feat: add simple nextclade datasets for all HA and NAs and code to ge… #10

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anna-parker wants to merge 5 commits into main from flu

data/flu/HA/ha_h10_h10n7/CY136094/unreleased/dataset.zip

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data/flu/HA/ha_h10_h10n7/CY136094/unreleased/genome_annotation.gff3

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+Diff line change
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+    ##gff-version 3
+    #!gff-spec-version 1.21
+    #!processor NCBI annotwriter
+    ##sequence-region CY136094.1 1 1703
+    ##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1228423
+    CY136094.1	Genbank	region	1	1703	.	+	.	ID=CY136094.1:1..1703;Dbxref=taxon:1228423;Name=4;bio-material=CEIRS#9BM11387#;country=USA: Alaska;gbkey=Src;lab-host=R0 passage(s);mol_type=viral cRNA;nat-host=northern pintail%3B gender F%3B age hatch year;note=Sample provided by University of Alaska Fairbanks;segment=4;serotype=H10N7;strain=A/northern pintail/Interior Alaska/9BM11387R0/2009
+    CY136094.1	Genbank	sequence_feature	1	1703	.	+	.	ID=id-CY136094.1:1..1703;Dbxref=IRD:NIGSP_CEIRS_CIP055_AK2_00216.HA;gbkey=misc_feature
+    CY136094.1	Genbank	gene	8	1693	.	+	.	ID=gene-HA;Name=HA;gbkey=Gene;gene=HA;gene_biotype=protein_coding
+    CY136094.1	Genbank	CDS	8	1693	.	+	0	ID=cds-AGG26198.1;Parent=gene-HA;Dbxref=NCBI_GP:AGG26198.1;Name=HA;gbkey=CDS;product=hemagglutinin;protein_id=AGG26198.1
+    CY136094.1	Genbank	signal_peptide_region_of_CDS	8	55	.	+	.	ID=id-AGG26198.1:1..16;Parent=cds-AGG26198.1;gbkey=Prot
+    CY136094.1	Genbank	mature_protein_region_of_CDS	56	1027	.	+	.	ID=id-AGG26198.1:17..340;Parent=cds-AGG26198.1;gbkey=Prot;product=HA1
+    CY136094.1	Genbank	mature_protein_region_of_CDS	1028	1690	.	+	.	ID=id-AGG26198.1:341..561;Parent=cds-AGG26198.1;gbkey=Prot;product=HA2

data/flu/HA/ha_h10_h10n7/CY136094/unreleased/pathogen.json

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+Diff line change
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+    {
+      "alignmentParams": {
+        "minSeedCover": 0.01
+      },
+      "schemaVersion": "3.0.0",
+      "attributes": {
+        "name": "ha_h10_h10n7",
+        "reference name": "Influenza A virus (A/northern pintail/Interior Alaska/9BM11387R0/2009(H10N7)) hemagglutinin (HA) gene, complete cds",
+        "reference accession": "CY136094"
+      },
+      "files": {
+        "reference": "reference.fasta",
+        "pathogenJson": "pathogen.json",
+        "genomeAnnotation": "genome_annotation.gff3"
+      }
+    }

data/flu/HA/ha_h10_h10n7/CY136094/unreleased/reference.fasta

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+    >CY136094.1 Influenza A virus (A/northern pintail/Interior Alaska/9BM11387R0/2009(H10N7)) hemagglutinin (HA) gene, complete cds
+    GGTCACAATGTACAAAATAGTACTAGTACTTGCGCTCCTTGGAGCGGTGCATGGTCTTGACAAAATATGC
+    CTTGGACATCATGCAGTCTCCAATGGCACCATTGTAAAGACTCTCACAAACGAAAAGGAAGAGGTGACCA
+    ATGCTACTGAAACAGTGGAGAGCAAAAGCCTGGACAAACTTTGCATGAAAAGTCGGAATTACAAGGACTT
+    AGGTAATTGCCACCCAATAGGGATGATAATAGGGACTCCTGCTTGTGACCTACACCTCACCGGAACATGG
+    GACACTTTAATAGAGAGAGACAATTCTATTGCCTACTGTTACCCGGGTGCCACTGTGAATGAAGAAGCAT
+    TAAGGCAGAAAATTATGGAAAGTGGAGGGATTGACAAGATAAGCACCGGGTTTACATATGGATCATCCAT
+    CAATTCAGCTGGAACCACTAAAGCATGCATGAGAAATGGGGGAAATAGTTTCTATGCGGAGCTAAAGTGG
+    CTAGTGTCGAAGAGCAAAGGACAAAACTTCCCACAAACAACAAACACATACAGAAATACAGATTCAGCAG
+    AACACCTTATAATCTGGGGAATTCATCACCCTTCAAGCACACAAGAAAAGAATGATCTGTATGGAACACA
+    ATCACTTTCCATTTCAGTAGGGAGTTCTACTTATCAAAACAACTTTGTGCCTGTGGTGGGAGCAAGACCA
+    CAAGTGAATGGCCAAAGTGGGCGGATTGTTTTCCATTGGGCGATGGTACAGCCAGGTGATAACATCACTT
+    TTTCGCATAATGGTGGATTGATAGCACCTAGCAGAGTGAGTAAACTAAAGGGAAGAGGCCTTGGCATCCA
+    ATCAGGAGCTTCAGTAGACAATGACTGTGAATCAAAATGTTTCTGGAAAGGTGGATCCATCAACACCAAA
+    CTCCCTTTTCAGAATCTTTCCCCAAGAACTGTGGGTCAATGCCCCAAGTATGTGAACAAAAAGAGCCTGT
+    TGCTTGCTACTGGAATGAGGAATGTGCCAGAGGTTGTCCAAGGAAGAGGCCTGTTTGGAGCAATAGCTGG
+    ATTCATAGAGAATGGATGGGAAGGAATGGTAGATGGTTGGTATGGTTTCCGACACCAAAATGCCCAAGGC
+    ACTGGCCAGGCCGCGGATTATAAAAGTACTCAGGCAGCTATAGATCAAATAACCGGGAAATTGAACAGAC
+    TGATAGAGAAGACAAACACAGAGTTCGAATCCATAGAATCTGAGTTCAGTGAAATAGAACATCAAATTGG
+    CAATGTAATAAACTGGACTAAGGATTCTATAACAGACATCTGGACGTACCAAGCTGAATTGCTGGTAGCA
+    ATGGAAAATCAGCATACAATTGACATGGCTGATTCAGAAATGCTGAATCTATATGAGAGGGTGAGGAAGC
+    AACTAAGGCAAAATGCAGAAGAAGATGGGAAAGGGTGCTTTGAAATATATCACAAATGCGATAACAATTG
+    TATGGAAAGCATCAGAAACAACACCTATGACCATACACAATACAGAGAAGAAGCACTCTTGAACAGACTC
+    AACATTAATCCGGTGAAACTCTCTTCTGGGTACAAAGATGTTATACTGTGGTTTAGCTTCGGGGCGTCAT
+    GCTTTGTACTTTTGGCTGTCATCATGGGGCTTGTTTTCTTCTGCTTGAAAAATGGAAACATGCGATGCAC
+    AATCTGTATTTAGTTAAAAACAC

data/flu/HA/ha_h11_h11n9/CY130070/unreleased/dataset.zip

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data/flu/HA/ha_h11_h11n9/CY130070/unreleased/genome_annotation.gff3

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+Diff line change
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+    ##gff-version 3
+    #!gff-spec-version 1.21
+    #!processor NCBI annotwriter
+    ##sequence-region CY130070.1 1 1735
+    ##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=402474
+    CY130070.1	Genbank	region	1	1735	.	+	.	ID=CY130070.1:1..1735;Dbxref=taxon:402474;Name=4;bio-material=CEIRS#162855#;collection-date=1974;country=USA: Memphis;gbkey=Src;mol_type=viral cRNA;nat-host=duck;segment=4;serotype=H11N9;strain=A/duck/Memphis/546/1974
+    CY130070.1	Genbank	sequence_feature	1	1735	.	+	.	ID=id-CY130070.1:1..1735;Dbxref=IRD:NIGSP_CEIRS_SJC001_WEB_00013.HA;gbkey=misc_feature
+    CY130070.1	Genbank	gene	21	1718	.	+	.	ID=gene-HA;Name=HA;gbkey=Gene;gene=HA;gene_biotype=protein_coding
+    CY130070.1	Genbank	CDS	21	1718	.	+	0	ID=cds-AGB50960.1;Parent=gene-HA;Dbxref=NCBI_GP:AGB50960.1;Name=HA;gbkey=CDS;product=hemagglutinin;protein_id=AGB50960.1
+    CY130070.1	Genbank	signal_peptide_region_of_CDS	21	68	.	+	.	ID=id-AGB50960.1:1..16;Parent=cds-AGB50960.1;gbkey=Prot
+    CY130070.1	Genbank	mature_protein_region_of_CDS	69	1046	.	+	.	ID=id-AGB50960.1:17..342;Parent=cds-AGB50960.1;gbkey=Prot;product=HA1
+    CY130070.1	Genbank	mature_protein_region_of_CDS	1047	1715	.	+	.	ID=id-AGB50960.1:343..565;Parent=cds-AGB50960.1;gbkey=Prot;product=HA2

data/flu/HA/ha_h11_h11n9/CY130070/unreleased/pathogen.json

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+Diff line change
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+    {
+      "alignmentParams": {
+        "minSeedCover": 0.01
+      },
+      "schemaVersion": "3.0.0",
+      "attributes": {
+        "name": "ha_h11_h11n9",
+        "reference name": "Influenza A virus (A/duck/Memphis/546/1974(H11N9)) hemagglutinin (HA) gene, complete cds",
+        "reference accession": "CY130070"
+      },
+      "files": {
+        "reference": "reference.fasta",
+        "pathogenJson": "pathogen.json",
+        "genomeAnnotation": "genome_annotation.gff3"
+      }
+    }

data/flu/HA/ha_h11_h11n9/CY130070/unreleased/reference.fasta

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+    >CY130070.1 Influenza A virus (A/duck/Memphis/546/1974(H11N9)) hemagglutinin (HA) gene, complete cds
+    GGAAATATCTAGAAATCAAAATGAAGAAAGTACTGCTTTTTGCAGCAATCATCATCTGTATTCGAGCAGA
+    CGAAATCTGCATTGGATACCTGAGCAACAACTCAACAGAGAAAGTGGACACAATAATTGAGAGTAATGTC
+    ACGGTTACTAGCTCGGTTGAACTGGTTGAAAATGAGTACACTGGATCATTCTGCTCAATCGATGGGAAAG
+    CACCAATAAGTCTTGGTGATTGCTCCTTTGCTGGGTGGATTCTTGGGAACCCAATGTGTGATGATTTGAT
+    TGGGAAAACATCATGGTCTTACATAGTAGAGAAACCGAATCCCATTAATGGCATATGCTACCCTGGTACT
+    CTAGAGAATGAAGAGGAATTGAGACTGAAGTTTAGTGGGGTCCTCGAATTCAACAAATTTGAAGCCTTCA
+    CTTCAAACGGATGGGGATCAGTGAATTCTGGTGCTGGTGTGACCGCAGCCTGCAAATTTGGAAGCAGTAA
+    CTCTTTTTTCAGAAACATGGTATGGTTGATACACCAATCAGGGACATATCCTGTGATACGGAGGACATTC
+    AACAACACCAAAGGGAGAGATGTATTAATGGTATGGGGAGTTCACCATCCTGCAACTCTAAAAGAACACC
+    AAGACTTGTACAAAAAGGACAACTCCTATGTAGCAGTGGGTTCAGAGAGTTATAACAGGAGGTTCACCCC
+    TGAGATCAGCACAAGGCCTAAAGTAAATGGTCAGGCTGGAAGAATGACCTTCTACTGGACCATAGTGAAG
+    CCTGAAGAGGCAATAACATTTGAGTCAAATGGTGCATTTCTCGCTCCTCGGTACGCTTTTGAGTTGGTGT
+    CCTTAGGGAATGGAAAATTGTTCAGAAGTGACTTAAATATTGAATCTTGCTCAACTAAATGCCAGTCTGA
+    AATTGGATGGATCAACACTAATAGAAGCTTCCACAGTGTCCATAGAAACACAATAGGAGACTGCCCCAAA
+    TATGTGAATGTTAAATCTTTAAAGCTTGCTACCGGACTCAGAAATGTCCCTGCGATTGCTGCAAGAGGCC
+    TGTTTGGTGCAATAGCTGGTTTCATAGAAGGTGGTTGGCCAGGTTTAATCAATGGTTGGTATGGATTCCA
+    ACATAGGAATGAAGAAGGTACAGGGATTGCTGCAGACAAAGAATCAACCCAGACAGCAATAGACCAGATA
+    ACCTCTAAAGTCAATAACATCGTTGATCGGATGAACACAAACTTTGAGTCTGTTCAACATGAATTCAGTG
+    AAATTGAAGAGAGAATAAATCAACTGTCAAAGCATGTGGATGATTCTGTTATTGACATATGGTCATACAA
+    TGCACAGCTCCTTGTTCTATTGGAAAATGAAAAGACACTAGATCTCCATGACTCTAATGTTCGAAACCTC
+    CATGAAAAAGTCAGACGAATGCTGAAGGATAATGCTAAAGATGAAGGGAATGGCTGTTTTACTTTCTATC
+    ACAAGTGTGATAACGAGTGCATTGAAAAAGTTAGGAATGGAACATATGACCACAAGGAATTTGAGGAGGA
+    GTCCAGACTAAACAGACAAGAAATTGAAGGAGTGAAACTGGATTCCAGTGGCAACGTCTACAAAATACTA
+    TCAATTTACAGCTGCATTGCAAGCAGTCTTGTGTTAGCAGCAATCATTATGGGGTTCATCTTTTGGGCGT
+    GTAGCAATGGATCATGTAGATGTACCATTTGCATTTAGAATTGCAGTAAAAACAC

data/flu/HA/ha_h12_h12n5/CY130078/unreleased/dataset.zip

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data/flu/HA/ha_h12_h12n5/CY130078/unreleased/genome_annotation.gff3

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+    ##gff-version 3
+    #!gff-spec-version 1.21
+    #!processor NCBI annotwriter
+    ##sequence-region CY130078.1 1 1712
+    ##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=385582
+    CY130078.1	Genbank	region	1	1712	.	+	.	ID=CY130078.1:1..1712;Dbxref=taxon:385582;Name=4;bio-material=CEIRS#14739#;collection-date=1976;country=Canada: Alberta;gbkey=Src;mol_type=viral cRNA;nat-host=duck;segment=4;serotype=H12N5;strain=A/duck/Alberta/60/1976
+    CY130078.1	Genbank	sequence_feature	1	1712	.	+	.	ID=id-CY130078.1:1..1712;Dbxref=IRD:NIGSP_CEIRS_SJC001_WEB_00014.HA;gbkey=misc_feature
+    CY130078.1	Genbank	gene	8	1702	.	+	.	ID=gene-HA;Name=HA;gbkey=Gene;gene=HA;gene_biotype=protein_coding
+    CY130078.1	Genbank	CDS	8	1702	.	+	0	ID=cds-AGB50971.1;Parent=gene-HA;Dbxref=NCBI_GP:AGB50971.1;Name=HA;gbkey=CDS;product=hemagglutinin;protein_id=AGB50971.1
+    CY130078.1	Genbank	signal_peptide_region_of_CDS	8	58	.	+	.	ID=id-AGB50971.1:1..17;Parent=cds-AGB50971.1;gbkey=Prot
+    CY130078.1	Genbank	mature_protein_region_of_CDS	59	1033	.	+	.	ID=id-AGB50971.1:18..342;Parent=cds-AGB50971.1;gbkey=Prot;product=HA1
+    CY130078.1	Genbank	mature_protein_region_of_CDS	1034	1699	.	+	.	ID=id-AGB50971.1:343..564;Parent=cds-AGB50971.1;gbkey=Prot;product=HA2

data/flu/HA/ha_h12_h12n5/CY130078/unreleased/pathogen.json

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+Diff line change
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+    {
+      "alignmentParams": {
+        "minSeedCover": 0.01
+      },
+      "schemaVersion": "3.0.0",
+      "attributes": {
+        "name": "ha_h12_h12n5",
+        "reference name": "Influenza A virus (A/duck/Alberta/60/1976(H12N5)) hemagglutinin (HA) gene, complete cds",
+        "reference accession": "CY130078"
+      },
+      "files": {
+        "reference": "reference.fasta",
+        "pathogenJson": "pathogen.json",
+        "genomeAnnotation": "genome_annotation.gff3"
+      }
+    }

data/flu/HA/ha_h12_h12n5/CY130078/unreleased/reference.fasta

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+Diff line change
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+    >CY130078.1 Influenza A virus (A/duck/Alberta/60/1976(H12N5)) hemagglutinin (HA) gene, complete cds
+    GGTCACAATGGAAAAATTCATCATTTTGAGTACTGTCTTGGCAGCAAGCTTTGCATATGACAAAATTTGC
+    ATTGGATACCAAACAAACAACTCGACTGAAACGGTAAACACACTAAGTGAACAAAACGTTCCGGTGACGC
+    AGGTGGAAGAACTTGTACATGGTGGGATTGATCCGATCCTGTGTGGAACGGAACTAGGATCACCACTAGT
+    GCTTGATGACTGTTCATTAGAGGGTCTAATCCTAGGCAATCCCAAATGTGATCTTTATTTGAATGGCAGG
+    GAATGGTCATACATAGTAGAGAGGCCCAAAGAGATGGAAGGAGTTTGCTATCCAGGGTCAATTGAAAACC
+    AGGAAGAGCTAAGATCTCTGTTTTCTTCCATCAAAAAATATGAAAGAGTGAAGATGTTTGATTTCACCAA
+    ATGGAATGTCACATACACTGGGACCAGCAAGGCCTGCAATAATACATCAAACCAAGGCTCATTCTATAGG
+    AGCATGAGATGGTTGACCTTAAAATCAGGACAATTTCCAGTCCAAACAGATGAGTACAAGAACACCAGAG
+    ATTCAGACATTGTATTCACCTGGGCCATTCACCACCCACCAACATCTGATGAACAAGTAAAATTATACAA
+    AAATCCTGATACTCTCTCTTCAGTCACCACCGATGAAATCAATAGGAGCTTCAAGCCTAATATAGGGCCA
+    AGACCACTCGTGAGAGGACAACAAGGGAGAATGGATTACTACTGGGCTGTTCTTAAACCTGGACAAACAG
+    TCAAAATACAAACCAATGGTAATCTTATTGCACCTGAATATGGTCACTTAATCACAGGGAAATCACATGG
+    CAGGATACTCAAGAATAATTTGCCCATGGGACAGTGTGTGACTGAATGTCAATTGAACGAGGGTGTAATG
+    AACACAAGCAAACCTTTCCAGAACACTAGTAAGCACTATATTGGGAAATGCCCCAAATACATACCATCAG
+    GGAGTTTAAAATTGGCAATAGGGCTCAGGAATGTCCCACAAGTTCAAGATCGGGGGCTCTTTGGAGCAAT
+    TGCAGGTTTCATAGAAGGCGGATGGCCAGGGCTAGTGGCTGGTTGGTACGGATTTCAGCATCAAAATGCG
+    GAGGGGACAGGCATAGCTGCAGACAGAGACAGCACCCAAAGGGCAATAGACAATATGCAAAACAAACTCA
+    ACAATGTCATCGACAAAATGAATAAACAATTTGAAGTGGTGAATCATGAGTTTTCAGAAGTGGAAAGCAG
+    AATAAACATGATTAATTCCAAAATTGATGATCAGATAACTGACATATGGGCATACAATGCTGAATTGCTT
+    GTCCTATTGGAAAATCAGAAGACATTAGATGAGCATGACGCTAATGTAAGGAATCTACATGATCGGGTCA
+    GAAGAGTCCTGAGGGAAAATGCAATTGACACAGGAGACGGCTGCTTTGAGATTTTACATAAATGTGACAA
+    CAATTGTATGGACACGATTAGAAACGGGACATACAATCACAAAGAGTATGAGGAAGAAAGCAAAATCGAA
+    CGACAGAAAGTCAATGGTGTGAAACTTGAGGAGAATTCTACATATAAAATTCTGAGCATCTACAGCAGTG
+    TTGCCTCAAGCTTAGTTCTACTGCTCATGATTATTGGGGGTTTCATTTTCGGGTGTCAAAATGGAAATGT
+    TCGTTGTACTTTCTGTATTTAATTAAAAACAC

data/flu/HA/ha_h13_h13n6/CY130086/unreleased/dataset.zip

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data/flu/HA/ha_h13_h13n6/CY130086/unreleased/genome_annotation.gff3

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+Diff line change
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+    ##gff-version 3
+    #!gff-spec-version 1.21
+    #!processor NCBI annotwriter
+    ##sequence-region CY130086.1 1 1743
+    ##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=384499
+    CY130086.1	Genbank	region	1	1743	.	+	.	ID=CY130086.1:1..1743;Dbxref=taxon:384499;Name=4;bio-material=CEIRS#80894#;collection-date=1977;country=USA: Maryland;gbkey=Src;mol_type=viral cRNA;nat-host=gull;segment=4;serotype=H13N6;strain=A/gull/Maryland/704/1977
+    CY130086.1	Genbank	sequence_feature	1	1743	.	+	.	ID=id-CY130086.1:1..1743;Dbxref=IRD:NIGSP_CEIRS_SJC001_WEB_00015.HA;gbkey=misc_feature
+    CY130086.1	Genbank	gene	30	1730	.	+	.	ID=gene-HA;Name=HA;gbkey=Gene;gene=HA;gene_biotype=protein_coding
+    CY130086.1	Genbank	CDS	30	1730	.	+	0	ID=cds-AGB51312.1;Parent=gene-HA;Dbxref=NCBI_GP:AGB51312.1;Name=HA;gbkey=CDS;product=hemagglutinin;protein_id=AGB51312.1
+    CY130086.1	Genbank	signal_peptide_region_of_CDS	30	83	.	+	.	ID=id-AGB51312.1:1..18;Parent=cds-AGB51312.1;gbkey=Prot
+    CY130086.1	Genbank	mature_protein_region_of_CDS	84	1058	.	+	.	ID=id-AGB51312.1:19..343;Parent=cds-AGB51312.1;gbkey=Prot;product=HA1
+    CY130086.1	Genbank	mature_protein_region_of_CDS	1059	1727	.	+	.	ID=id-AGB51312.1:344..566;Parent=cds-AGB51312.1;gbkey=Prot;product=HA2

data/flu/HA/ha_h13_h13n6/CY130086/unreleased/pathogen.json

-Original file line number
+Diff line change
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+    {
+      "alignmentParams": {
+        "minSeedCover": 0.01
+      },
+      "schemaVersion": "3.0.0",
+      "attributes": {
+        "name": "ha_h13_h13n6",
+        "reference name": "Influenza A virus (A/gull/Maryland/704/1977(H13N6)) hemagglutinin (HA) gene, complete cds",
+        "reference accession": "CY130086"
+      },
+      "files": {
+        "reference": "reference.fasta",
+        "pathogenJson": "pathogen.json",
+        "genomeAnnotation": "genome_annotation.gff3"
+      }
+    }

data/flu/HA/ha_h13_h13n6/CY130086/unreleased/reference.fasta

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+Diff line change
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+    >CY130086.1 Influenza A virus (A/gull/Maryland/704/1977(H13N6)) hemagglutinin (HA) gene, complete cds
+    GGAAATCTTAACAATCAGAAACAAACAAGATGGCTCTAAATGTCATTGCAACTTTGACACTTATAAGTGT
+    ATGTGTACATGCAGACAGAATATGCGTGGGGTATCTGAGCACCAATTCATCAGAAAGGGTCGACACGCTC
+    CTTGAAAATGGGGTCCCAGTCACCAGCTCCATTGATCTGATTGAGACAAACCACACAGGAACATACTGTT
+    CTCTAAATGGAGTCAGTCCAGTGCATTTGGGAGATTGCAGCTTTGAAGGATGGATTGTAGGAAACCCAGC
+    CTGCACCAGCAACTTTGGGATCAGAGAGTGGTCATACCTGATTGAGGACCCCGCGGCCCCTCATGGGCTT
+    TGCTACCCTGGAGAATTAAACAACAATGGTGAACTCAGACACTTGTTCAGTGGAATCAGGTCATTCAGTA
+    GAACGGAATTGATCCCACCTACCTCCTGGGGGGAAGTACTTGACGGTACAACATCTGCTTGCAGAGATAA
+    CACGGGAACCAACAGCTTCTATCGAAATTTAGTTTGGTTTATAAAGAAGAATAATAGATATCCAGTTATC
+    AGTAAGACCTACAACAATACAACGGGAAGGGATGTTTTAGTTTTATGGGGAATACATCACCCAGTGTCTG
+    TGGATGAGACAAAGACTCTGTATGTCAATAGTGATCCATACACACTGGTTTCCACCAAGTCTTGGAGCGA
+    GAAATATAAACTAGAAACGGGAGTCCGACCTGGCTATAATGGACAGAGGAGCTGGATGAAAATTTATTGG
+    TCTTTGATACATCCAGGGGAGATGATTACTTTCGAGAGTAATGGTGGATTTTTAGCCCCAAGATATGGGT
+    ACATAATTGAAGAATATGGAAAAGGAAGGATTTTCCAGAGTCGCATCAGAATGTCTAGGTGCAACACCAA
+    GTGCCAGACTTCGGTTGGAGGGATAAACACAAACAGAACGTTCCAAAACATCGATAAGAATGCTCTTGGT
+    GACTGTCCCAAATACATAAAGTCTGGCCAACTCAAGCTAGCCACTGGACTCAGAAATGTGCCAGCTATAT
+    CGAATAGAGGATTGTTCGGAGCAATTGCAGGGTTCATAGAAGGAGGCTGGCCAGGTTTAATCAATGGTTG
+    GTACGGTTTTCAGCATCAAAATGAACAGGGAACAGGAATAGCTGCAGACAAAGAATCAACACAGAAAGCT
+    ATAGACCAGATAACAACCAAAATAAATAACATTATTGATAAAATGAATGGGAACTATGATTCAATTAGGG
+    GTGAATTCAATCAAGTTGAGAAGCGTATAAACATGCTTGCAGACAGAATAGATGATGCCGTGACGGACAT
+    TTGGTCATACAATGCCAAACTTCTTGTATTGCTGGAAAATGATAAAACTTTAGATATGCATGATGCTAAT
+    GTAAAGAATTTACATGAGCAAGTACGAAGAGAATTGAAGGACAATGCAATTGACGAAGGAAATGGCTGTT
+    TTGAACTCCTTCATAAATGCAATGACTCCTGCATGGAAACTATAAGAAATGGAACGTATGACCACACTGA
+    GTATGCAGAGGAGTCAAAGTTAAAGAGGCAAGAAATCGATGGGATCAAACTCAAATCAGAAGACAACGTT
+    TACAAAGCATTATCAATATACAGTTGCATTGCAAGTAGTGTTGTACTAGTAGGACTCATACTCTCTTTCA
+    TCATGTGGGCCTGTAGTAGTGGGAATTGCCGATTCAATGTTTGTATATAAGTAGAAAAAACAC

data/flu/HA/ha_h14_h14n5/JN696314/unreleased/dataset.zip

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data/flu/HA/ha_h14_h14n5/JN696314/unreleased/genome_annotation.gff3

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+Diff line change
@@ -0,0 +1,8 @@
+    ##gff-version 3
+    #!gff-spec-version 1.21
+    #!processor NCBI annotwriter
+    ##sequence-region JN696314.2 1 1749
+    ##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1088701
+    JN696314.2	Genbank	region	1	1749	.	+	.	ID=JN696314.2:1..1749;Dbxref=taxon:1088701;Name=4;collected-by=Chad Courtney;collection-date=16-Nov-2010;country=USA;gbkey=Src;genome=genomic;mol_type=viral cRNA;nat-host=Clangula hyemalis (long-tailed duck);segment=4;serotype=H14N6;strain=A/long-tailed duck/Wisconsin/10OS3912/2010
+    JN696314.2	Genbank	gene	18	1724	.	+	.	ID=gene-HA;Name=HA;gbkey=Gene;gene=HA;gene_biotype=protein_coding
+    JN696314.2	Genbank	CDS	18	1724	.	+	0	ID=cds-AEP68847.2;Parent=gene-HA;Dbxref=NCBI_GP:AEP68847.2;Name=HA;gbkey=CDS;product=hemagglutinin;protein_id=AEP68847.2

data/flu/HA/ha_h14_h14n5/JN696314/unreleased/pathogen.json

-Original file line number
+Diff line change
@@ -0,0 +1,16 @@
+    {
+      "alignmentParams": {
+        "minSeedCover": 0.01
+      },
+      "schemaVersion": "3.0.0",
+      "attributes": {
+        "name": "ha_h14_h14n5",
+        "reference name": "Influenza A virus (A/long-tailed duck/Wisconsin/10OS3912/2010(H14N6)) segment 4 hemagglutinin (HA) gene, complete cds",
+        "reference accession": "JN696314"
+      },
+      "files": {
+        "reference": "reference.fasta",
+        "pathogenJson": "pathogen.json",
+        "genomeAnnotation": "genome_annotation.gff3"
+      }
+    }

data/flu/HA/ha_h14_h14n5/JN696314/unreleased/reference.fasta

-Original file line number
+Diff line change
@@ -0,0 +1,27 @@
+    >JN696314.2 Influenza A virus (A/long-tailed duck/Wisconsin/10OS3912/2010(H14N6)) segment 4 hemagglutinin (HA) gene, complete cds
+    AGCAAAAGCAGGGGAAAATGATTGCATTCATAGTGATTGCACTGGCTCTGAGCCACACTACTTACTCCCA
+    GATCACAAATGGAAACACAGGAAACCCTGTTATATGCTTGGGTCACCATGCAGTGGAGAATGGCACATCT
+    GTTAAAACATTAACAGACAATCATATAGAGGTTGTGTCGGCTAAAGAATTAGTTGAGACAAACCACATTA
+    ATGAACTATGCCCAAGTCCTCTGAAGCTTGTCGATGGACAAGACTGCGACCTTATCAACGGTGCATTGGG
+    AAGCCCAGGCTGTGACCACTTACAAGACACTACTTGGGATGTTTTCATTGAAAGGCCAACGGCAATGGAC
+    ACGTGCTATCCATTCGATGTTCCAGATTACCAGAGCCTTAGAAGCATCTTGGCAAGCAGTGGGAGTCTGG
+    AATTCATTGCCGAACAATTCACTTGGAATGGTGTCACAGTTGACGGATCAAGCAGTGCTTGTTTGAGGGG
+    CGGCCGCAATGGCTTCTTCACCCGACTGAACTGGCTAACCAGAGTAAAAAACGGGAACTATGGGCCTATT
+    AATGTCACAAAAGAAAATACAGGGTCTTACGTCAGGCTCTATCTCTGGGGAGTGCACCATCCATCAAGTG
+    ATACTGAGCAAACGGATCTTTACAAAGTTGCAACGGGAAGAGTAACGGTGTCTACTCGCTCAGATCAAAT
+    CAGCATTATTCCCAATATAGGAAGTAGACCAAGGGTGAGGAATCAGAGCGGCAGAATAAGCATCTACTGG
+    ACTCTAGTAAACCCAGGGGATTCCATCATCTTTAACAGCATTGGAAACCTAATTGCACCAAGAGGCCACT
+    ACAAAATAAATAAATCTACAAAGGGCACTGTGCTTAAAAGTGACAAGAAGATTGGATCATGCACAAGCCC
+    TTGTTTAACCGATAAAGGTTCAATCCAAAGTGACAAACCTTTTCAGAATGTGTCCAGAATCGCTATAGGA
+    AACTGCCCGAAGTATGTGAAGCAAGGCTCACTGATGTTGGCAACTGGAATGCGTAACATCCCTGACAAGC
+    AGACGAAGGGCTTATTTGGAGCAATTGCTGGATTCATTGAAAATGGTTGGCAAGGCCTGATTGATGGGTG
+    GTATGGATTCAGGCACCAAAATGCTGAGGGAACAGGAACTGCTGCGGATTTGAAATCAACCCAGGCAGCC
+    ATTGACCAAATAAATGGCAAACTAAACAGATTGATAGAGAAGACAAATGAAAAATATCACCAAATCGAAA
+    AAGAATTCGAGCAAGTGGAAGGAAGAATACAGGACCTTGAGAAATACGTTGAGGACACTAAAATTGATCT
+    GTGGTCATACAATGCTGAGCTATTGGTGGCCCTAGAAAATCAGCACACAATAGATGTTACAGACTCCGAG
+    ATGAACAAACTCTTTGAGAGGGTGAGAAGACAACTTAGGGAAAATGCGGAAGATCAAGGCAACGGATGTT
+    TCGAGATATTCCATCAGTGTGACAACAACTGTATAGAAAGTATCAGAAATGGAACCTATGATCACAACAT
+    CTACAGGGATGAAGCCATTAACAATCGGATTAAAATAAATCCCGTCAATTTGACGATGGGTTACAAGGAC
+    ATAATACTGTGGATTTCTTTCTCCATGTCATGCTTTGTCTTTGTGGCACTGATTTTGGGATTTGTTCTTT
+    GGGCTTGTAAGAACGGAAATATCCGATGCCAAATTTGTATATAAAGAAAAAAACACCCTTGTTTCTACT

data/flu/HA/ha_h15_h15n9/CY006010/unreleased/dataset.zip

Binary file not shown.

data/flu/HA/ha_h15_h15n9/CY006010/unreleased/genome_annotation.gff3

-Original file line number
+Diff line change
@@ -0,0 +1,13 @@
+    ##gff-version 3
+    #!gff-spec-version 1.21
+    #!processor NCBI annotwriter
+    ##sequence-region CY006010.1 1 1763
+    ##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=352560
+    CY006010.1	Genbank	region	1	1763	.	+	.	ID=CY006010.1:1..1763;Dbxref=taxon:352560;Name=4;collection-date=1979;country=Australia: Western Australia;gbkey=Src;mol_type=viral cRNA;nat-host=Avian;segment=4;serotype=H15N9;strain=A/wedge-tailed shearwater/Western Australia/2576/1979
+    CY006010.1	Genbank	primer_binding_site	1	19	.	+	.	ID=id-CY006010.1:1..19;Note=PCR amplification primer sequence;gbkey=primer_bind
+    CY006010.1	Genbank	gene	22	1734	.	+	.	ID=gene-HA;Name=HA;gbkey=Gene;gene=HA;gene_biotype=protein_coding
+    CY006010.1	Genbank	CDS	22	1734	.	+	0	ID=cds-ABB88138.1;Parent=gene-HA;Dbxref=NCBI_GP:ABB88138.1;Name=HA;gbkey=CDS;product=hemagglutinin;protein_id=ABB88138.1
+    CY006010.1	Genbank	signal_peptide_region_of_CDS	22	75	.	+	.	ID=id-ABB88138.1:1..18;Parent=cds-ABB88138.1;gbkey=Prot
+    CY006010.1	Genbank	mature_protein_region_of_CDS	76	1068	.	+	.	ID=id-ABB88138.1:19..349;Parent=cds-ABB88138.1;gbkey=Prot;product=HA1
+    CY006010.1	Genbank	mature_protein_region_of_CDS	1069	1731	.	+	.	ID=id-ABB88138.1:350..570;Parent=cds-ABB88138.1;gbkey=Prot;product=HA2
+    CY006010.1	Genbank	primer_binding_site	1744	1763	.	-	.	ID=id-CY006010.1:1744..1763;Note=PCR amplification primer sequence;gbkey=primer_bind

data/flu/HA/ha_h15_h15n9/CY006010/unreleased/pathogen.json

-Original file line number
+Diff line change
@@ -0,0 +1,16 @@
+    {
+      "alignmentParams": {
+        "minSeedCover": 0.01
+      },
+      "schemaVersion": "3.0.0",
+      "attributes": {
+        "name": "ha_h15_h15n9",
+        "reference name": "Influenza A virus (A/wedge-tailed shearwater/Western Australia/2576/1979(H15N9)) segment 4, complete sequence",
+        "reference accession": "CY006010"
+      },
+      "files": {
+        "reference": "reference.fasta",
+        "pathogenJson": "pathogen.json",
+        "genomeAnnotation": "genome_annotation.gff3"
+      }
+    }

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