RGI: add mappings for antibiotics and hit positions

zwets · zwets · commit 39a6a673dde1 · 2025-01-15T03:06:16.000+03:00
- Closes #100
diff --git 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
@@ -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
@@ -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
@@ -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
diff --git a/test/test_parsing_validity.py b/test/test_parsing_validity.py
