESPRFPAIGKSFYEQGPQQSYLLLSERLAAVAPHMDEETLYAVACQFLEMLKADLFLKALSVADFQPTMALLETRLKLSVDIIACYLEHLSQSPAQG MNDASPRLTERGRQRRRAMLDAATQAFLEHGFEGTTLDMVIERAGGSRGTLYSSFGGKEGLFAAVIAHMIGEIFDDSADQPRPAATLSATLEHFGRRFLTSLLDPRCQSLYRLVVAESPRFPAIGKSFYEQGPQQSYLLLSERLAAVAPHMDEETLYAVACQFLEMLKADLFLKALSVADFQPTMALLETRLKLSVDIIACYLEHLSQSPAQG 100.00 gnl|BL_ORD_ID|2132|hsp_num:0 1670 diff --git a/test/test_parsing_validity.py b/test/test_parsing_validity.py index e989e88..a79b073 100644 --- a/test/test_parsing_validity.py +++ b/test/test_parsing_validity.py @@ -315,11 +315,11 @@ def test_resfinder(): seen_genes += 1 # it reports these 4 agents separately (even if all on one gene) - assert (result.antimicrobial_agent, result.drug_class) in [ + assert (result.antimicrobial_agent, result.drug_class) in [ ('ciprofloxacin', 'quinolone'), ('nalidixic acid', 'quinolone'), ('trimethoprim', 'folate pathway antagonist'), - ('chloramphenicol', 'amphenicol') ] + ('chloramphenicol', 'amphenicol')] # assert mandatory fields (5) assert result.gene_symbol == "OqxA" @@ -330,7 +330,10 @@ def test_resfinder(): # optional fields (12) assert result.predicted_phenotype == "ciprofloxacin, nalidixic acid, trimethoprim, chloramphenicol" - assert result.predicted_phenotype_confidence_level == "Must be in an operon with oqxB,phenotype differs based on genomic location of the operon PMID 25801572,also nitrofurantoin resistance PMID 26552976. Natural in K. pneumoniae. PMIDs: 18440636" + assert result.predicted_phenotype_confidence_level == ( + "Must be in an operon with oqxB," + + "phenotype differs based on genomic location of the operon PMID 25801572," + + "also nitrofurantoin resistance PMID 26552976. Natural in K. pneumoniae. PMIDs: 18440636") assert result.coverage_percentage == 100.0 assert result.input_sequence_id == "contig1" assert result.input_gene_length == 1176 @@ -372,7 +375,9 @@ def test_resfinder(): assert result.antimicrobial_agent == "ampicillin" assert result.drug_class == "beta-lactam" assert result.predicted_phenotype == "ampicillin" - assert result.predicted_phenotype_confidence_level == "The nineteen pbp5 mutations must be present simultaneously for resistance phenotype. PMIDs: 25182648" + assert result.predicted_phenotype_confidence_level == ( + "The nineteen pbp5 mutations must be present simultaneously " + + "for resistance phenotype. PMIDs: 25182648") assert result.coverage_percentage == 100.0 assert result.input_sequence_id == "contig2" assert result.input_gene_length == 2037 @@ -385,9 +390,13 @@ def test_resfinder(): assert result.sequence_identity == 95.34 # mutation fields (3) - assert result.amino_acid_mutation == "p.V24A, p.S27G, p.R34Q, p.G66E, p.A68T, p.E85D, p.E100Q, p.K144Q, p.T172A, p.L177I, p.D204G, p.A216S, p.T324A, p.N496K, p.A499T, p.E525D, p.P667S" + assert result.amino_acid_mutation == ( + "p.V24A, p.S27G, p.R34Q, p.G66E, p.A68T, p.E85D, p.E100Q, p.K144Q, p.T172A, " + + "p.L177I, p.D204G, p.A216S, p.T324A, p.N496K, p.A499T, p.E525D, p.P667S") assert result.nucleotide_mutation is None - assert result.nucleotide_mutation_interpretation == "Codon changes: gta>gca agt>ggt cgg>cag gga>gaa gca>aca gaa>gat gag>cag aaa>caa aca>gca tta>ata gac>ggc gca>tcc aca>gca aat>aaa gca>aca gag>gat ccc>tcg" + assert result.nucleotide_mutation_interpretation == ( + "Codon changes: gta>gca agt>ggt cgg>cag gga>gaa gca>aca gaa>gat gag>cag aaa>caa " + + "aca>gca tta>ata gac>ggc gca>tcc aca>gca aat>aaa gca>aca gag>gat ccc>tcg") # not set (10) assert result.coverage_depth is None @@ -408,6 +417,7 @@ def test_resfinder(): assert seen_genes == 4 assert seen_variants == 1 + def test_rgi_variants(): metadata = { "analysis_software_version": "5.2.0", @@ -435,6 +445,8 @@ def test_rgi_variants(): assert result.drug_class == "aminocoumarin antibiotic" assert result.sequence_identity == 99.88 assert result.resistance_mechanism == "antibiotic target alteration" + assert result.antimicrobial_agent == '' + def test_rgi_orf_mode(): metadata = { @@ -447,30 +459,27 @@ def test_rgi_orf_mode(): for result in parsed_report: # assert mandatory fields assert result.input_file_name == "Dummy ORF" - assert result.gene_symbol == "NDM-5" - assert ( - result.gene_name - == "NDM beta-lactamase" - ) + assert result.gene_symbol == "NDM-1" + assert result.gene_name == "NDM beta-lactamase" assert result.reference_database_name == "CARD" assert result.reference_database_version == "3.2.5" - assert result.reference_accession == "3000467" + assert result.reference_accession == "3000589" assert result.analysis_software_name == "rgi" assert result.analysis_software_version == "6.0.0" assert result.genetic_variation_type == "gene_presence_detected" # optional fields - present in dummy dataset - assert result.input_sequence_id == "gb|AEN03071.1|+|NDM-5 [Escherichia coli]" - assert result.input_gene_start == '' - assert result.input_gene_stop == '' - assert result.strand_orientation == '' - assert ( - result.drug_class - == "carbapenem; cephalosporin; cephamycin; penam" - ) + assert result.input_sequence_id == "ndm-1_1" + assert result.input_gene_start == 1 + assert result.input_gene_stop == 813 + assert result.strand_orientation == '+' + assert result.drug_class == "carbapenem; cephalosporin; penicillin beta-lactam" assert result.sequence_identity == 100 assert result.coverage_percentage == 100 assert result.resistance_mechanism == "antibiotic inactivation" + assert result.reference_gene_start == 0 + assert result.reference_gene_stop == 810 + assert result.antimicrobial_agent == "ertapenem; meropenem; imipenem" def test_rgi(): @@ -501,28 +510,27 @@ def test_rgi(): assert result.input_gene_start == 1333608 assert result.input_gene_stop == 1334783 assert result.strand_orientation == "-" - assert ( - result.drug_class - == "fluoroquinolone antibiotic; glycylcycline; tetracycline antibiotic; diaminopyrimidine antibiotic; nitrofuran antibiotic" - ) + assert result.drug_class == ( + "fluoroquinolone antibiotic; glycylcycline; tetracycline antibiotic; " + + "diaminopyrimidine antibiotic; nitrofuran antibiotic") assert result.sequence_identity == 99.49 assert result.coverage_percentage == 100 assert result.resistance_mechanism == "antibiotic efflux" # missing data in report - assert result.reference_gene_length is None assert result.coverage_depth is None - assert result.input_gene_length is None - assert result.antimicrobial_agent is None - assert result.reference_protein_length is None assert result.coverage_ratio is None + assert result.input_gene_length is None assert result.input_protein_length is None assert result.input_protein_start is None assert result.input_protein_stop is None + assert result.reference_gene_length is None + assert result.reference_gene_start == 0 + assert result.reference_gene_stop == 1173 + assert result.reference_protein_length is None assert result.reference_protein_start is None assert result.reference_protein_stop is None - assert result.reference_gene_start is None - assert result.reference_gene_stop is None + assert result.antimicrobial_agent == 'tigecycline; ciprofloxacin; nitrofurantoin; trimethoprim' def test_srax(): @@ -825,11 +833,9 @@ def test_tbprofiler(): def test_mykrobe_empty(): metadata = {} - parsed_report = hAMRonization.parse( - "data/dummy/mykrobe/empty.json", metadata, "mykrobe" - ) + parsed_report = hAMRonization.parse("data/dummy/mykrobe/empty.json", metadata, "mykrobe") for result in parsed_report: - assert False # there should be none + assert False # there should be none def test_mykrobe(): @@ -958,6 +964,7 @@ def test_resfams(): assert result.genetic_variation_type == "gene_presence_detected" assert result.reference_database_name == "resfams_hmms" + def test_fargene(): metadata = { 'analysis_software_version': '0.1', From 6140f96fd0df7cc38cb0e8244af5bad14bac0573 Mon Sep 17 00:00:00 2001 From: Marco van Zwetselaar Date: Wed, 15 Jan 2025 03:25:17 +0300 Subject: [PATCH 3/3] Fix failing GitHub workflow --- .github/workflows/test_package.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test_package.yml b/.github/workflows/test_package.yml index b569835..84e2bbb 100644 --- a/.github/workflows/test_package.yml +++ b/.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