Add ribosomal issue test files

pha4ge · Dec 27, 2024 · 2b8c724 · 2b8c724
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diff --git a/test/data/raw_outputs/amrfinderplus/afp_non_coding.tsv b/test/data/raw_outputs/amrfinderplus/afp_non_coding.tsv
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+Name	Protein identifier	Contig id	Start	Stop	Strand	Gene symbol	Sequence name	Scope	Element type	Element subtype	Class	Subclass	Method	Target length	Reference sequence length	% Coverage of reference sequence	% Identity to reference sequence	Alignment length	Accession of closest sequence	Name of closest sequence	HMM id	HMM description
+DAWXTK010000082_noncoding_test	NA	DAWXTK010000082.1:68-2970	1	2903	+	23S_A2062G	Neisseria gonorrhoeae azithromycin resistant 23S	core	AMR	POINT	MACROLIDE	AZITHROMYCIN	POINTN	2903	2910	100.00	99.35	2910	NC_002946.2:1119158-1116249	23S ribosomal RNA	NA	NA
diff --git a/test/data/raw_outputs/amrfinderplus/hamronized_non_coding.tsv b/test/data/raw_outputs/amrfinderplus/hamronized_non_coding.tsv
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+input_file_name	gene_symbol	gene_name	reference_database_name	reference_database_version	reference_accession	analysis_software_name	analysis_software_version	genetic_variation_type	antimicrobial_agent	coverage_percentage	coverage_depth	coverage_ratio	drug_class	input_gene_length	input_gene_start	input_gene_stop	input_protein_length	input_protein_start	input_protein_stop	input_sequence_id	nucleotide_mutation	nucleotide_mutation_interpretation	predicted_phenotype	predicted_phenotype_confidence_level	amino_acid_mutation	amino_acid_mutation_interpretation	reference_gene_length	reference_gene_start	reference_gene_stop	reference_protein_length	reference_protein_start	reference_protein_stop	resistance_mechanism	strand_orientation	sequence_identity
+DAWXTK010000082_noncoding_test	23S	Neisseria gonorrhoeae azithromycin resistant 23S	NCBI Reference Gene Database	2024-07-22.1	NC_002946.2:1119158-1116249	amrfinderplus	3.12.18	nucleotide_variant_detected	AZITHROMYCIN	100.0			MACROLIDE		1	2903	2903			DAWXTK010000082.1:68-2970	c.2062A>G									2910				+	99.35
diff --git a/test/data/raw_outputs/amrfinderplus/non_coding_contig.fasta b/test/data/raw_outputs/amrfinderplus/non_coding_contig.fasta
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+>DAWXTK010000082.1:68-2970 TPA_asm: Neisseria gonorrhoeae strain WHO_V SAMEA3905804-rid23293863.denovo.083, whole genome shotgun sequence
+TGAAATGATAGGGTCAAGTGAATAAGTGCATCAGGCGGATGCCTTGGCGATGATAGGCGACGAAGGACGT
+GTAAGCCTGCGAAAAGCGCGGGGGAGCTGGCAATAAAGCTATGATTCCGCGATGTCCGAATGGGGAAACC
+CACTGCATTCTGTGCAGTATCCTAAGTTGAATACATAGGCTTAGAGAAGCGAACCCGGAGAACTGAACCA
+TCTAAGTACCCGGAGGAAAAGAAATCAACCGAGATTCCGCAAGTAGTGGCGAGCGAACGCGGAGGAGCCT
+GTACGTAATAACTGTCGAGATAGAAGAACAAGCTGGGAAGCTTGACCATAGCGGGTGACAGTCCCGTATT
+CGAAATCTCAACAGCGGTACTAAGCGTACGAAAAGTAGGGCGGGACACGTGAAATCCTGTCTGAATATGG
+GGGGACCATCCTCCAAGGCTAAATACTCATCATCGACCGATAGTGAACCAGTACCGTGAGGGAAAGGCGA
+AAAGAACCCCGGGAGGGGAGTGAAACAGAACCTGAAACCTGATGCATACAAACAGTGGGAGCGCCCTAGT
+GGTGTGACTGCGTACCTTTTGTATAATGGGTCAACGACTTACATTCAGTAGCGAGCTTAACCGGATAGGG
+GAGGCGTAGGGAAACCGAGTCTTAATAGGGCGATGAGTTGCTGGGTGTAGACCCGAAACCGAGTGATCTA
+TCCATGGCCAGGTTGAAGGTGCCGTAACAGGTACTGGAGGACCGAACCCACGCATGTTGCAAAATGCGGG
+GATGAGCTGTGGGTAGGGGTGAAAGGCTAAACAAACTCGGAGATAGCTGGTTCTCCCCGAAAACTATTTA
+GGTAGTGCCTCGAGCAAGACACTGATGGGGGTAAAGCACTGTTATGGCTAGGGGGTTATTGCAACTTACC
+AACCCATGGCAAACTCAGAATACCATCAAGTGGTTCCTCGGGAGACAGACAGCGGGTGCTAACGTCCGTT
+GTCAAGAGGGAAACAACCCAGACCGCCGGCTAAGGTCCCAAATGATAGATTAAGTGGTAAACGAAGTGGG
+AAGGCACAGACAGCCAGGATGTTGGCTTAGAAGCAGCCATCATTTAAAGAAAGCGTAATAGCTCACTGGT
+CGAGTCGTCCTGCGCGGAAGATGTAACGGGGCTCAAATCTATAACCGAAGCTGCGGATGCCGGTTTACCG
+GCATGGTAGGGGAGCGTTCTGTAGGCTGATGAAGGTGCATTGTAAAGTGTGCTGGAGGTATCAGAAGTGC
+GAATGTTGACATGAGTAGCGATAAAGCGGGTGAAAAGCCCGCTCGCCGAAAGCCCAAGGTTTCCTACGCA
+ACGTTCATCGGCGTAGGGTAAGTCGGCCCCTAAGGCGAGGCAGAAATGCGTAGTCGATGGGAAACAGGTT
+AATATTCCTGTACTTGATTCAAATGCGATGTGGGGACGGAGAAGGTTAGGTTGGCAAGCTGTTGGAATAG
+CTTGTTTAAGCCGGTAGGTGGAAGACTTAGGCAAATCCGGGTTTTCTTAACACCGAGAAGTGATGACGAG
+TGTCTACGGACACGAAGCAACCGATACCACGCTTCCAGGAAAAGCCACTAAGCTTCAGTTTGAATCGAAC
+CGTACCGCAAACCGACACAGGTGGGCAGGATGAGAATTCTAAGGCGCTTGAGAGAACTCGGGAGAAGGAA
+CTCGGCAAATTGATACCGTAACTTCGGGAGAAGGTATGCCCTCTAAGGTTAAGGACTTGCTCCGTAAGCC
+CCGGAGGGTCGCAGAGAATAGGTGGCTGCGACTGTTTATTAAAAACACAGCACTCTGCCAACACGAAAGT
+GGACGTATAGGGTGTGACGCCTGCCCGGTGCCGGAAGGTTAATTGAAGATGTGCAAGCATCGGATCGAAG
+CCCCGGTAAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGAC
+CCGCACGAATGGCGTAACGATGGCCACACTGTCTCCTCCCGAGACTCAGCGAAGTTGAAGTGGTTGTGAA
+GATGCAATCTACCCGCTGCTAGACGGAGAGACCCCGTGAACCTTTACTGTAGCTTTGCATTGGACTTTGA
+AGTCACTTGTGTAGGATAGGTGGGAGGCTTGGAAGCAGAGACGCCAGTCTCTGTGGAGTCGTCCTTGAAA
+TACCACCCTGGTGTCTTTGAGGTTCTAACCCAGACCCGTCATCCGGGTCGGGGACCGTGCATGGTAGGCA
+GTTTGACTGGGGCGGTCTCCTCCCAAAGCGTAACGGAGGAGTTCGAAGGTTACCTAGGTCCGGTCGGAAA
+TCGGACTGATAGTGCAATGGCAAAAGGTAGCTTAACTGCGAGACCGACAAGTCGGGCAGGTGCGAAAGCA
+GGACATAGTGATCCGGTGGTTCTGTATGGAAGGGCCATCGCTCAACGGATAAAAGGTACTCCGGGGATAA
+CAGGCTGATTCCGCCCAAGAGTTCATATCGACGGCGGAGTTTGGCACCTCGATGTCGGCTCATCACATCC
+TGGGGCTGTAGTCGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGTGAGCTGGGTTTAAAAC
+GTCGTGAGACAGTTTGGTCCCTATCTGCAGTGGGCGTTGGAAGTTTGACGGGGGCTGCTCCTAGTACGAG
+AGGACCGGAGTGGACGAACCTCTGGTGTACCGGTTGTAACGCCAGTTGCATAGCCGGGTAGCTAAGTTCG
+GAAGAGATAAGCGCTGAAAGCATCTAAGCGCGAAACTCGCCTGAAGATGAGACTTCCCTTGCGGTTTAAC
+CGCACTAAAGGGTCGTTCGAGACCAGGACGTTGATAGGTGGGGTGTGGAAGCGCGGTAACGCGTGAAGCT
+AACCCATACTAATTGCCCGTGAGGCTTGACTCT
+
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		Name Protein identifier Contig id Start Stop Strand Gene symbol Sequence name Scope Element type Element subtype Class Subclass Method Target length Reference sequence length % Coverage of reference sequence % Identity to reference sequence Alignment length Accession of closest sequence Name of closest sequence HMM id HMM description
		DAWXTK010000082_noncoding_test NA DAWXTK010000082.1:68-2970 1 2903 + 23S_A2062G Neisseria gonorrhoeae azithromycin resistant 23S core AMR POINT MACROLIDE AZITHROMYCIN POINTN 2903 2910 100.00 99.35 2910 NC_002946.2:1119158-1116249 23S ribosomal RNA NA NA
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		input_file_name gene_symbol gene_name reference_database_name reference_database_version reference_accession analysis_software_name analysis_software_version genetic_variation_type antimicrobial_agent coverage_percentage coverage_depth coverage_ratio drug_class input_gene_length input_gene_start input_gene_stop input_protein_length input_protein_start input_protein_stop input_sequence_id nucleotide_mutation nucleotide_mutation_interpretation predicted_phenotype predicted_phenotype_confidence_level amino_acid_mutation amino_acid_mutation_interpretation reference_gene_length reference_gene_start reference_gene_stop reference_protein_length reference_protein_start reference_protein_stop resistance_mechanism strand_orientation sequence_identity
		DAWXTK010000082_noncoding_test 23S Neisseria gonorrhoeae azithromycin resistant 23S NCBI Reference Gene Database 2024-07-22.1 NC_002946.2:1119158-1116249 amrfinderplus 3.12.18 nucleotide_variant_detected AZITHROMYCIN 100.0 MACROLIDE 1 2903 2903 DAWXTK010000082.1:68-2970 c.2062A>G 2910 + 99.35