From 4ab368065fa846b070ac6982e324b6ae20869748 Mon Sep 17 00:00:00 2001 From: anna-parker <50943381+anna-parker@users.noreply.github.com> Date: Mon, 26 Jan 2026 15:02:44 +0100 Subject: [PATCH 1/5] feat: add simple nextclade datasets for all HA and NAs and code to generate the datasets --- .../CY136094/unreleased/dataset.zip | Bin 0 -> 2038 bytes .../unreleased/genome_annotation.gff3 | 13 +++ .../CY136094/unreleased/pathogen.json | 16 +++ .../CY136094/unreleased/reference.fasta | 27 +++++ .../CY130070/unreleased/dataset.zip | Bin 0 -> 1932 bytes .../unreleased/genome_annotation.gff3 | 13 +++ .../CY130070/unreleased/pathogen.json | 16 +++ .../CY130070/unreleased/reference.fasta | 27 +++++ .../CY130078/unreleased/dataset.zip | Bin 0 -> 1929 bytes .../unreleased/genome_annotation.gff3 | 13 +++ .../CY130078/unreleased/pathogen.json | 16 +++ .../CY130078/unreleased/reference.fasta | 27 +++++ .../CY130086/unreleased/dataset.zip | Bin 0 -> 1944 bytes .../unreleased/genome_annotation.gff3 | 13 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ID=id-AGB50960.1:343..565;Parent=cds-AGB50960.1;gbkey=Prot;product=HA2 + diff --git a/data/flu/HA/ha_h11_h11n9/CY130070/unreleased/pathogen.json b/data/flu/HA/ha_h11_h11n9/CY130070/unreleased/pathogen.json new file mode 100644 index 0000000..3c705e3 --- /dev/null +++ b/data/flu/HA/ha_h11_h11n9/CY130070/unreleased/pathogen.json @@ -0,0 +1,16 @@ +{ + "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" + } +} diff --git a/data/flu/HA/ha_h11_h11n9/CY130070/unreleased/reference.fasta b/data/flu/HA/ha_h11_h11n9/CY130070/unreleased/reference.fasta new file mode 100644 index 0000000..ca13c8b --- /dev/null +++ b/data/flu/HA/ha_h11_h11n9/CY130070/unreleased/reference.fasta @@ -0,0 +1,27 @@ +>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 + diff --git a/data/flu/HA/ha_h12_h12n5/CY130078/unreleased/dataset.zip b/data/flu/HA/ha_h12_h12n5/CY130078/unreleased/dataset.zip new file mode 100644 index 0000000000000000000000000000000000000000..444906b3c399b6328c2f5d152204bd30e383c473 GIT binary patch literal 1929 zcmZ`)c{Cg77Ec7x)-Fh?t;Aki`ihd47{*#*FidPIv9)3sraZL`Q%Z$aRVYP8h}fpY zQfrCYN@`!*OsJujQVhk*%sc13H}ht`?|kQ;@1A?_AHVba-5<&d#0dca06c(b{8iU{ zdwewr2mp}TkB^-V#)SI?`C@Sz0bxNntgXSVZY{xuW3?nD$pjhg=!X1$LZossviO@O zx)PcaewIKimOE{$6UjG9k$l-Vk6(n{ROg1F$IMTp)cwS-*IN}O7Qtd=uNZ`xNlsl< zdoAlK-c4Xi1sr^}R$46E>nOGx^|s@VT4q~c3Yt>_j0UGvyYibAv9S9^i8?MsNr`d$nZ@uaSRY``s@hC%+02p`tOz}X*n&E-Gveuz zvGyObwtJ5SIEP1VL?b=0j*$F7!$ycb;?d)M?tNYz;Ba^N5$8*|+~N3q#tpqA>C_e# z&yre29qBKK<6bFG#d@dIfG@CSvpCd$(28QC_1L@OTQd#-fWZj>h_TUP0~HjA^}yh8 zLE)Hi{~(-(ua6J>Az?NnUrX=@YX3K=5Eo4FU7{d4)EUc2Q=V}ke~;DIlAA~Krj z+4~6-Hg#o|jN~zt9@#&I@3n@ueD*L>Rcw-sXtj-`>^<;EfJW5*xLHOwR*{=$h1UhE ztRQ7z3|WK1@}(7E6#vVlvBJEQ4m;=`n5SiVm03NcZF*iAU;f$se!^0e;l;ur=zGWe zdb7p$t(=P=Dwm#J;}TKHI9ob2wkyhl9d+GPmr&?0nx#F$FL&tXTsOEh)tOPIPyhAy z!YlO_pA0Qzq-H^&JM1<*(4yppXLIR4yhEBXUDS%&9>0e+GGey31p1EsK9tc&s`Q_X z50WkDTQ!UDPSE7192=E#E-4x_0A$Z-m^18FK@S*GOig$F1*XqsH-zq#v-DUFM+U{= zP8U9{I2gNtCb@BQ_Z0Vq@VOS`hSGFjX2)}`pt3}FsPk?cKhf9dh0$l@E}1sZaqW8-l>!Q_oTA&0}iKYzI+{8Su|9lD7kkg7fiMnRdg^`gbR+Abii26n1%$n75 z<*3cgl3#r0$?&8!y^_8`V_yT3zl#%iNRPSdQbx<0WZ-?fEpMpRrL_5QJ=m)gu7y$3 zytiVJvj@rZbZ02cz0RRCu^Fpyc*ibCa3#;LS2@A)V zIwCSf?0DA~sZ%;xf)++|#);mvtx*)Mn3o0<&qBX(Lv~X8;LOyR+Y1|aUi2|*cc$Av zE(A61%Pej@*Br>)iEuyJP|80cx>r*fudifIc8}aIXdltcJzmDOOvg62qY>*1vBx#; 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ID=id-AGB51312.1:344..566;Parent=cds-AGB51312.1;gbkey=Prot;product=HA2 + diff --git a/data/flu/HA/ha_h13_h13n6/CY130086/unreleased/pathogen.json b/data/flu/HA/ha_h13_h13n6/CY130086/unreleased/pathogen.json new file mode 100644 index 0000000..ebcc669 --- /dev/null +++ b/data/flu/HA/ha_h13_h13n6/CY130086/unreleased/pathogen.json @@ -0,0 +1,16 @@ +{ + "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" + } +} diff --git a/data/flu/HA/ha_h13_h13n6/CY130086/unreleased/reference.fasta b/data/flu/HA/ha_h13_h13n6/CY130086/unreleased/reference.fasta new file mode 100644 index 0000000..1726319 --- /dev/null +++ b/data/flu/HA/ha_h13_h13n6/CY130086/unreleased/reference.fasta @@ -0,0 +1,27 @@ +>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 + diff --git a/data/flu/HA/ha_h14_h14n5/JN696314/unreleased/dataset.zip b/data/flu/HA/ha_h14_h14n5/JN696314/unreleased/dataset.zip new file mode 100644 index 0000000000000000000000000000000000000000..82080dd2dbff65da895b766d7443795f05b3e75a GIT binary patch literal 1882 zcmZ`)c{JN=8vdcgmc|-eEVqrNmY@`EEp0=mYDw%%wWN_CLlVT!pn|kotr}~K3bmx@ z(7LsxMb(m0E~(a96jjSe#qGsaF}ZinnVH*j=ljlg-t)cZecwNx^E}Usb`Uxw2LOO5 zkPvgq4}2A>tsnpZ{rm^!XUP~!FewN}L=YlLL>$_R^wLObW>>!2QDX$IbxdZ4j`(}3 z=Q+Y(C{c*)sl}V2ndP*DE1(P1S99}8(=!RyPQa1SryujjlOOcFvoj=%Q>1*~oThWf zU@Q@{TW-?SEv9-zQx(*Pbt=q)<^ly-wFQ5EJ~mrY-G2F|!Pg&^x10O-`i2!^e$w{{ zysp_b7r($*p&dwxTM(vB7DDZ@-d1sM!FlLtuKDh$vvPE?Y|aZ#Q=T_G%e|7_-2ZG~ zLK0T{0=oE9kOyOhiGO2sS-}MT$`lkbiA0v3$=@(Oe9@k$(=vhZ8gN`3*#UXbBD})y zugx5#=~2`&XFxwUi&dL%v{5=YQK)H0fqVJl_=S<#2LD#8?7%vPZhK(SeeDDEe-Mo4 zBbc96fSu-}CnW>`P(Ffu@JL}ee+-dGqF^W?BqAaRk2eW(9mt+ElDnMwnA}t4k(Y^l zrPrh@!YEofV)xLapg$auZFkjeN`SlFj8Uu_)31B9XSu94JAa20Jum%K`XYTKV5e*E z6R>`QRw38Eb5>8JSLfD^rEU|tt8T*R%WGuh}Snc+2QBwgL_@kO#Zhtd8^Ch$+uB>K9fj zT?%|q7J9v{jm6^j(9Hv@O%kT??)iR2?OF2*C1>pLj+L+~O7zQHu|j-|K$2;qub*&y zTm5o;CnpAcvfZF3?@qg{#5rOSgSyC>*Y~=Y93TVf)|ExPXy{{ym|Y)DbZYkhS%k;M z@wh+UUfaF*Qlj3Rmsgq=i(3{wsi|LE(s19rMBcUk+j+L?*z*LV9f?2k;bZzoq!^zI z;UEBj@c9sd!{Z`wL@W-0$3#*vb{NTT_=|8R%%LKN&5!vg$_f&cErR(jcp!IAgUaXw`QYR?lE zgEroHG;Bc%mYbHereB2|>LTrbvCNs`mQ-(H`mFoJ%S{w-2PF3r$6qh(45^CRD~iE| z@F|I>Q-CKJ6(XTR+Uo;h4oE4|oHOSnL}R! 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ID=id-CY006010.1:1744..1763;Note=PCR amplification primer sequence;gbkey=primer_bind + diff --git a/data/flu/HA/ha_h15_h15n9/CY006010/unreleased/pathogen.json b/data/flu/HA/ha_h15_h15n9/CY006010/unreleased/pathogen.json new file mode 100644 index 0000000..bd92a5f --- /dev/null +++ b/data/flu/HA/ha_h15_h15n9/CY006010/unreleased/pathogen.json @@ -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" + } +} diff --git a/data/flu/HA/ha_h15_h15n9/CY006010/unreleased/reference.fasta b/data/flu/HA/ha_h15_h15n9/CY006010/unreleased/reference.fasta new file mode 100644 index 0000000..71d64ac --- /dev/null +++ b/data/flu/HA/ha_h15_h15n9/CY006010/unreleased/reference.fasta @@ -0,0 +1,28 @@ +>CY006010.1 Influenza A virus (A/wedge-tailed shearwater/Western Australia/2576/1979(H15N9)) segment 4, complete sequence +AGCAAAAGCAGGGGAAACAAAATGAACACTCAAATCATTGTCATTCTAGTCCTCGGACTGTCAATGGTGA +AATCTGACAAGATTTGTCTCGGGCACCATGCCGTAGCAAATGGGACAAAAGTCAACACACTAACTGAGAG +AGGAGTGGAAGTGGTCAATGCCACGGAGACAGTGGAGATTACCGGAATAGATAAAGTGTGCACAAAAGGG +AAGAAAGCAGTGGACCTGGGGTCTTGTGGAATACTGGGAACTATCATTGGGCCTCCACAATGTGATCTTC +ATCTTGAATTCAAAGCTGATCTGATAATAGAAAGAAGAAATTCAAGTGACATCTGTTACCCAGGAAGATT +CACTAATGAGGAAGCACTGAGACAAATAATCAGAGAATCTGGAGGAATTGACAAAGAGTCAATGGGCTTT +AGATATTCAGGAATAAGAACAGACGGGGCAACCAGTGCGTGTAAGAGAACAGTGTCCTCTTTCTACTCAG +AAATGAAATGGCTTTCATCCAGCATGAATAACCAGGTGTTCCCACAACTGAATCAGACATACAGGAACAC +CAGAAAAGAACCAGCCCTAATTGTCTGGGGAGTACATCATTCAAGTTCCTTGGATGAGCAAAATAAGCTA +TATGGAACTGGGAACAAGCTGATAACAGTAGGAAGCTCAAAGTACCAACAATCGTTTTCACCAAGTCCAG +GGGCCAGGCCCAAAGTGAATGGTCAGGCCGGGAGGATCGACTTTCATTGGATGCTATTGGACCCAGGGGA 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ID=CY125945.1:1..1771;Dbxref=taxon:1395524;Name=4;collection-date=2010;country=Peru: Truenococha;gbkey=Src;isolation-source=rectal swab;mol_type=viral cRNA;nat-host=Artibeus planirostris%3B gender M;note=Complete sequence%2C ends confirmed by RACE-PCR.;segment=4;serotype=H18N11;strain=A/flat-faced bat/Peru/033/2010 +CY125945.1 Genbank gene 29 1714 . + . ID=gene-HA;Name=HA;gbkey=Gene;gene=HA;gene_biotype=protein_coding +CY125945.1 Genbank CDS 29 1714 . + 0 ID=cds-AGX84934.1;Parent=gene-HA;Dbxref=NCBI_GP:AGX84934.1;Name=AGX84934.1;gbkey=CDS;gene=HA;product=hemagglutinin;protein_id=AGX84934.1 +CY125945.1 Genbank signal_peptide_region_of_CDS 29 70 . + . ID=id-AGX84934.1:1..14;Parent=cds-AGX84934.1;gbkey=Prot +CY125945.1 Genbank mature_protein_region_of_CDS 71 1045 . + . ID=id-AGX84934.1:15..339;Parent=cds-AGX84934.1;gbkey=Prot;product=HA1 +CY125945.1 Genbank mature_protein_region_of_CDS 1046 1711 . + . ID=id-AGX84934.1:340..561;Parent=cds-AGX84934.1;gbkey=Prot;product=HA2 + diff --git a/data/flu/HA/ha_h18_h18n11/CY125945/unreleased/pathogen.json b/data/flu/HA/ha_h18_h18n11/CY125945/unreleased/pathogen.json new file mode 100644 index 0000000..806bdd2 --- /dev/null +++ b/data/flu/HA/ha_h18_h18n11/CY125945/unreleased/pathogen.json @@ -0,0 +1,16 @@ +{ + "alignmentParams": { + "minSeedCover": 0.01 + }, + "schemaVersion": "3.0.0", + "attributes": { + "name": "ha_h18_h18n11", + "reference name": "Influenza A virus (A/flat-faced bat/Peru/033/2010(H18N11)) hemagglutinin (HA) gene, complete cds", + "reference accession": "CY125945" + }, + "files": { + "reference": "reference.fasta", + "pathogenJson": "pathogen.json", + "genomeAnnotation": "genome_annotation.gff3" + } +} diff --git a/data/flu/HA/ha_h18_h18n11/CY125945/unreleased/reference.fasta b/data/flu/HA/ha_h18_h18n11/CY125945/unreleased/reference.fasta new file mode 100644 index 0000000..6ff2547 --- /dev/null +++ b/data/flu/HA/ha_h18_h18n11/CY125945/unreleased/reference.fasta @@ -0,0 +1,28 @@ +>CY125945.1 Influenza A virus (A/flat-faced bat/Peru/033/2010(H18N11)) hemagglutinin (HA) gene, complete cds +AGCAGAAGCAGGGTGATTATTATTCAGAATGATTACAATACTTATCTTGGTACTCCCTATTGTTGTAGGT +GACCAAATATGCATTGGCTATCATTCAAATAATTCAACACAAACAGTGAATACTCTCCTTGAATCAAATG +TACCAGTGACTTCCTCTCACAGCATCCTAGAAAAAGAACACAATGGTTTGCTTTGCAAGCTAAAAGGGAA +AGCACCCTTGGACCTTATTGACTGCTCTCTTCCTGCATGGCTTATGGGAAACCCAAAATGTGACGAACTC +TTAACAGCAAGCGAATGGGCCTACATAAAAGAAGACCCAGAACCTGAAAATGGAATCTGTTTTCCAGGAG +ATTTTGATTCTTTAGAGGATCTGATTTTATTGGTTTCTAACACTGACCATTTCAGAAAAGAGAAAATAAT +AGACATGACCAGATTCTCTGATGTGACTACAAACAACGTAGACAGTGCATGCCCATATGACACAAATGGT +GCTTCCTTTTACAGAAATCTAAACTGGGTGCAGCAAAACAAAGGCAAGCAACTGATTTTTCACTACCAGA +ATTCTGAAAACAACCCACTTTTGATAATTTGGGGAGTACACCAGACATCTAATGCTGCAGAACAAAACAC +ATACTATGGCTCACAGACTGGCTCAACAACCATCACTATTGGGGAAGAAACAAACACTTATCCACTAGTG +ATAAGTGAAAGTTCTATTCTTAACGGTCACTCTGATAGAATAAATTACTTTTGGGGAGTTGTCAATCCTA 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ID=NC_007362.1:1..1760;Dbxref=taxon:93838;Name=4;gbkey=Src;genome=genomic;mol_type=viral cRNA;old-name=Influenza A virus (A/Goose/Guangdong/1/96(H5N1));segment=4;serotype=H5N1;strain=A/goose/Guangdong/1/1996 +NC_007362.1 RefSeq gene 22 1728 . + . ID=gene-FLUAVH5N1_s4gp1;Dbxref=GeneID:3654620;Name=HA;gbkey=Gene;gene=HA;gene_biotype=protein_coding;locus_tag=FLUAVH5N1_s4gp1 +NC_007362.1 RefSeq CDS 22 1728 . + 0 ID=cds-YP_308669.1;Parent=gene-FLUAVH5N1_s4gp1;Dbxref=GenBank:YP_308669.1,GeneID:3654620;Name=YP_308669.1;gbkey=CDS;gene=HA;locus_tag=FLUAVH5N1_s4gp1;product=hemagglutinin;protein_id=YP_308669.1 +NC_007362.1 RefSeq signal_peptide_region_of_CDS 22 69 . + . ID=id-YP_308669.1:1..16;Parent=cds-YP_308669.1;gbkey=Prot +NC_007362.1 RefSeq mature_protein_region_of_CDS 70 1059 . + . ID=id-YP_308669.1:17..346;Parent=cds-YP_308669.1;gbkey=Prot;product=HA1;protein_id=YP_529486.1 +NC_007362.1 RefSeq mature_protein_region_of_CDS 1060 1725 . + . ID=id-YP_308669.1:347..568;Parent=cds-YP_308669.1;gbkey=Prot;product=HA2;protein_id=YP_529487.1 + diff --git a/data/flu/HA/ha_h5_h5n1/NC_007362.1/unreleased/pathogen.json b/data/flu/HA/ha_h5_h5n1/NC_007362.1/unreleased/pathogen.json new file mode 100644 index 0000000..dc42ac8 --- /dev/null +++ b/data/flu/HA/ha_h5_h5n1/NC_007362.1/unreleased/pathogen.json @@ -0,0 +1,16 @@ +{ + "alignmentParams": { + "minSeedCover": 0.01 + }, + "schemaVersion": "3.0.0", + "attributes": { + "name": "ha_h5_h5n1", + "reference name": "Influenza A virus (A/goose/Guangdong/1/1996(H5N1)) hemagglutinin (HA) gene, complete cds", + "reference accession": "NC_007362.1" + }, + "files": { + "reference": "reference.fasta", + "pathogenJson": "pathogen.json", + "genomeAnnotation": "genome_annotation.gff3" + } +} diff --git a/data/flu/HA/ha_h5_h5n1/NC_007362.1/unreleased/reference.fasta b/data/flu/HA/ha_h5_h5n1/NC_007362.1/unreleased/reference.fasta new file mode 100644 index 0000000..344aa03 --- /dev/null +++ b/data/flu/HA/ha_h5_h5n1/NC_007362.1/unreleased/reference.fasta @@ -0,0 +1,28 @@ +>NC_007362.1 Influenza A virus (A/goose/Guangdong/1/1996(H5N1)) hemagglutinin (HA) gene, complete cds +GCAGGGGTATAATCTGTCAAAATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTCAAAAGTG +ATCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACACAATAATGGAAAAGAACGT +TACTGTTACACATGCCCAAGACATACTGGAAAAGACACACAATGGGAAGCTCTGCGATCTAAATGGAGTG +AAGCCTCTCATTTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCTATGTGTGACGAATTCA +TCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAGTCCAGCCAATGACCTCTGTTACCCAGGGGA +TTTCAACGACTATGAAGAACTGAAACACCTATTGAGCAGAACAAACCATTTTGAGAAAATTCAGATCATC +CCCAAAAGTTCTTGGTCCAATCATGATGCCTCATCAGGGGTGAGCTCAGCATGTCCATACCATGGGAGGT +CCTCCTTTTTCAGAAATGTGGTATGGCTTATCAAAAAGAACAGTGCATACCCAACAATAAAGAGGAGCTA +CAATAATACCAACCAAGAAGATCTTTTAGTACTGTGGGGGATTCACCATCCTAATGATGCGGCAGAGCAG +ACAAAGCTCTATCAAAACCCAACCACTTACATTTCCGTTGGAACATCAACACTGAACCAGAGATTGGTTC +CAGAAATAGCTACTAGACCCAAAGTAAACGGGCAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAA 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https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=402473 +CY130030.1 Genbank region 1 1714 . + . ID=CY130030.1:1..1714;Dbxref=taxon:402473;Name=4;bio-material=CEIRS#162849#;collection-date=1965;country=USA: Massachusetts;gbkey=Src;mol_type=viral cRNA;nat-host=turkey;segment=4;serotype=H6N2;strain=A/turkey/Massachusetts/3740/1965 +CY130030.1 Genbank sequence_feature 1 1714 . + . ID=id-CY130030.1:1..1714;Dbxref=IRD:NIGSP_CEIRS_SJC001_WEB_00006.HA;gbkey=misc_feature +CY130030.1 Genbank gene 4 1707 . + . ID=gene-HA;Name=HA;gbkey=Gene;gene=HA;gene_biotype=protein_coding +CY130030.1 Genbank CDS 4 1707 . + 0 ID=cds-AGB50905.1;Parent=gene-HA;Dbxref=NCBI_GP:AGB50905.1;Name=AGB50905.1;gbkey=CDS;gene=HA;product=hemagglutinin;protein_id=AGB50905.1 +CY130030.1 Genbank signal_peptide_region_of_CDS 4 51 . + . ID=id-AGB50905.1:1..16;Parent=cds-AGB50905.1;gbkey=Prot +CY130030.1 Genbank mature_protein_region_of_CDS 52 1038 . + . ID=id-AGB50905.1:17..345;Parent=cds-AGB50905.1;gbkey=Prot;product=HA1 +CY130030.1 Genbank mature_protein_region_of_CDS 1039 1704 . + . ID=id-AGB50905.1:346..567;Parent=cds-AGB50905.1;gbkey=Prot;product=HA2 + diff --git a/data/flu/HA/ha_h6_h6n2/CY130030/unreleased/pathogen.json b/data/flu/HA/ha_h6_h6n2/CY130030/unreleased/pathogen.json new file mode 100644 index 0000000..365142b --- /dev/null +++ b/data/flu/HA/ha_h6_h6n2/CY130030/unreleased/pathogen.json @@ -0,0 +1,16 @@ +{ + "alignmentParams": { + "minSeedCover": 0.01 + }, + "schemaVersion": "3.0.0", + "attributes": { + "name": "ha_h6_h6n2", + "reference name": "Influenza A virus (A/turkey/Massachusetts/3740/1965(H6N2)) hemagglutinin (HA) gene, complete cds", + "reference accession": "CY130030" + }, + "files": { + "reference": "reference.fasta", + "pathogenJson": "pathogen.json", + "genomeAnnotation": "genome_annotation.gff3" + } +} diff --git a/data/flu/HA/ha_h6_h6n2/CY130030/unreleased/reference.fasta b/data/flu/HA/ha_h6_h6n2/CY130030/unreleased/reference.fasta new file mode 100644 index 0000000..64f1f5a --- /dev/null +++ b/data/flu/HA/ha_h6_h6n2/CY130030/unreleased/reference.fasta @@ -0,0 +1,27 @@ +>CY130030.1 Influenza A virus (A/turkey/Massachusetts/3740/1965(H6N2)) hemagglutinin (HA) gene, complete cds +AAAATGATTGCAATCATAATAATCGCGGTAGTGGCCTCTACCAGCAAATCAGACAAGATCTGCATTGGGT +ATCATGCCAACAACTCGACAACACAAGTGGACACAATATTAGAGAAGAATGTGACAGTGACGCACTCTGT +AGAGCTCCTAGAAAGTCAGAAGGAGGAGAGATTCTGCAGAGTGTTGAATAAAACACCTCTGGATCTAAAG +GGTTGCACCATTGAAGGATGGATTCTTGGAAACCCCCAATGTGACATCTTACTTGGTGACCAAAGTTGGT +CATACATAGTAGAGAGGCCTGGAGCCCAAAATGGGATATGTTACCCAGGGGTGCTGAACGAAGTGGAAGA +ACTGAAAGCATTCATTGGGTCCGGAGAGAAAGTACAGAGATTTGAAATGTTTCCCAAGAGCACGTGGACC +GGAGTGGACACTAACAGTGGAGTTACGAGAGCTTGCCCCTATACTACCAGTGGATCATCCTTTTACAGGA +ATCTTTTGTGGATAATAAAAACAAGGTCTGCTGCATACCCAGTAATTAAGGGAACATACAATAATACTGG +CTCCCAGCCAATCCTATATTTCTGGGGTGTGCATCATCCTCCAAATACCGATGAGCAAAATACCTTATAT +GGCTCTGGTGACAGGTATGTTAGAATGGGAACTGAAAGCATGAATTTTGCCAAGAGTCCTGAAATAGCAG +CCAGGCCAGCTGTGAATGGGCAAAGAGGAAGAATTGATTATTATTGGTCTGTACTGAAACCAGGAGAAAC +CTTAAATGTAGAATCCAATGGAAATTTAATAGCTCCTTGGTATGCTTACAAGTTCACAAGTTCCAACAAC +AAAGGAGCTATCTTCAAATCAAACCTCCCAATTGAGAATTGTGATGCTGTATGTCAAACTGTTGCTGGAG +CACTAAAGACAAACAAAACTTTCCAAAATGTTAGTCCACTCTGGATTGGAGAATGTCCCAAATATGTTAA +GAGTGAGAGCCTAAGACTGGCAACTGGTCTGAGGAATGTCCCACAGGCAGAAACAAGAGGATTGTTTGGA +GCCATAGCTGGGTTTATAGAAGGAGGGTGGACAGGTATGATAGACGGATGGTACGGGTACCATCATGAGA +ACTCACAGGGGTCGGGTTATGCAGCAGATAAAGAAAGTACCCAGAAAGCAATTGACGGGATCACCAATAA +AGTAAATTCCATCATTGACAAGATGAACACACAGTTTGAAGCAGTAGAGCATGAGTTCTCAAATCTCGAA +AGGAGAATAGACAATTTAAACAAAAGAATGGAAGATGGATTTTTGGATGTGTGGACGTACAATGCTGAAC +TTTTAGTTCTACTGGAAAATGAAAGGACCCTGGATCTGCACGATGCCAATGTGAAGAACCTATACGAGAA +GGTGAAATCACAATTGAGAGATAATGCAAAGGATTTGGGTAATGGGTGTTTTGAATTTTGGCACAAATGC +GACGATGAATGCATCAACTCAGTTAAGAATGGCACATACGATTACCCAAAGTACCAAGACGAGAGCAAAC +TTAACAGACAGGAGATAGACTCAGTGAAGCTGGAAAATCTGGGCGTATATCAAATTCTTGCTATTTATAG +TACGGTATCGAGCAGTCTAGTTTTGGTGGGGCTGATCATTGCCATGGGTCTTTGGATGTGCTCAAATGGC +TCAATGCAATGCAGGATATGTATATAATTAGGAA + diff --git a/data/flu/HA/ha_h7_h7n9/NC_026425.1/unreleased/dataset.zip b/data/flu/HA/ha_h7_h7n9/NC_026425.1/unreleased/dataset.zip new file mode 100644 index 0000000000000000000000000000000000000000..41126add3dcc3842130a45fde3adbcdbdc582197 GIT binary patch literal 1932 zcmZ`)X*e6`7LFxoMW`iqwX3D7L>EbFYiEkaR${a@M8wugh}3rNB zYpZ<=irN)bd(mi%QdHf{+#hpi?%eNtzUMsOdCoaM-sgSKYiY*8DGUGrcmVhP_3pg& z3ng>10RYcgkB^o0MibrfZdjbAr!O9dwSe7i*AjSpqz<;Yz^Ok%ChFJ^gL4JmdzKE^ zqsj*iDLT-lW;=qj(3u&++(uIa7eH>;`nh~fcA-`JC%#g!Uo<6HQIARH^@wpbNr5fY zY$=Zr>7Rb7O5%WNYY2762*r$h?jvpm^*Y-uVWr1syZG=b&oIzxdYojW{q}&DzTmOE zjdxNIRKRwv+!!L=3soPM@9T4KzI<;{40K{ndi)*liPw)%6)v&6wxGx~)DUQW=CP8y z`O2~FJqhh?(HMs;k+O{iB}V)51ZsD%Oaq1gDTRIw07w7<00;{%7E*XGtRotS!xPa& z4?IrO&DB+hN-@LJw1i0$OLkhl1aeFS{OsLiWtxeokS+3Jr4e{Wtk~)1v`0pmV*@lK z4y9w%v+$;A6&3@NsyMn*%l))YI8;w8)OW6)wD2^xjdLof*oEzu*)l#wH1&#zQ3h>+ zYt-q|sJB1B${;7a4wi|PQCZXwC-uA-RD4ozT%*p-wCk!0lDXEscwV?OAtn!J)LNX# zIDAjOa$PR-CNX!(DvD453gO}H3frROK#>#;$;MNkO3}?ESlQ#<#MPz7p+nqUpGcrD zA)#%^Yhi5Du=R;pfo>Qs?qU@iW!`99SGcR@q^W0k2kjldt)U=obW=LoN~NNtHYbgV zo4;D~TMI}-JF$QyTAOqqXMQ&EU#0F$(TPkTWR#OSN-n`FgdlH&jWC&Vi7B2)@vll^ zy>}6NVR9uAy0Qyd~cYkm+HVM-B0kh@zVf#Cy7=pMb6)XaA!&O z_7q<|{f1B-Vg`X#M=h}wlL zP1dXPljKC8$>j%5weQ%o5z~Reb2WoSD>sJp@VUB;(T$nIcQ&^*BdvB1?gs3)9*?w` z5324gjZD>6z(a=lbh&~1;(IT5+?R62kWDt(By`5WcavkK-@dSa;f5j)I1VVo^5(N? 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ID=id-YP_009118475.1:340..560;Parent=cds-YP_009118475.1;gbkey=Prot;product=HA2;protein_id=YP_009118483.1 + diff --git a/data/flu/HA/ha_h7_h7n9/NC_026425.1/unreleased/pathogen.json b/data/flu/HA/ha_h7_h7n9/NC_026425.1/unreleased/pathogen.json new file mode 100644 index 0000000..0b90209 --- /dev/null +++ b/data/flu/HA/ha_h7_h7n9/NC_026425.1/unreleased/pathogen.json @@ -0,0 +1,16 @@ +{ + "alignmentParams": { + "minSeedCover": 0.01 + }, + "schemaVersion": "3.0.0", + "attributes": { + "name": "ha_h7_h7n9", + "reference name": "Influenza A virus (A/Shanghai/02/2013(H7N9)) segment 4 hemagglutinin (HA) gene, complete cds", + "reference accession": "NC_026425.1" + }, + "files": { + "reference": "reference.fasta", + "pathogenJson": "pathogen.json", + "genomeAnnotation": "genome_annotation.gff3" + } +} diff --git a/data/flu/HA/ha_h7_h7n9/NC_026425.1/unreleased/reference.fasta b/data/flu/HA/ha_h7_h7n9/NC_026425.1/unreleased/reference.fasta new file mode 100644 index 0000000..93d4c91 --- /dev/null +++ b/data/flu/HA/ha_h7_h7n9/NC_026425.1/unreleased/reference.fasta @@ -0,0 +1,27 @@ +>NC_026425.1 Influenza A virus (A/Shanghai/02/2013(H7N9)) segment 4 hemagglutinin (HA) gene, complete cds +ATGAACACTCAAATCCTGGTATTCGCTCTGATTGCGATCATTCCAACAAATGCAGACAAAATCTGCCTCG +GACATCATGCCGTGTCAAACGGAACCAAAGTAAACACATTAACTGAAAGAGGAGTGGAAGTCGTCAATGC +AACTGAAACAGTGGAACGAACAAACATCCCCAGGATCTGCTCAAAAGGGAAAAGGACAGTTGACCTCGGT +CAATGTGGACTCCTGGGGACAATCACTGGACCACCTCAATGTGACCAATTCCTAGAATTTTCAGCCGATT +TAATTATTGAGAGGCGAGAAGGAAGTGATGTCTGTTATCCTGGGAAATTCGTGAATGAAGAAGCTCTGAG +GCAAATTCTCAGAGAATCAGGCGGAATTGACAAGGAAGCAATGGGATTCACATACAGTGGAATAAGAACT +AATGGAGCAACCAGTGCATGTAGGAGATCAGGATCTTCATTCTATGCAGAAATGAAATGGCTCCTGTCAA +ACACAGATAATGCTGCATTCCCGCAGATGACTAAGTCATATAAAAATACAAGAAAAAGCCCAGCTCTAAT +AGTATGGGGGATCCATCATTCCGTATCAACTGCAGAGCAAACCAAGCTATATGGGAGTGGAAACAAACTG +GTGACAGTTGGGAGTTCTAATTATCAACAATCTTTTGTACCGAGTCCAGGAGCGAGACCACAAGTTAATG +GTCTATCTGGAAGAATTGACTTTCATTGGCTAATGCTAAATCCCAATGATACAGTCACTTTCAGTTTCAA 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ID=CY125947.1:1..1426;Dbxref=taxon:1395524;Name=6;collection-date=2010;country=Peru: Truenococha;gbkey=Src;isolation-source=rectal swab;mol_type=viral cRNA;nat-host=Artibeus planirostris%3B gender M;note=Complete sequence%2C ends confirmed by RACE-PCR.;segment=6;serotype=H18N11;strain=A/flat-faced bat/Peru/033/2010 +CY125947.1 Genbank gene 24 1367 . + . ID=gene-NA;Name=NA;gbkey=Gene;gene=NA;gene_biotype=protein_coding +CY125947.1 Genbank CDS 24 1367 . + 0 ID=cds-AGX84936.1;Parent=gene-NA;Dbxref=NCBI_GP:AGX84936.1;Name=AGX84936.1;gbkey=CDS;gene=NA;product=neuraminidase-like protein;protein_id=AGX84936.1 + diff --git a/data/flu/NA/na_n11_h18n11/CY125947/unreleased/pathogen.json b/data/flu/NA/na_n11_h18n11/CY125947/unreleased/pathogen.json new file mode 100644 index 0000000..273a75d --- /dev/null +++ b/data/flu/NA/na_n11_h18n11/CY125947/unreleased/pathogen.json @@ -0,0 +1,16 @@ +{ + "alignmentParams": { + "minSeedCover": 0.01 + }, + "schemaVersion": "3.0.0", + "attributes": { + "name": "na_n11_h18n11", + "reference name": "Influenza A virus (A/flat-faced bat/Peru/033/2010(H18N11)) neuraminidase-like protein (NA) gene, complete cds", + "reference accession": "CY125947" + }, + "files": { + "reference": "reference.fasta", + "pathogenJson": "pathogen.json", + "genomeAnnotation": "genome_annotation.gff3" + } +} diff --git a/data/flu/NA/na_n11_h18n11/CY125947/unreleased/reference.fasta b/data/flu/NA/na_n11_h18n11/CY125947/unreleased/reference.fasta new file mode 100644 index 0000000..1e370cb --- /dev/null +++ b/data/flu/NA/na_n11_h18n11/CY125947/unreleased/reference.fasta @@ -0,0 +1,23 @@ +>CY125947.1 Influenza A virus (A/flat-faced bat/Peru/033/2010(H18N11)) neuraminidase-like protein (NA) gene, complete cds +AGCAGAAGCAGGAGTTTTTCATAATGTCGTTTCAAACATCGACATGTCTGTTGATTGTTTCCCTAATATG +TGGGATACTAACAGTCTGCCTTCAGGTACTGTTACCCTTCATATTGATATGGACAAATACAGAACCAAAT +TATTCCTGTGAGTGTCCAGCTCCCAACATCAGTCTTAGCTGTCCAAACGGGACTTCTGTAACATATGACA +GTAAAAATATAACTGAAAACAGCTTCTACAGTTCAACAACAAACTACCTGTCCCCTGTCATTGCAACCCC +TCTGGTGCTAGGAGAGAATCTGTGCAGCATAAATGGGTGGGTTCCAACCTACAGAGGAGAAGGAACAACC +GGAAAAATTCCTGATGAACAAATGCTGACCAGACAGAACTTTGTATCCTGCTCAGATAAAGAGTGTCGAA +GATTTTTTGTGAGTATGGGATACGGAACTACCACAAATTTTGCAGACCTAATTGTGTCAGAACAAATGAA +TGTTTACAGTGTAAAGTTAGGAGACCCTCCAACACCTGACAAGTTAAAATTTGAAGCTGTTGGCTGGAGT 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https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=384499 +CY130088.1 Genbank region 1 1442 . + . 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ID=KC110598.1:1..1423;Dbxref=taxon:1088701;Name=6;collection-date=16-Nov-2010;country=USA;gbkey=Src;genome=genomic;mol_type=viral cRNA;nat-host=Clangula hyemalis (long-tailed duck);segment=6;serotype=H14N6;strain=A/long-tailed duck/Wisconsin/10OS3912/2010 +KC110598.1 Genbank gene 19 1423 . + . ID=gene-NA;Name=NA;end_range=1423,.;gbkey=Gene;gene=NA;gene_biotype=protein_coding;partial=true +KC110598.1 Genbank CDS 19 1423 . + 0 ID=cds-AFX81873.1;Parent=gene-NA;Dbxref=NCBI_GP:AFX81873.1;Name=AFX81873.1;end_range=1423,.;gbkey=CDS;gene=NA;partial=true;product=neuraminidase;protein_id=AFX81873.1 + diff --git a/data/flu/NA/na_n6_h14n6/KC110598/unreleased/pathogen.json b/data/flu/NA/na_n6_h14n6/KC110598/unreleased/pathogen.json new file mode 100644 index 0000000..3015f1b --- /dev/null +++ b/data/flu/NA/na_n6_h14n6/KC110598/unreleased/pathogen.json @@ -0,0 +1,16 @@ +{ + "alignmentParams": { + "minSeedCover": 0.01 + }, + "schemaVersion": "3.0.0", + "attributes": { + "name": "na_n6_h14n6", + "reference name": "Influenza A virus (A/long-tailed duck/Wisconsin/10OS3912/2010(H14N6)) segment 6 neuraminidase (NA) gene, partial cds", + "reference accession": "KC110598" + }, + "files": { + "reference": "reference.fasta", + "pathogenJson": "pathogen.json", + "genomeAnnotation": "genome_annotation.gff3" + } +} diff --git a/data/flu/NA/na_n6_h14n6/KC110598/unreleased/reference.fasta b/data/flu/NA/na_n6_h14n6/KC110598/unreleased/reference.fasta new file mode 100644 index 0000000..805091a --- /dev/null +++ b/data/flu/NA/na_n6_h14n6/KC110598/unreleased/reference.fasta @@ -0,0 +1,23 @@ +>KC110598.1 Influenza A virus (A/long-tailed duck/Wisconsin/10OS3912/2010(H14N6)) segment 6 neuraminidase (NA) gene, partial cds +AGCAAAAGCAGGGTGAAAATGAATCCAAATCAAAAGATAATATGCATTTCAGCCACAGGAATGACACTAT +CGGTAGTAAGCCTGCTGATAGGAATTGCCAATTTGGGCCTAAACATCGGACTCCATTATAAGGTGGGTGA +TACACCAGATGTGAGCATCCCAAACATGAATGAGACCAACTCAACAACAACAATAATAAACAATAATACC +CAAAATAATTTCACAAATATCACTAACATTATAGTGAATAAAAACGAGGGAAAAATGTTCCTAAATCTGA +CCAAGCCCCTATGTGAGGTAAACTCATGGCACATCTTGTCGAAAGACAATGCAATAAGAATAGGAGAAGA +TGCTCATATACTAGTCACAAGGGAGCCCTACCTGTCTTGCGATCCACAAGGCTGCAGGATGTTTGCTCTG +AGCCAAGGAACAACACTCAGAGGGCGACATGCGAATGGGACTATACATGATAGAAGTCCATTTCGAGCTC 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ID=gene-NA;Name=NA;gbkey=Gene;gene=NA;gene_biotype=protein_coding +CY130072.1 Genbank CDS 7 1419 . + 0 ID=cds-AGB50963.1;Parent=gene-NA;Dbxref=NCBI_GP:AGB50963.1;Name=AGB50963.1;gbkey=CDS;gene=NA;product=neuraminidase;protein_id=AGB50963.1 + diff --git a/data/flu/NA/na_n9_h11n9/CY130072/unreleased/pathogen.json b/data/flu/NA/na_n9_h11n9/CY130072/unreleased/pathogen.json new file mode 100644 index 0000000..dbd60f7 --- /dev/null +++ b/data/flu/NA/na_n9_h11n9/CY130072/unreleased/pathogen.json @@ -0,0 +1,16 @@ +{ + "alignmentParams": { + "minSeedCover": 0.01 + }, + "schemaVersion": "3.0.0", + "attributes": { + "name": "na_n9_h11n9", + "reference name": "Influenza A virus (A/duck/Memphis/546/1974(H11N9)) neuraminidase (NA) gene, complete cds", + "reference accession": "CY130072" + }, + "files": { + "reference": "reference.fasta", + "pathogenJson": "pathogen.json", + "genomeAnnotation": "genome_annotation.gff3" + } +} diff --git a/data/flu/NA/na_n9_h11n9/CY130072/unreleased/reference.fasta b/data/flu/NA/na_n9_h11n9/CY130072/unreleased/reference.fasta new file mode 100644 index 0000000..f18b4b0 --- /dev/null +++ b/data/flu/NA/na_n9_h11n9/CY130072/unreleased/reference.fasta @@ -0,0 +1,23 @@ +>CY130072.1 Influenza A virus (A/duck/Memphis/546/1974(H11N9)) neuraminidase (NA) gene, complete cds +GTCAAGATGAATCCAAATCAGAAGATTCTATGCACTTCTGCCACTGCTATCGTAATAGGCACAATTGCAG +TACTCATAGGAATAGCGAACTTAGGATTGAATATAGGACTACATCTGAAACCGAGCTGCAATTGCTCACA +CTCACAACCTGAAGCAATCAATGCAAGCCAAACAATAATAAACAACTACTATAATGAAACAAACATCACC +CAAATAAGTAATACCAACATCCAAGTAGAGGAAAGGGCAAACAGAGACTTCAATAACTTAACTAGAGGGC +TCTGTACTATAAATTCATGGCACATATTTGGGAAAGACAATGCGGTAAGAATTGGGGAGGACTCAGATGT +TTTAGTCACAAGAGAACCCTATGTCTCCTGTGACCCAGATGAGTGCAGGTTCTATGCTCTCAGCCAAGGG +ACAACAATCAGAGGGAAACATTCAAATGGAACAATACACGATAGATCCCAATACCGCGCCCTGATAAGCT +GGCCACTGTCATCACCGCCCACAGTATACAATAGCAGAGTGGAATGCATTGGATGGTCAAGCACTAGTTG +CCATGATGGCAAAGCCAGGATGTCAATATGTATATCGGGCCCGAACAACAATGCATCAGCAGTAATCTGG +TACAATAGAAGACCTGTTACAGAAATCAACACATGGGCCCGAAACATACTAAGAACACAAGAATCTGAAT +GTGTATGCCACAACGGTGTTTGCCCGGTAGTGTTCACAGATGGGTCTGCCACTGGACCTGCAGAGACAAG +AATATACTATTTTAAGGAAGGAAAGACATTAAAATGGGAACCTCTGACTGGAACGGCTAAACATATCGAA +GAATGCTCATGTTACGGGGAGCGGGCAGGGATTACTTGCACATGCAGGGATAATTGGCAGGGCTCAAATA +GGCCAGTAATTCAGATAGATCCAGTGGCGATGACACACACTAGTCAGTATATATGTAGCCCTGTTCTTAC +AGACAACCCCCGACCGAATGATCCAACTGTAGGTAAGTGTAACGACCCTTATCCAGGCAATAACAACAAC +GGGGTCAAAGGGTTTTCATACCTGGATGGGAGTAATACCTGGTTGGGGAGGACAATAAGCACAGCTTCAA +GATCCGGATATGAGATGCTAAAGGTGCCAAATGCATTGACAGACGATAGATCAAAGCCCACTCAAGGTCA +GACTATCGTATTAAACACTGACTGGAGTGGTTACAGTGGGTCCTTCATGGACTATTGGGCTGAGGGGGAA +TGCTACCGAGCGTGCTTTTACGTGGAGTTAATACGTGGAAGACCTAAGGAGGATAAAGTATGGTGGACCA +GTAATAGTATAGTATCAATGTGTTCCAGCACAGAATTCCTTGGACAATGGAACTGGCCTGATGGGGCTAA +AATAGAGTACTTCCTCTAAGATACAGAAAAAAGAC + diff --git a/data/flu/NA/na_n9_h15n9/CY005407/unreleased/dataset.zip b/data/flu/NA/na_n9_h15n9/CY005407/unreleased/dataset.zip new file mode 100644 index 0000000000000000000000000000000000000000..4b1d790d4a1fb33f1c5d2fabbbb1b64b63e52993 GIT binary patch literal 1798 zcmWIWW@Zs#U|`^2;H|KVx%@tvNq~`oVLuS_0!0fFOEU7)Q}gt)iu3bQ{e82W9R&9N z))w>UTvBIZnv_4u`?j;DNL1CNm3H=B*2{KhGx7d>AL~2C!SC?z88g54^$F;0^*t(- zbI)Vqm3NCRqHb|*dRV^TMp?DSX|_0lsE1pmrj^7wUt*tbkE8nn_lk92v0t#FAbmw+2yxUKX$UKDwqWPF#jySH_qryud>$%X|n{Q@eH-EMI$i8T(1m%>f|` zWQ3Ahe@*!_RqgbYN|TkFGVeIVIlS1Rqo`iSe#d0R@gwzu$N#3-bnQLozU+!ySi&{w zl|?JNwjRx^Y@amS-iZJI28~4T-lglGt#1i0)!ZIb@SY>{;EAPIpHF(PA*ZR~pqSbf zD|tbBb${E7(E4e-9KUe^8@~$e^r|9^tL&<%X<5#36ECsu|BPSXvA85SbJs4Io%E2J~CHs zzpj6Gx?n5frfT1uXNT+J_TImDf34Z>-*?Y0Kl|XY?CG&OVMC3A_5%||Qy4RYke|iT{{;UE2C3UR$gQb z^2Ck%k57OngKI9ARuWg_2I(!Ucdcqn@+vqI!1UHzwPbmkPf^1Jr&6AhX3d4tWxXdB zu?I$odpo7=Ss>;R$1P`e!&z9M-+Ym0kMi;SiOfE0*k;mJ~yO+0COL1uE|xjts6BNQ(0OkV73$lup{ z!ccOB&#PX(T$wt>crLLin?&YTTB@;Hxad6!c|Ge#lf_I8HqXabyt&RN_cZi(I;tt{ zo+Cbqw{)?hldRe$=TFUbB}T;}OBIeiI2dTR_AhgQHzSh>Gwxagn3%y}Nh63tsYB4U xqL-QwjSLJ+8m)n4DfTiH*$iwM31LPKuq;N)Rsr6u!2HI*zzl?YfV2si2LJ_I1cv|s literal 0 HcmV?d00001 diff --git a/data/flu/NA/na_n9_h15n9/CY005407/unreleased/genome_annotation.gff3 b/data/flu/NA/na_n9_h15n9/CY005407/unreleased/genome_annotation.gff3 new file mode 100644 index 0000000..75cec76 --- /dev/null +++ b/data/flu/NA/na_n9_h15n9/CY005407/unreleased/genome_annotation.gff3 @@ -0,0 +1,11 @@ +##gff-version 3 +#!gff-spec-version 1.21 +#!processor NCBI annotwriter +##sequence-region CY005407.1 1 1459 +##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=352560 +CY005407.1 Genbank region 1 1459 . + . 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ID=id-CY005407.1:1439..1459;Note=PCR amplification primer sequence;gbkey=primer_bind + diff --git a/data/flu/NA/na_n9_h15n9/CY005407/unreleased/pathogen.json b/data/flu/NA/na_n9_h15n9/CY005407/unreleased/pathogen.json new file mode 100644 index 0000000..dd3d694 --- /dev/null +++ b/data/flu/NA/na_n9_h15n9/CY005407/unreleased/pathogen.json @@ -0,0 +1,16 @@ +{ + "alignmentParams": { + "minSeedCover": 0.01 + }, + "schemaVersion": "3.0.0", + "attributes": { + "name": "na_n9_h15n9", + "reference name": "Influenza A virus (A/wedge-tailed shearwater/Western Australia/2576/1979(H15N9)) segment 6, complete sequence", + "reference accession": "CY005407" + }, + "files": { + "reference": "reference.fasta", + "pathogenJson": "pathogen.json", + "genomeAnnotation": "genome_annotation.gff3" + } +} diff --git a/data/flu/NA/na_n9_h15n9/CY005407/unreleased/reference.fasta b/data/flu/NA/na_n9_h15n9/CY005407/unreleased/reference.fasta new file mode 100644 index 0000000..c9d1f05 --- /dev/null +++ b/data/flu/NA/na_n9_h15n9/CY005407/unreleased/reference.fasta @@ -0,0 +1,23 @@ +>CY005407.1 Influenza A virus (A/wedge-tailed shearwater/Western Australia/2576/1979(H15N9)) segment 6, complete sequence +AGCAAAAGCAGGGTCAAGATGAATCCAAATCAGAAGATTCTATGCACATCTGCCACTGCCATCGCAATAG +GCACAATTGCTGTGTTAATAGGAATAGCAAACCTAGGTTTGAACATAGGACTACACCTGAAACCGGGCTG +CAACTGCTCCAATCCCACTCCTGAAGCCACAAATGTGAGCCAAACAATAATAAACAATTACCACAATGAA +ACAAATATTACTCAAATAAGCAATACAAACATTCAACATATGGGGGAAACTGACAGAGACTTCAACAATC +TGACCAAAGGGCTCTGCACAATAAATTCGTGGCATATATTCGGGAAGGACAATGCTATAAGAATAGGGGA +GAACTCTGATGTTTTAGTCACAAGAGAGCCATATGTTTCTTGTGATCCAGATGGATGCAGATTTTATGCT +CTTAGCCAAGGAACAACGATAAGGGGAAAGCACTCAAATGGAACAATACACGATAGATCCCAATACCGTG +CTTTAGTGAGCTGGCCTTTATCATCACCACCCACTGTATACAATACCAGGGTAGAATGCATTGGATGGTC +CAGCACAAGCTGCCATGATGGGAAAGCACGAATGTCTATATGTGTTTCAGGTCCCAACAACAATGCATCA +GCAGTGATTTGGTACAAAGGGAGGCCTATCACAGAAATCAATACGTGGGCCCGAAACATATTGAGAACCC +AAGAGTCTGAGTGTGTGTGCCACAATGGAGTATGTCCAGTAGTGTTCACTGACGGTTCTGCTACTGGCCC +AGCAGAAACTAGGATATACTACTTCAAAGAGGGGAAAATCCTTAAATGGGAGCCACTAACTGGAACTGCC +AAGCACATTGAGGAATGCTCTTGCTATGGGAAAGACTCAGAAATAACATGCACATGTAGAGACAATTGGC +AAGGCTCGAATAGACCAGTGATACAAATAAATCCCACAATGATGACGCACACTAGTCAATACATATGCAG +CCCTGTCCTCACAGACAATCCACGTCCCAATGACCCCGCGGTAGGCAAGTGTAATGATCCTTATCCAGGG +AACAACAATAATGGGGTCAAAGGATTCTCATATTTAGATGGTGACAATACGTGGCTAGGAAGAACAATAA +GCACAGCTTCTAGGTCTGGATATGAAATGCTGAAAGTGCCTAATGCACTGACAGATGATAGATCAAAACC +TACTCAAGGTCAGACAATTGTGTTAAACACAGACTGGAGTGGTTACAGTGGGTCTTTCATTGATTACTGG +GCAAAAGGGGAGTGCTATAGAGCATGCTTCTATGTTGAGCTGATCCGTGGGAGGCCAAAGGAGGACAAAG +TGTGGTGGACCAGTAATAGCATAGTATCGATGTGTTCCAGCACAGAGTTCCTTGGACAATGGAACTGGCC +AGATGGGGCTAAAATAGAGTACTTCCTCTAAGATGTAGAAAAAGACCCTTGTTTCTACT + diff --git a/data/flu/NA/na_n9_h7n9/NC_026429.1/unreleased/dataset.zip b/data/flu/NA/na_n9_h7n9/NC_026429.1/unreleased/dataset.zip new file mode 100644 index 0000000000000000000000000000000000000000..e2963342f910bd19aa7cd417e07e8104182cd594 GIT binary patch literal 1722 zcmWIWW@Zs#U|`^2;I6QW30uzS!o6^t)4P z>c{wpuM*rfPO2~ZW)bIMZPGdEis1IUIYz$zT>CwwEjKCuwJF-OzaV4nwEL5nF4u8$ z-Q2VB*`jy+F*;GlGlZ6ON;idmK9@A3qh8Q!hli~s$EhDzl*?^TS)6>N=5uXtJ6NQ;v;Rou+V6TV|7_mwdl%31*toot6PSoC9uRef_6Os22=nu1A`bauz=x|pPL$=n3tDdl30?NpQo3emS$W!DL((Ug2>VN zbNwG`_Rrq9akGx0Q}AS;Y7{vPmYZB^l9ABJJirDQ-#rFZww$8-<9xV zsYqF%-~D9C<=m&|Y%esMtm*xE_*a|8vq^5z?)jz5lTTN1o)Vg`cwt`TX_h0V7HZMa z$L*D7QvB+*GAsUUE>H+PTB`p*EjbcSKqw&LL419|rBUwCBQT|4(+9sU;Q)xnvh^sPJf<+}b?(QBDij!N(Ra+#1DihFm?vt;)vS z@Z|uPNS|BR>}xM|O;?wEJR0^?@5IC>Hy<7e3b?J3cB#LBtAj~aEP;gRi)9W9hKf~u z3eowK3QV>qT)4i~Xin% z-`ri~C#ab+S7zPAu=O+Us4sauf#>Y)lAUbsx&phnGmb4_y3iu@q3D5jXxBV{qt?B0 zYCjLM$p@`alVM$vSsp( zo~4HW7z4Z+nM9azm-N823I{4kFFKH+=FOjU|7mxAbKpyv~W8IHix Y6fM^Tc(byB6fgtf9w7Y!n7J4j028DI0{{R3 literal 0 HcmV?d00001 diff --git a/data/flu/NA/na_n9_h7n9/NC_026429.1/unreleased/genome_annotation.gff3 b/data/flu/NA/na_n9_h7n9/NC_026429.1/unreleased/genome_annotation.gff3 new file mode 100644 index 0000000..1252237 --- /dev/null +++ b/data/flu/NA/na_n9_h7n9/NC_026429.1/unreleased/genome_annotation.gff3 @@ -0,0 +1,9 @@ +##gff-version 3 +#!gff-spec-version 1.21 +#!processor NCBI annotwriter +##sequence-region NC_026429.1 1 1398 +##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1332244 +NC_026429.1 RefSeq region 1 1398 . + . ID=NC_026429.1:1..1398;Dbxref=taxon:1332244;Name=6;collection-date=05-Mar-2013;country=China;gbkey=Src;genome=genomic;mol_type=viral cRNA;nat-host=Homo sapiens;note=passage details: E1;segment=6;serotype=H7N9;strain=A/Shanghai/02/2013 +NC_026429.1 RefSeq gene 1 1398 . + . ID=gene-TS66_s6gp1;Dbxref=GeneID:23104238;Name=NA;gbkey=Gene;gene=NA;gene_biotype=protein_coding;locus_tag=TS66_s6gp1 +NC_026429.1 RefSeq CDS 1 1398 . + 0 ID=cds-YP_009118481.1;Parent=gene-TS66_s6gp1;Dbxref=GenBank:YP_009118481.1,GeneID:23104238;Name=YP_009118481.1;gbkey=CDS;gene=NA;locus_tag=TS66_s6gp1;product=neuraminidase;protein_id=YP_009118481.1 + diff --git a/data/flu/NA/na_n9_h7n9/NC_026429.1/unreleased/pathogen.json b/data/flu/NA/na_n9_h7n9/NC_026429.1/unreleased/pathogen.json new file mode 100644 index 0000000..79aa837 --- /dev/null +++ b/data/flu/NA/na_n9_h7n9/NC_026429.1/unreleased/pathogen.json @@ -0,0 +1,16 @@ +{ + "alignmentParams": { + "minSeedCover": 0.01 + }, + "schemaVersion": "3.0.0", + "attributes": { + "name": "na_n9_h7n9", + "reference name": "Influenza A virus (A/Shanghai/02/2013(H7N9)) segment 6 neuraminidase (NA) gene, complete cds", + "reference accession": "NC_026429.1" + }, + "files": { + "reference": "reference.fasta", + "pathogenJson": "pathogen.json", + "genomeAnnotation": "genome_annotation.gff3" + } +} diff --git a/data/flu/NA/na_n9_h7n9/NC_026429.1/unreleased/reference.fasta b/data/flu/NA/na_n9_h7n9/NC_026429.1/unreleased/reference.fasta new file mode 100644 index 0000000..63f3bfe --- /dev/null +++ b/data/flu/NA/na_n9_h7n9/NC_026429.1/unreleased/reference.fasta @@ -0,0 +1,22 @@ +>NC_026429.1 Influenza A virus (A/Shanghai/02/2013(H7N9)) segment 6 neuraminidase (NA) gene, complete cds +ATGAATCCAAATCAGAAGATTCTATGCACTTCAGCCACTGCTATCATAATAGGCGCAATCGCAGTACTCA +TTGGAATGGCAAACCTAGGATTGAACATAGGACTGCATCTAAAACCGGGCTGCAATTGCTCACACTCACA +ACCTGAAACAACCAACACAAGCCAAACAATAATAAACAACTATTATAATGAAACAAACATCACCAAYATC +CAAATGGAAGAGAGAACAAGCAGGAATTTCAATAACTTAACTAAAGGGCTCTGTACTATAAATTCATGGC +ACATATATGGGAAAGACAATGCAGTAAGAATTGGAGAGAGCTCGGATGTTTTAGTCACAAGAGAACCCTA +TGTTTCATGCGACCCAGATGAATGCAGGTTCTATGCTCTCAGCCAAGGAACAACAATCAGAGGGAAACAC +TCAAACGGAACAATACACGATAGGTCCCAGTATCGCGCCCTGATAAGCTGGCCACTATCATCACCGCCCA +CAGTGTACAACAGCAGGGTGGAATGCATTGGGTGGTCAAGTACTAGTTGCCATGATGGCAAATCCAGGAT +GTCAATATGTATATCAGGACCAAACAACAATGCATCTGCAGTAGTATGGTACAACAGAAGGCCTGTTGCA +GAAATTAACACATGGGCCCGAAACATACTAAGAACACAGGAATCTGAATGTGTATGCCACAACGGCGTAT +GCCCAGTAGTGTTCACCGATGGGTCTGCCACTGGACCTGCAGACACAAGAATATACTATTTTAAAGAGGG +GAAAATATTGAAATGGGAGTCTCTGACTGGAACTGCTAAGCATATTGAAGAATGCTCATGTTACGGGGAA +CGAACAGGAATTACCTGCACATGCAGGGACAATTGGCAGGGCTCAAATAGACCAGTGATTCAGATAGACC +CAGTAGCAATGACACACACTAGTCAATATATATGCAGTCCTGTTCTTACAGACAATCCCCGACCGAATGA +CCCAAATATAGGTAAGTGTAATGACCCTTATCCAGGTAATAATAACAATGGAGTCAAGGGATTCTCATAC +CTGGATGGGGCTAACACTTGGCTAGGGAGGACAATAAGCACAGCCTCGAGGTCTGGATACGAGATGTTAA +AAGTGCCAAATGCATTGACAGATGATAGATCAAAGCCCATTCAAGGTCAGACAATTGTATTAAACGCTGA +CTGGAGTGGTTACAGTGGATCTTTCATGGACTATTGGGCTGAAGGGGACTGCTATCGAGCGTGTTTTTAT +GTGGAGTTGATACGTGGAAGACCCAAGGAGGATAAAGTGTGGTGGACCAGCAATAGTATAGTATCGATGT +GTTCCAGTACAGAATTCCTGGGACAATGGAACTGGCCTGATGGGGCTAAAATAGAGTACTTCCTCTAA + diff --git a/flu-dataset-generator/config.yml b/flu-dataset-generator/config.yml new file mode 100644 index 0000000..6c9e631 --- /dev/null +++ b/flu-dataset-generator/config.yml @@ -0,0 +1,39 @@ +HA: + ha_h3_h3n8: CY028836 + ha_h4_h4n6: CY181241 + ha_h5_h5n1: NC_007362.1 + ha_h5_h5n2: KU143256 + ha_h6_h6n2: CY130030 + ha_h7_h7n9: NC_026425.1 + ha_h8_h8n4: CY136131 + ha_h9_h9n2: NC_004908.1 + ha_h10_h10n7: CY136094 + ha_h11_h11n9: CY130070 + ha_h12_h12n5: CY130078 + ha_h13_h13n6: CY130086 + ha_h14_h14n5: JN696314 + ha_h15_h15n9: CY006010 + ha_h16_h16n3: CY136630 + ha_h17_h17n10: CY103876 + ha_h18_h18n11: CY125945 + +NA: + na_n1_h5n1: NC_007361.1 + na_n2_h6n2: CY130032 + na_n2_h9n2: NC_004909.1 + na_n2_h5n2: KU143347 + na_n3_h16n3: CY136632 + na_n4_h8n4: CY136133 + na_n5_h12n5: CY130080 + na_n6_h4n6: CY181243 + na_n6_h13n6: CY130088 + na_n6_h14n6: KC110598 + na_n7_h10n7: CY136096 + na_n8_h3n8: CY028838 + na_n9_h7n9: NC_026429.1 + na_n9_h11n9: CY130072 + na_n9_h15n9: CY005407 + na_n10_h17n10: CY103878 + na_n11_h18n11: CY125947 + +output_dir: ../data/flu diff --git a/flu-dataset-generator/generator.py b/flu-dataset-generator/generator.py new file mode 100644 index 0000000..dc03b61 --- /dev/null +++ b/flu-dataset-generator/generator.py @@ -0,0 +1,103 @@ +import json +from pathlib import Path +import sys +import zipfile +import yaml +from Bio import Entrez, SeqIO +from dataclasses import dataclass +import click + +# Set your email address (required by NCBI) +Entrez.email = "your_email@example.com" + +InsdcAccession = str +SequenceName = str + +PATHOGEN_TEMPLATE = { + "alignmentParams": {"minSeedCover": 0.01}, + "schemaVersion": "3.0.0", + "attributes": { + "name": "TODO", + "reference name": "TODO", + "reference accession": "TODO", + }, + "files": { + "reference": "reference.fasta", + "pathogenJson": "pathogen.json", + "genomeAnnotation": "genome_annotation.gff3", + }, +} + + +@dataclass +class Config: + HA: dict[SequenceName, InsdcAccession] + NA: dict[SequenceName, InsdcAccession] + output_dir: str + + +def fetch_genbank_description(accession: str): + with Entrez.efetch( + db="nucleotide", + id=accession, + rettype="gb", + retmode="text", + ) as handle: + return SeqIO.read(handle, "genbank").description + +def generate_dataset(out_dir: Path, ref_name: str, accession: str): + out_dir.mkdir(parents=True, exist_ok=True) + fasta_path = out_dir / "reference.fasta" + gff_path = out_dir / "genome_annotation.gff3" + pathogen_path = out_dir / "pathogen.json" + zip_path = out_dir / "dataset.zip" + + try: + fasta = Entrez.efetch( + db="nucleotide", id=accession, rettype="fasta", retmode="text" + ) + fasta_path.write_text(fasta.read()) + + gff3 = Entrez.efetch( + db="nucleotide", id=accession, rettype="gff3", retmode="text" + ) + gff_path.write_text(gff3.read()) + + pathogen_json = PATHOGEN_TEMPLATE.copy() + pathogen_json["attributes"]["name"] = ref_name + pathogen_json["attributes"]["reference name"] = fetch_genbank_description(accession) + pathogen_json["attributes"]["reference accession"] = accession + + pathogen_path.write_text( + json.dumps(pathogen_json, indent=2, ensure_ascii=False) + "\n" + ) + except Exception as e: + print(f" {out_dir} Failed: {e}", file=sys.stderr) + + with zipfile.ZipFile(zip_path, "w", zipfile.ZIP_DEFLATED) as zf: + for path in out_dir.rglob("*"): + if path == zip_path: + continue # don’t zip the zip + zf.write(path, arcname=path.relative_to(out_dir)) + +def create_datasets(config: Config) -> None: + for ref_name, accession in config.HA.items(): + out_dir = Path(config.output_dir) / "HA" / ref_name / accession / "unreleased" + generate_dataset(out_dir, ref_name, accession) + for ref_name, accession in config.NA.items(): + out_dir = Path(config.output_dir) / "NA" / ref_name / accession / "unreleased" + generate_dataset(out_dir, ref_name, accession) + + +@click.command() +@click.option("--config-file", required=True, type=click.Path(exists=True)) +def main(config_file: str) -> None: + with open(config_file, encoding="utf-8") as file: + full_config = yaml.safe_load(file) + relevant_config = {key: full_config[key] for key in Config.__annotations__} + config = Config(**relevant_config) + create_datasets(config) + + +if __name__ == "__main__": + main() From e2cfb071821199a49dbd9458dad3b16537642348 Mon Sep 17 00:00:00 2001 From: anna-parker <50943381+anna-parker@users.noreply.github.com> Date: Mon, 26 Jan 2026 15:32:57 +0100 Subject: [PATCH 2/5] add to index --- .../CY136094/unreleased/dataset.zip | Bin 2038 -> 2038 bytes .../CY130070/unreleased/dataset.zip | Bin 1932 -> 1932 bytes .../CY130078/unreleased/dataset.zip | Bin 1929 -> 1929 bytes .../CY130086/unreleased/dataset.zip | Bin 1944 -> 1944 bytes .../JN696314/unreleased/dataset.zip | Bin 1882 -> 1882 bytes .../CY006010/unreleased/dataset.zip | Bin 1991 -> 1991 bytes .../CY136630/unreleased/dataset.zip | Bin 1981 -> 1981 bytes .../CY103876/unreleased/dataset.zip | Bin 2014 -> 2014 bytes .../CY125945/unreleased/dataset.zip | Bin 1967 -> 1967 bytes .../CY028836/unreleased/dataset.zip | Bin 1846 -> 1846 bytes .../CY181241/unreleased/dataset.zip | Bin 1904 -> 1904 bytes .../NC_007362.1/unreleased/dataset.zip | Bin 1923 -> 1923 bytes .../KU143256/unreleased/dataset.zip | Bin 1899 -> 1899 bytes .../CY130030/unreleased/dataset.zip | Bin 1937 -> 1937 bytes .../NC_026425.1/unreleased/dataset.zip | Bin 1932 -> 1932 bytes .../CY136131/unreleased/dataset.zip | Bin 2035 -> 2035 bytes .../NC_004908.1/unreleased/dataset.zip | Bin 1832 -> 1832 bytes .../CY103878/unreleased/dataset.zip | Bin 1784 -> 1784 bytes .../CY125947/unreleased/dataset.zip | Bin 1788 -> 1788 bytes .../NC_007361.1/unreleased/dataset.zip | Bin 1700 -> 1700 bytes .../KU143347/unreleased/dataset.zip | Bin 1717 -> 1717 bytes .../CY130032/unreleased/dataset.zip | Bin 1753 -> 1753 bytes .../NC_004909.1/unreleased/dataset.zip | Bin 1716 -> 1716 bytes .../CY136632/unreleased/dataset.zip | Bin 1797 -> 1797 bytes .../CY136133/unreleased/dataset.zip | Bin 1868 -> 1868 bytes .../CY130080/unreleased/dataset.zip | Bin 1732 -> 1732 bytes .../CY130088/unreleased/dataset.zip | Bin 1735 -> 1735 bytes .../KC110598/unreleased/dataset.zip | Bin 1778 -> 1778 bytes .../CY181243/unreleased/dataset.zip | Bin 1720 -> 1720 bytes .../CY136096/unreleased/dataset.zip | Bin 1858 -> 1858 bytes .../CY028838/unreleased/dataset.zip | Bin 1645 -> 1645 bytes .../CY130072/unreleased/dataset.zip | Bin 1740 -> 1740 bytes .../CY005407/unreleased/dataset.zip | Bin 1798 -> 1798 bytes .../NC_026429.1/unreleased/dataset.zip | Bin 1722 -> 1722 bytes data/index.json | 752 +++++++++++++++++- flu-dataset-generator/config.yml | 2 +- flu-dataset-generator/generator.py | 67 +- 37 files changed, 802 insertions(+), 19 deletions(-) diff --git a/data/flu/HA/ha_h10_h10n7/CY136094/unreleased/dataset.zip b/data/flu/HA/ha_h10_h10n7/CY136094/unreleased/dataset.zip index 46124e9c121c3b2e44f25f36c8c98bf33a0dc6a9..2f97f56f752136f81e0ff84c5f62442337a14ba6 100644 GIT binary patch delta 58 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zcmaFM^OlDvz?+#xgn@y9gW-4eMjk~*reD>Y^%<{#X;$V%OiaJ4C$D6+1PV`n!s-N~ HG}v4L6_pda delta 58 zcmaFM^OlDvz?+#xgn@y9gMqtZBab2@6IaD%ea0(bnw5DG6BBpE2LLBcSe0C5M9B10z^-CVzUHMwQNox>L8md E0OF1k^8f$< delta 58 zcmZqUYvbby@MdNaVPIh3VBoFT$YaUK#9Oi1ol&2OiKk+71@j3eAb+wGn None: for ref_name, accession in config.HA.items(): - out_dir = Path(config.output_dir) / "HA" / ref_name / accession / "unreleased" - generate_dataset(out_dir, ref_name, accession) + dataset_dir = Path(config.output_dir) / "flu" / "HA" / ref_name / accession / "unreleased" + generate_dataset(dataset_dir, ref_name, accession, config.output_dir) for ref_name, accession in config.NA.items(): - out_dir = Path(config.output_dir) / "NA" / ref_name / accession / "unreleased" - generate_dataset(out_dir, ref_name, accession) + dataset_dir = Path(config.output_dir) / "flu" / "NA" / ref_name / accession / "unreleased" + generate_dataset(dataset_dir, ref_name, accession, config.output_dir) @click.command() From 14df83631f08e8fc47fb2abfa7b17753d6eb9afc Mon Sep 17 00:00:00 2001 From: anna-parker <50943381+anna-parker@users.noreply.github.com> Date: Mon, 26 Jan 2026 15:45:32 +0100 Subject: [PATCH 3/5] fix CDS name in gff3 files --- .../CY136094/unreleased/dataset.zip | Bin 2038 -> 2032 bytes .../unreleased/genome_annotation.gff3 | 3 +- .../CY130070/unreleased/dataset.zip | Bin 1932 -> 1926 bytes .../unreleased/genome_annotation.gff3 | 3 +- .../CY130078/unreleased/dataset.zip | Bin 1929 -> 1923 bytes .../unreleased/genome_annotation.gff3 | 3 +- .../CY130086/unreleased/dataset.zip | Bin 1944 -> 1937 bytes .../unreleased/genome_annotation.gff3 | 3 +- .../JN696314/unreleased/dataset.zip | Bin 1882 -> 1876 bytes .../unreleased/genome_annotation.gff3 | 3 +- .../CY006010/unreleased/dataset.zip | Bin 1991 -> 1985 bytes .../unreleased/genome_annotation.gff3 | 3 +- .../CY136630/unreleased/dataset.zip | Bin 1981 -> 1975 bytes .../unreleased/genome_annotation.gff3 | 3 +- .../CY103876/unreleased/dataset.zip | Bin 2014 -> 2010 bytes .../unreleased/genome_annotation.gff3 | 3 +- .../CY125945/unreleased/dataset.zip | Bin 1967 -> 1963 bytes .../unreleased/genome_annotation.gff3 | 3 +- .../CY028836/unreleased/dataset.zip | Bin 1846 -> 1840 bytes .../unreleased/genome_annotation.gff3 | 3 +- .../CY181241/unreleased/dataset.zip | Bin 1904 -> 1898 bytes .../unreleased/genome_annotation.gff3 | 3 +- .../NC_007362.1/unreleased/dataset.zip | Bin 1923 -> 1916 bytes .../unreleased/genome_annotation.gff3 | 3 +- .../KU143256/unreleased/dataset.zip | Bin 1899 -> 1895 bytes .../unreleased/genome_annotation.gff3 | 3 +- .../CY130030/unreleased/dataset.zip | Bin 1937 -> 1931 bytes .../unreleased/genome_annotation.gff3 | 3 +- .../NC_026425.1/unreleased/dataset.zip | Bin 1932 -> 1924 bytes .../unreleased/genome_annotation.gff3 | 3 +- .../CY136131/unreleased/dataset.zip | Bin 2035 -> 2029 bytes .../unreleased/genome_annotation.gff3 | 3 +- .../NC_004908.1/unreleased/dataset.zip | Bin 1832 -> 1825 bytes .../unreleased/genome_annotation.gff3 | 3 +- .../CY103878/unreleased/dataset.zip | Bin 1784 -> 1779 bytes .../unreleased/genome_annotation.gff3 | 3 +- .../CY125947/unreleased/dataset.zip | Bin 1788 -> 1782 bytes .../unreleased/genome_annotation.gff3 | 3 +- .../NC_007361.1/unreleased/dataset.zip | Bin 1700 -> 1693 bytes .../unreleased/genome_annotation.gff3 | 3 +- .../KU143347/unreleased/dataset.zip | Bin 1717 -> 1711 bytes .../unreleased/genome_annotation.gff3 | 3 +- .../CY130032/unreleased/dataset.zip | Bin 1753 -> 1748 bytes .../unreleased/genome_annotation.gff3 | 3 +- .../NC_004909.1/unreleased/dataset.zip | Bin 1716 -> 1708 bytes .../unreleased/genome_annotation.gff3 | 3 +- .../CY136632/unreleased/dataset.zip | Bin 1797 -> 1792 bytes .../unreleased/genome_annotation.gff3 | 3 +- .../CY136133/unreleased/dataset.zip | Bin 1868 -> 1861 bytes .../unreleased/genome_annotation.gff3 | 3 +- .../CY130080/unreleased/dataset.zip | Bin 1732 -> 1727 bytes .../unreleased/genome_annotation.gff3 | 3 +- .../CY130088/unreleased/dataset.zip | Bin 1735 -> 1729 bytes .../unreleased/genome_annotation.gff3 | 3 +- .../KC110598/unreleased/dataset.zip | Bin 1778 -> 1771 bytes .../unreleased/genome_annotation.gff3 | 3 +- .../CY181243/unreleased/dataset.zip | Bin 1720 -> 1715 bytes .../unreleased/genome_annotation.gff3 | 3 +- .../CY136096/unreleased/dataset.zip | Bin 1858 -> 1852 bytes .../unreleased/genome_annotation.gff3 | 3 +- .../CY028838/unreleased/dataset.zip | Bin 1645 -> 1640 bytes .../unreleased/genome_annotation.gff3 | 3 +- .../CY130072/unreleased/dataset.zip | Bin 1740 -> 1734 bytes .../unreleased/genome_annotation.gff3 | 3 +- .../CY005407/unreleased/dataset.zip | Bin 1798 -> 1793 bytes .../unreleased/genome_annotation.gff3 | 3 +- .../NC_026429.1/unreleased/dataset.zip | Bin 1722 -> 1716 bytes .../unreleased/genome_annotation.gff3 | 3 +- data/index.json | 18 ++++++------ flu-dataset-generator/generator.py | 26 +++++++++++++++++- 70 files changed, 68 insertions(+), 78 deletions(-) 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b/data/flu/HA/ha_h10_h10n7/CY136094/unreleased/genome_annotation.gff3 index 8ca1de6..5ea22c2 100644 --- a/data/flu/HA/ha_h10_h10n7/CY136094/unreleased/genome_annotation.gff3 +++ b/data/flu/HA/ha_h10_h10n7/CY136094/unreleased/genome_annotation.gff3 @@ -6,8 +6,7 @@ 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=AGG26198.1;gbkey=CDS;gene=HA;product=hemagglutinin;protein_id=AGG26198.1 +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 - diff --git a/data/flu/HA/ha_h11_h11n9/CY130070/unreleased/dataset.zip b/data/flu/HA/ha_h11_h11n9/CY130070/unreleased/dataset.zip index 3f620e360cb748f5ccafe85a45f3955a38ef4fb4..1b070953bc1cafaf0a6bb9a79c9a822b67698139 100644 GIT binary patch delta 711 zcmV;&0yzDQ4~7p6P)h>@6aWAK2mthau?#H%67+mJTqXFt2SEY=0K^0U02Tm~AqNqR2o8M)3i^PaSp+1VrRA~<=@W^P{u|#O;MD@ zdCz&?b8+2rv+-U)DkgY0>bM{5w`zdC9fqhEn)5~q3Q7stT};OFF5z70y<{3>$8{C_ z*a4^DNhod1e8phDC0zXTcLDb?C5i*psayw zgEqB_R{Ic!i$SKeB#h@H-^%<`YCnln--2&7;5-7n0it&j{%8d&y!X2?f0_;#^Vw>N z+p_WMaS{X}{&qjcfq9A0!{}6hSj`kYGj91PfrHbt@bK;ex2K-T(Kh-mmx+PQ{%ViR z6PpRNT`=3GfpJVl!FYL#GnuZgFoDI;LV2UvI0*)+(Pm2`ZFkS`Q>}J?@oYK#MR;w? zq|S^1(|Vn6p(bTn?KIcJT3+kqwTxrpKj zp(IWI$40O76HrS71QY-O00;o|e6zL#5Ca1Ae3QrqISurDI$S0Ayaz!7006|34hJ_M t^n5y8&-l$p;{pHxMh5@@4*&oF0000000000q=BT9WCtP!v<3hG007V4OWptg delta 687 zcmV;g0#N;i4~!2CP)h>@6aWAK2mtDPu?#H%4e5J2T>5y@_D2E$0M(O50Uv+cj@mE~ zhOfg@Q020UlaK=oQB-kQu~aHTORK6^mT`t)ZDOakS(dl29ZtI~+p3D9#P)c;|DPGx zEjJtQ8Kh!@ccYH`!LC&U^s*VEUTF3kDJUo0p0-7I|+Z3f)(ET)tEm{hl}}awZyG$y!t!| zf)IbdALGFMMCf63GFE>xMbC^|I!fT+^ejBQyTa|RXL7WKzT`4@AhSp9mic1Sfwl@} z+B7hZsVEpPZ*eBm)f-G;F|<(LXf{rQL26>NC6TteXZXphonJg#4qpYfvRQkKhdtU>HDu5jDWsvVDg@dD2@@6aWAK2mtAOv#5y@_D2E$0M(NS2R8!g Vdy_#290976UI!uux&{CM001B3OV9uS diff --git a/data/flu/HA/ha_h11_h11n9/CY130070/unreleased/genome_annotation.gff3 b/data/flu/HA/ha_h11_h11n9/CY130070/unreleased/genome_annotation.gff3 index 922a962..4d04d00 100644 --- a/data/flu/HA/ha_h11_h11n9/CY130070/unreleased/genome_annotation.gff3 +++ b/data/flu/HA/ha_h11_h11n9/CY130070/unreleased/genome_annotation.gff3 @@ -6,8 +6,7 @@ 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=AGB50960.1;gbkey=CDS;gene=HA;product=hemagglutinin;protein_id=AGB50960.1 +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 - diff --git a/data/flu/HA/ha_h12_h12n5/CY130078/unreleased/dataset.zip b/data/flu/HA/ha_h12_h12n5/CY130078/unreleased/dataset.zip index 6f216a23809deeacd35beead3058ca2094d16b06..8cfb5e5a95daaf9b937034cdfcfe8c89f79ed7e6 100644 GIT binary patch delta 710 zcmV;%0y+JO4}%X3P)h>@6aWAK2mtkbu?#E$67_sKT%rZP96$m90Kxuebr#3IYv3 zcOVJ~6;$rb_yvTWL-mHEFvszLXP`?-Hr|J zgi(il%mgdhz#rBtP==9e^$dr6sS47_nwrBF@)xdH?H5n;ArZ`k8>vlR?uuukp=v-F z3%A|MW9}nv&oiQpVqE0I$fZSZrK3(9IrKdT&NHBEU}mS_4=;Eber(6=X)>74rppCA z_Dz>x$8n75_lFUU?MsRthi`pK?yU91uu&Szeh6^spS(V+y>*>3*;FVxC-NM%J66k3;sa(^O>a2HAGnH$t(^SsF ze{1KYZecatLpH~O(6hu_WY+g^oFpGodk7_I`=8v4Esw*yZU0q+6_9$k)9-(zB1sd3 zvQGLxGTN@6aWAK2mthav$O*b0|NDYlf?!(4fT9FT%rZP96$m90K$_C2R9$| sd^%ibz_I$`0ssIm2LJ#M00000000000001_fufUP2O@6aWAK2mtGQu?#E$4eEP3T$p63S4IK=0MnC20U>{zFc5~X z$x~2qSz&O1oDiyVSY^|TDB4u2dSy8?A zz)=|X2MD|7>Eo`=F+~|Dcc*{#UX6m_cswGWZy4fLjX2w(QoID;=&RtOJ_QpgjtZpB z()1POCHumPEE*)qpxe2Ycjmx1ls`Ky*ujpaImr2J-o-4tW{xmIb}yZ6UL|ZZZAqiH zV7jC=WO2G-!mp{Z#AuaG9~Mt*56Asz=%u-+D#*1#_=QQx@UY)A!2^HS@{~;}rv)9k z<7xv^)3n??!zo+KJgr4V^l1;-3zM{R^QYxF$Rp^5;}RSp(MwZrq9{_YrrO zNvgD@jA!G(rUh@MgI*X|^t}$8XF#?<^+CcPycs@zOVIL!$uBf!FJ+t4O+UrZ^tI zjBcm%3s6e~1QY-O00;o;d$XU)zu S2OI&YlUoNO2Db(P0001=SwsK; diff --git a/data/flu/HA/ha_h12_h12n5/CY130078/unreleased/genome_annotation.gff3 b/data/flu/HA/ha_h12_h12n5/CY130078/unreleased/genome_annotation.gff3 index 9e8d09d..c2e3df4 100644 --- a/data/flu/HA/ha_h12_h12n5/CY130078/unreleased/genome_annotation.gff3 +++ b/data/flu/HA/ha_h12_h12n5/CY130078/unreleased/genome_annotation.gff3 @@ -6,8 +6,7 @@ CY130078.1 Genbank region 1 1712 . + . ID=CY130078.1:1..1712;Dbxref=taxon:385582;Name=4;bio-material=CEIRS#14739#;collection-date=1976;country=Canada: Alberta;gbkey=Src;mol_type=viral cRNA;nat-host=duck;segment=4;serotype=H12N5;strain=A/duck/Alberta/60/1976 CY130078.1 Genbank sequence_feature 1 1712 . + . ID=id-CY130078.1:1..1712;Dbxref=IRD:NIGSP_CEIRS_SJC001_WEB_00014.HA;gbkey=misc_feature CY130078.1 Genbank gene 8 1702 . + . ID=gene-HA;Name=HA;gbkey=Gene;gene=HA;gene_biotype=protein_coding -CY130078.1 Genbank CDS 8 1702 . + 0 ID=cds-AGB50971.1;Parent=gene-HA;Dbxref=NCBI_GP:AGB50971.1;Name=AGB50971.1;gbkey=CDS;gene=HA;product=hemagglutinin;protein_id=AGB50971.1 +CY130078.1 Genbank CDS 8 1702 . + 0 ID=cds-AGB50971.1;Parent=gene-HA;Dbxref=NCBI_GP:AGB50971.1;Name=HA;gbkey=CDS;product=hemagglutinin;protein_id=AGB50971.1 CY130078.1 Genbank signal_peptide_region_of_CDS 8 58 . + . ID=id-AGB50971.1:1..17;Parent=cds-AGB50971.1;gbkey=Prot CY130078.1 Genbank mature_protein_region_of_CDS 59 1033 . + . ID=id-AGB50971.1:18..342;Parent=cds-AGB50971.1;gbkey=Prot;product=HA1 CY130078.1 Genbank mature_protein_region_of_CDS 1034 1699 . + . ID=id-AGB50971.1:343..564;Parent=cds-AGB50971.1;gbkey=Prot;product=HA2 - diff --git a/data/flu/HA/ha_h13_h13n6/CY130086/unreleased/dataset.zip b/data/flu/HA/ha_h13_h13n6/CY130086/unreleased/dataset.zip index a0b60a6a8e2545e2c5fef3aa74b2b2cd455c1cdf..6d09e2c8c71d8e14bacc0176dbda1373409668a9 100644 GIT binary patch delta 712 zcmV;(0yq7b50MWHP)h>@6aWAK2mtncu?#H%683yLT(BGUhe84X0L26V02Tm~Ee9BX zm6F?z+At7?uftQM%4HQNCIJFgRB@>OP}fqq%jsm{G9jcsDy~6wJg>wP^6g5&XsM7H5blob+uhYI-|d|@wA z$m$eKlswj;Y?fv(C@c5}o~Ka~$HQUgD(}oeY?yd*&R_>SmgXSmz4PB&VppgDoA6p;nJ^|DT%W(oqk+AuDv8ohOtL7S(cD#gYa{ckmBKgU|@m= zq17qofB+{74cxpga2xfFM$_qwmbnAO9yKBJ zP0a|JHkftOzy-}@&P8#LGo7t(Frmd{dF_wqlOB$67h$qu%C@(Kzt(COn9f(DUlMO^ z8EIk+@6aWAK2mtGQu?#H%4eNV4T;65r z#$Sg|ktr{yI57zjh@y!<6=l*8Dx0RgvW#;CtBK7VQ_8oW9U5pix@kfo$>n^%=eax2 zE4Ewz2~^FcaHEd*!M@jfV3#09U2NieB^lJURPJ&*S-4aPsgH_lP#w>!;pYJa17AU5 z&rE;dC=8Q6!mjxZ;>hNhq8xu}cc=Bf9tFYictnD2I1*)r1mB@TJ_TRtvlOyA1rsHY zH7J{<=`&&l|HShwO5%7p>|Dz`a}XOU9-TAT!H%Ul$oXil#VosKjxa*@TRPi3E7)e* zl1Ar(>5^8E#p#AizoNzxr)4(1TRg12Bus{}moizFz_da5xk%`!GqB1lzm%| zNA4G@P9+t2T5KNSl&uv@D_IhK+C%ol6)j!%upFm?YJVqdofU_&Olv4A5Za)PSJ~v= z<7nAWYpp03**LIiL0dZ*gmGZew>r?yfNX*4gMvSL!E^upb}Sxdqvc}0UXjK(S%02} zAtvANCL}ZuJ#;^QaaMovnzf8uItmcrM4^G3zYE+(eN&_9^re!yJV!eq`xaf>sZt>0imi(z@~kLQyfj&K*@bVZeIZwr6%Y8RNySEE;njjUJiXL$y3 zQD+3@2d1+fRJ16{gXV&Zw3TUg^LqN`ba)|XN%pYUJO^@KS0Y!p+vt{r7!p6o4)_5!3Y?d0d@!Psfgkj zpwB}Y0~!MY>wA;U200Dudpca+W&Q0*0ssKklM@Fw X0_%H|Oa~kRtdnU6A_m3=00000Xv;v> diff --git a/data/flu/HA/ha_h13_h13n6/CY130086/unreleased/genome_annotation.gff3 b/data/flu/HA/ha_h13_h13n6/CY130086/unreleased/genome_annotation.gff3 index 0663a4f..533bbd4 100644 --- a/data/flu/HA/ha_h13_h13n6/CY130086/unreleased/genome_annotation.gff3 +++ b/data/flu/HA/ha_h13_h13n6/CY130086/unreleased/genome_annotation.gff3 @@ -6,8 +6,7 @@ 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=AGB51312.1;gbkey=CDS;gene=HA;product=hemagglutinin;protein_id=AGB51312.1 +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 - diff --git a/data/flu/HA/ha_h14_h14n5/JN696314/unreleased/dataset.zip b/data/flu/HA/ha_h14_h14n5/JN696314/unreleased/dataset.zip index 23691458e4bb56cb44fd48b7664511d42204b21f..3bfdb89c66d455ea85babad6557b49aca2da7e04 100644 GIT binary patch delta 604 zcmcb`cZH89z?+#xgn@y9gW-G4Mji)7p>H)-F)`nG7GGmzVEE6(z#zsj`8}INeQwa{ zzFP(&vF+E~Rf)Si0yD3w7R~8So_OO*S;L>dHx36_UDeS!{k`zq z&g114Pkz^yFy*#PdYEDG=fVAF9B=Xkj!G7NTpY&J6KJI~jo)8!YS7KiVq#wsEKEKu zXFjQL=|JuI?MXJ${Q+|6id+{}=Kqvp*E&$&vURJwvHzscKV`hbx+2VSbzEhOOTFqY zbx&ILb~5|gb8K7IZ~7u+thcYDYe9+C+$9+W$NA+Pr-jHhX%{yz`HLSpm|i|F>`9!Z zd*PeniqJTdH=SQYK8L%+ToCihGOovnj+Rpf&V3-~0`X_nNl&E#K_6H(_mHT+hahv$#CPPX4z& znV&dglG_QErT4clmOLf2{)a95TtAKrS0raVEoZJZiPB$}%C%`kmR>g9kP^VAdE2gb}D?RJVb^&4%!Y3P)h>@6aWAK2mtJRu?#=~4(xk6T$YQMW847%01yL{S^*}1aK)xo zm4`#bE3zsEs+s8`MWt1j$Z;-?MPgIi0rK~?VHl>>EUc^hJm((Y;gIik;SsbEN}|zV z_`&<;0PHo0qZGUNK`REvD2A3tbyGN65xrRRuo@kLYw zC)4R9!Grt!;1Og=K@@y;?|DV;m2(_LK9{e`vxXh99%}wFF)wHfB+Hp< z8ekTxu7-GYSx-1C#<{VY3P~36|2^?ELLT;I=gyiqxELWR-n3)3#~W)m7armW#@6aWAK2mtqdu?#u^68C&MT#@8wfK~zk0A2+E02Tm~Tn89` zom5?Kqc9MBroVzy9#0quNeDscL{h2kOBA&yo$d)aupw5#=4>Z4|Nhn?X__9rFCjoI z>zUcvwFiT8vvKwy6%*VJZU&#sw`w4N4fO*t33l}v-Y84MKs z*a6SMkx-g7i|?K{@qCZ?HeTT*FgXZ+%0Ss$ts6CS-L`EB&)1CbswSLmNh$X3SNbBj zs1NR3idKO%S(?6(ykuWkkp$!6c;ek$;H^90Ys#Okj@a@o!)6idGu{uk$t82<6Jq|w zx9b-Pn?xI?SqB&|X${FJ&P7#0t`W#7sD{Lk!U%&quH_*~cS=iIF*>uqfx^0fx&0c7 z%k?uHk|&wRwWuAJleEwDz;%cHICRFn0;=4^{M1H6nzRx;9w1h*p*;(VKq_bKJ9GBcL#-Q5EUQC z5WW$$a|dTn1LIjPOdWkZi`%Cw8qd(=g>usQd^+`mDe>bKmB#fm`DqT!G-r3K*_*^` zSqL4YfMS>HWD7Md%W9_?XFNX3!oj?(?o+2&$!V1}&}ddb*3D`rHrYvLb~wK3$OY`! zk?C3ayLvi#D-_YkSyR1}kexMNbA}Vk_a@U1StCM%QS?XNS6}Ya-nxIQ0R=>+Vg5%d zg0V-)IQ0HS#_+GVK{y(n&kCn^FJQvy#Q5(G@e@!>0|XQR000O8_k6S111SRn_k5EB z2RRM*d^%i_@6aWAK2mtMSu?#u^f9-oZT<#9c$Xo&d0B;2V02TlM0B2=x zZ*65?VQy}3bYXO9Z*DGUW@a;;RNHQ&Fc5tvU%@JmD-47XLJ(S!RBHPYMeRzfeL{|z z5UXIbwiBAaUpwT|bm`uN05OcuIdf+0;jr9noIMChIkSVo@RRwL4UkLFMbjYI2_@zF1rF)6AW6-uTpb!n_f-F~$VdVXbjL~0ji)cJPpB+x`7v9hbrxWDA zH^|^8P)h>@6aWAK2mtJRv(f`80|M=Pll=xc4efh6T<#9c$Xo&d0B@5+2R8!jdy{+z R90AOenFk^U^#%X{008MxRj~j7 diff --git a/data/flu/HA/ha_h15_h15n9/CY006010/unreleased/genome_annotation.gff3 b/data/flu/HA/ha_h15_h15n9/CY006010/unreleased/genome_annotation.gff3 index 3cad754..d99d9d9 100644 --- a/data/flu/HA/ha_h15_h15n9/CY006010/unreleased/genome_annotation.gff3 +++ b/data/flu/HA/ha_h15_h15n9/CY006010/unreleased/genome_annotation.gff3 @@ -6,9 +6,8 @@ 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=ABB88138.1;gbkey=CDS;gene=HA;product=hemagglutinin;protein_id=ABB88138.1 +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 - diff --git a/data/flu/HA/ha_h16_h16n3/CY136630/unreleased/dataset.zip b/data/flu/HA/ha_h16_h16n3/CY136630/unreleased/dataset.zip index 026d40584bb9af4e5c950c4077a1161b00918fbf..19f5fffb0f3d5b25f84ff3afd4a8c67ddd4d5a8a 100644 GIT binary patch delta 731 zcmV<10wn#t54R5tP)h>@6aWAK2mtteu?#l>4)}aJT!;+pyJrFb0R04$Q2`x)lHHD* zFc5{W$x~2q)2hN?U`Yr`ujGX@ULBpO z;0Fn!jZ)+VWd;32^8|Y%KNxz0OMPPjY)jaaaZ)z0(aIUf_^9vYJh?=UF+%OXc)ooR zuuD`cH9l92SEPa@h_{s6712#mQYN#{%g2p{gCKB2E6#XXLZ-Bco$H8y1V{E4a+f2sh97=K^0^(x(1jl3}vbZE$d(WjxK4Y^cQj!AR%MWqI%Tyg}NS>)6 zrI|ghCNU%G6k3v|*i%-RMN^isgrWkbG@^EecS-j+T=}t7f>4%BoU3@JhcKt)=;$6J zrv<%bTtB;X2Shaj{;-gL=JwkzE+6OP)pD^}r=45r=3(Z#IDMGTQrEq6N9cZX_MxIO z>osn16u`jnd@b&|7xDJg)-}5Myw=h=+Ft$Wj`Ta#gX>JuYpQ^DU;+D>AzPXZd zTbV4E_GGc}!YB$6j@Q~bZFVny?zLU~bg>@)5_pZJOUD`@Z!(pC?4cq>Q8tP)%HkeN z@9-u2<}_%*NSW49E1E-k+Uk_=(lhojx*E)-ST~rcC;zRV6W&@w+|sPNnWR1AwdTk* zup5ltQuSPf{J{IC?yE2Nlbe12l|chUdSH0?7KI=92;GHu|AXNTegaTS0|XQR000O8 z_O(3n=ryuF$Pu3o1&~Q+vGAQ{r)!{tBjxn{_zt%MTcB zU={H_`-J`5;S1%0W?wIV|EuP1zO-K9?AoBMGFIp6_Pgsu2Ol}bWw^_gwZ3rQ#PD+! 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ID=CY028836.1:1..1725;Dbxref=taxon:387222;Name=4;collection-date=1963;country=USA: Florida;gbkey=Src;mol_type=viral cRNA;nat-host=Equine;segment=4;serotype=H3N8;strain=A/equine/Miami/1/1963 CY028836.1 Genbank gene 11 1708 . + . ID=gene-HA;Name=HA;gbkey=Gene;gene=HA;gene_biotype=protein_coding -CY028836.1 Genbank CDS 11 1708 . + 0 ID=cds-ABY81492.1;Parent=gene-HA;Dbxref=NCBI_GP:ABY81492.1;Name=ABY81492.1;gbkey=CDS;gene=HA;product=hemagglutinin;protein_id=ABY81492.1 +CY028836.1 Genbank CDS 11 1708 . + 0 ID=cds-ABY81492.1;Parent=gene-HA;Dbxref=NCBI_GP:ABY81492.1;Name=HA;gbkey=CDS;product=hemagglutinin;protein_id=ABY81492.1 CY028836.1 Genbank signal_peptide_region_of_CDS 11 58 . + . ID=id-ABY81492.1:1..16;Parent=cds-ABY81492.1;gbkey=Prot CY028836.1 Genbank mature_protein_region_of_CDS 59 1042 . + . ID=id-ABY81492.1:17..344;Parent=cds-ABY81492.1;gbkey=Prot;product=HA1 CY028836.1 Genbank mature_protein_region_of_CDS 1043 1705 . + . 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@+J}0Jpn~#Rj)k z^rAOYy5?%8l%5Out-My{(rCDateXMhv&6T^Ue}4j`0ib5AE7wu{gZoX%fskq*?-kw z1Ptu_lJ``^Ns3S}?f;LAZm07LP)h>@6aWAK2ms}Kv$+Ed0|MoHlg9=*4dr_}T%C-R zcT55R0OFGk2R9$(dpcb34i4Gh0ssIx2LJ#M00000000000001_fwPli2O@6aWAK2mtYXu?#H%67YOFTy!AxO+x|z00jjA02Tm~AqNA!KoE zpZ9rR&S1dy``{6j=2G~{)!>W!)-BN2B1SQ`^;Ss=T1(|`7T0T^2qDc;aRcgVFwpRD z06`&8z}%h9qKM*A8V?cn?K6%h?vU+&%0c^;F|D43;qiDxg6=pHb%O-25R;GL9eI*M zHmC4f$)g74P8srqDC6IGnd2mh<21c`C*a+}ehUv?C+%U+$$7~8YTxxTe|K_*5ptW^ za`&WQpBtw&duf?%NCSDAQCZhOjcpZ_#6TVmgI`1iafB1QcMwLM@Fs8o31WguYLl;IBYjO;4nk)(L&#gAHDTbFURKi4XgoSERW4VJ~vy9H`7cTMYzc4;kF`zRfLC896GkXL@W=uJVuk`Ee}@=?zW>* zp;Ol4a~3~sdA*#)369b@9(QSftmZE!-L7-lmF!yVct>T&!T=Wql_eJ}t0g_?!Vs3f zN%WyDmfQDakt3s}4u0PhQ8dMPl8)`^?1m_p!spD_MBL9lUix;~idF8V%&e30Kuumj zLl~<-hn-@wbiygm<8=j80TCyNgM z#`5$@H^dwi6ldIz(!-&LBRsySK1C==rvIe>8r5o!`vaQ9{Q+I1w1^Wo6452jB#jUn zj-vksjXwcREa)FlO9KQH000080PuXXx&sUY0`Yv4$ObtL@O(O4bRhIiLjnK*1(Oa3 vHy`kPI$X!37!Kb8001xt000jF0000000000005+crjuj`A_lSs00000d<8%U delta 691 zcmV;k0!;mc4~!2CP)h>@6aWAK2mt1Lu?#H%4d#0~TsgJEO-lj*02-4<0Uv)$Z=*02 zh1cX)Fv@a#IhdUgy z{XVz{rMVP-Iv9R)-@1k3rHH}=*?OyF0a{DtZvYE2pVB^b(UJ@@6aWAK2ms}Kv$6vW0|MrIlfVW!4d#0~TsgJEO-lj*02-49 Z2R8!cdy_v0909JATn8csx&{CM005X~MDPFr diff --git a/data/flu/HA/ha_h7_h7n9/NC_026425.1/unreleased/genome_annotation.gff3 b/data/flu/HA/ha_h7_h7n9/NC_026425.1/unreleased/genome_annotation.gff3 index 4475a6e..0479d6b 100644 --- a/data/flu/HA/ha_h7_h7n9/NC_026425.1/unreleased/genome_annotation.gff3 +++ b/data/flu/HA/ha_h7_h7n9/NC_026425.1/unreleased/genome_annotation.gff3 @@ -5,8 +5,7 @@ ##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1332244 NC_026425.1 RefSeq region 1 1708 . + . ID=NC_026425.1:1..1708;Dbxref=taxon:1332244;Name=4;collection-date=05-Mar-2013;country=China;gbkey=Src;genome=genomic;mol_type=viral cRNA;nat-host=Homo sapiens;note=passage details: E1;segment=4;serotype=H7N9;strain=A/Shanghai/02/2013 NC_026425.1 RefSeq gene 1 1683 . + . ID=gene-TS66_s4gp1;Dbxref=GeneID:23104227;Name=HA;gbkey=Gene;gene=HA;gene_biotype=protein_coding;locus_tag=TS66_s4gp1 -NC_026425.1 RefSeq CDS 1 1683 . + 0 ID=cds-YP_009118475.1;Parent=gene-TS66_s4gp1;Dbxref=GenBank:YP_009118475.1,GeneID:23104227;Name=YP_009118475.1;gbkey=CDS;gene=HA;locus_tag=TS66_s4gp1;product=hemagglutinin;protein_id=YP_009118475.1 +NC_026425.1 RefSeq CDS 1 1683 . + 0 ID=cds-YP_009118475.1;Parent=gene-TS66_s4gp1;Dbxref=GenBank:YP_009118475.1,GeneID:23104227;Name=HA;gbkey=CDS;locus_tag=TS66_s4gp1;product=hemagglutinin;protein_id=YP_009118475.1 NC_026425.1 RefSeq signal_peptide_region_of_CDS 1 54 . + . ID=id-YP_009118475.1:1..18;Parent=cds-YP_009118475.1;gbkey=Prot NC_026425.1 RefSeq mature_protein_region_of_CDS 55 1017 . + . ID=id-YP_009118475.1:19..339;Parent=cds-YP_009118475.1;gbkey=Prot;product=HA1;protein_id=YP_009118482.1 NC_026425.1 RefSeq mature_protein_region_of_CDS 1018 1680 . + . ID=id-YP_009118475.1:340..560;Parent=cds-YP_009118475.1;gbkey=Prot;product=HA2;protein_id=YP_009118483.1 - diff --git a/data/flu/HA/ha_h8_h8n4/CY136131/unreleased/dataset.zip b/data/flu/HA/ha_h8_h8n4/CY136131/unreleased/dataset.zip index 8a97d3620c9e8fa7a725519c8c19191ca2994f6d..681be11cb8cc2a7f827b67371985fa9a82623537 100644 GIT binary patch delta 743 zcmVOP)h>@6aWAK2mtbYu?#!`4e@+BT>bOL?~4Ke06&ve0WE*r2n|G0 z6`*BNwFp7?p-+*M9D=opo!SPLzpu?@S+;DeDvA=@$1`(g>~_0ctvXu}l5&RpR{Nb9 z%Lel2Nf&#ro^J%tK}s&rY&4uA!WdUOK^2HryDj0@23QUq0j1e9`sw;T*LSgt^z+&6 zn;H#DL87%%jU3qaZnwiM&nSOpRgD>4T{zPt zB?x74V!xJQPnmH*M}2?9vQHK)9NTl8{w?><2OwPmQ5yk&_cTcY+{IzI&2!V9;V>}ZHX#?MfC3q)q=Fr~k# z4*%ee_ErI9Y0eAE%3Cy}@$w~$V_5P+c9O}&>v=&JyV0BoWBPxY`_!qqJLzOTcu{z* zN+U;_zu4p|UPDdFvf3!hD2vXj^fkEbzL^Cr8L83+8l_K2db}7ZU!_OYL3owQ1?!l~ zS@^4Vj_T%G!!64C5J-BKcug7fE!Xk;Z?c9M``zw8d7o{$OK!IPR}HSybxdBtTPpl+ zfN{|4{f`W<^&1ROO9KQH000080P%dY4+I_q0`h#5F9$gd@q9X5{qx4}ivj=uKa+I_ ZHv;i|ldcCG0{sJ%%m*O`8wUUY005+eR&4+P delta 749 zcmV@6aWAK2mt4Mu?#!`4d;70T)hYKfRO?K08o=v0WE)AAT$s~ zRe+X7)glDlhdxCnIRtAHJGBige_uP{vb$wlRZ*1KKAxE~W4GJ+X4Bb&kd!mjZMEN- zv8*7yOuE=}^?W6G3Q}@`=Ht-}5yrSW2&zD|+HDEHcED2T2*}Nz@lUtgce^fjk$yhA z15=|xDM++cs**$7J{%61rE7nRSy5s}w>al}`v-aAjF(4yB=|vsFja~?;WVdTXcoDi z7X-b2>xyqpfvpL9v>Im1wG5qwtxx)$O`>b%(8buSg_HG@fK8+f)$oKE&PfSTFI-dJ zDT!{1k|G*^oh?`G!RS74ok2TH`Hm@Zj2>3;5XA+Nk0i|3k8q4uA`O2FvhHlTRMFBw z6_JwU@IihIOI{@ESV6R>f)prS&f|~~)s!+W)D{Fo6=jOh;(d37a$p$oFfOH&tnn8xvNA$pG9hN#GzBwsF-v|}P7#T{)OJGWOrw!$`n7d%E zM@kUNqS$^d!=5qYfR2B3&f8JUmXqOpHeD@} z+VW&PTR6U-#NWNdaXin#ck#*TlFIbVaZ87G53E3QJHeIPOm;Lxo$&=qZ-LM()l>SL z=-ASg4;j_Y8 z)w6MVv^>fBz%)JUHHL^ zl&)A!O6Nviwb!UzXbrb0%Q~RsEb%3!Kd@YgBdy^>#ISuD~I$XU6@_>;7 f002;vZwEI5=6jQ<2OI(e1e3-GAqF7_00000x?x_a diff --git a/data/flu/HA/ha_h8_h8n4/CY136131/unreleased/genome_annotation.gff3 b/data/flu/HA/ha_h8_h8n4/CY136131/unreleased/genome_annotation.gff3 index 7512472..8fcfae2 100644 --- a/data/flu/HA/ha_h8_h8n4/CY136131/unreleased/genome_annotation.gff3 +++ b/data/flu/HA/ha_h8_h8n4/CY136131/unreleased/genome_annotation.gff3 @@ -6,8 +6,7 @@ CY136131.1 Genbank region 1 1719 . + . ID=CY136131.1:1..1719;Dbxref=taxon:1228846;Name=4;bio-material=CEIRS#9BM8109#;country=USA: Alaska;gbkey=Src;lab-host=R0 passage(s);mol_type=viral cRNA;nat-host=northern pintail%3B gender M%3B age hatch year;note=Sample provided by University of Alaska Fairbanks;segment=4;serotype=H8N4;strain=A/northern pintail/Interior Alaska/9BM8109R0/2009 CY136131.1 Genbank sequence_feature 1 1719 . + . ID=id-CY136131.1:1..1719;Dbxref=IRD:NIGSP_CEIRS_CIP055_AK2_00220.HA;gbkey=misc_feature CY136131.1 Genbank gene 8 1708 . + . ID=gene-HA;Name=HA;gbkey=Gene;gene=HA;gene_biotype=protein_coding -CY136131.1 Genbank CDS 8 1708 . + 0 ID=cds-AGG26254.1;Parent=gene-HA;Dbxref=NCBI_GP:AGG26254.1;Name=AGG26254.1;gbkey=CDS;gene=HA;product=hemagglutinin;protein_id=AGG26254.1 +CY136131.1 Genbank CDS 8 1708 . + 0 ID=cds-AGG26254.1;Parent=gene-HA;Dbxref=NCBI_GP:AGG26254.1;Name=HA;gbkey=CDS;product=hemagglutinin;protein_id=AGG26254.1 CY136131.1 Genbank signal_peptide_region_of_CDS 8 58 . + . ID=id-AGG26254.1:1..17;Parent=cds-AGG26254.1;gbkey=Prot CY136131.1 Genbank mature_protein_region_of_CDS 59 1039 . + . ID=id-AGG26254.1:18..344;Parent=cds-AGG26254.1;gbkey=Prot;product=HA1 CY136131.1 Genbank mature_protein_region_of_CDS 1040 1705 . + . ID=id-AGG26254.1:345..566;Parent=cds-AGG26254.1;gbkey=Prot;product=HA2 - diff --git a/data/flu/HA/ha_h9_h9n2/NC_004908.1/unreleased/dataset.zip b/data/flu/HA/ha_h9_h9n2/NC_004908.1/unreleased/dataset.zip index 3f0e0f61566e2a8ad843d763dbda34d1f42ff39f..82ffe96e87ffab7d8c9ec54065076e62605fa337 100644 GIT binary patch delta 628 zcmZ3%w~&t~z?+#xgn@y9gW*%nMjmZOp-(kdF;|u@sd~)Fz|hCcz#zsjc`utpeQQu` z{w)KMTE6{C!u`z0)ij?tUp#W$Y*CqHbJ?YNiv;wJX>DAY%k}5?&D0Q)Repgn2oZ^j-+S<3&qeV+U`TzW;EW0Td92hy5a0bU;F@_a_ypTxYFn`ME$8GPPB@n`HNe13p*AvN>XoF}7l)sT7A&u{HxzVO zwXHb1p#FH^Jx`GfQaj9iyiQO0xaEB>>+*MNe^#)3uhH+iSDYVl@T0Z(Gu>PN%D!Lt ze^abWZ1V#xsst342x?X)2tx z#&v6Gt6pZ6>X&&JA7*?zroPQ?b!*o1$x3@VH{5qtnK|WBTm1+5-}b*huGf(Mw=*;K zPR!y?kwUYXNj;tdu?|Pxvxx^twEoa_`Lp5j?zThO8d@6aWAK2mt7Nu?#B#4d;70Ty9Y%RO$f$0HBjZ0V;ok#3m`^ zL(#;?wnXhR2JNIhMIl^_Rbo@y6!`bG%Rm&+rYNy;?)ACn9J|>hi$(htgruC=UZeTR z{L3{|ClEUwtnszr6-dd2oeu|@T{6biR!{|^(QHb1*#N7cEr6Ik`LIC94^iM?TR%PQ znUB}$jNh8TVhS(TVX}oSGtF|W&-%?q$ysNF9mf>o(QGGRktj1NIxxn0SwrH-WcCdE zWGbqdfR+Kt`$DU@=Bq;O*C)W9WtWK3U_V{_nb)jUw!KQ5bd)4wmI#3#Mp1 z93Z_GGs@o$=z~;1SyAyhWh7qlY9k9(lH_X8Euq8F^n*@hbXIfO&c{V?7b36c;CNgL z6T*Mw|LjMHz=%pp&BpHv;E- UliUUz0ZWtl1|kMl1^@s60Ls7*4*&oF diff --git a/data/flu/HA/ha_h9_h9n2/NC_004908.1/unreleased/genome_annotation.gff3 b/data/flu/HA/ha_h9_h9n2/NC_004908.1/unreleased/genome_annotation.gff3 index 22cd32b..97bb398 100644 --- a/data/flu/HA/ha_h9_h9n2/NC_004908.1/unreleased/genome_annotation.gff3 +++ b/data/flu/HA/ha_h9_h9n2/NC_004908.1/unreleased/genome_annotation.gff3 @@ -5,5 +5,4 @@ ##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=130760 NC_004908.1 RefSeq region 1 1714 . + . ID=NC_004908.1:1..1714;Dbxref=taxon:130760;Name=4;gbkey=Src;genome=genomic;mol_type=genomic RNA;note=subtype H9N2;segment=4;strain=A/Hong Kong/1073/99 NC_004908.1 RefSeq gene 32 1714 . + . ID=gene-FLUAVAHHH9N2s4gp1;Dbxref=GeneID:1460996;Name=ha;gbkey=Gene;gene=ha;gene_biotype=protein_coding;locus_tag=FLUAVAHHH9N2s4gp1 -NC_004908.1 RefSeq CDS 32 1714 . + 0 ID=cds-NP_859037.1;Parent=gene-FLUAVAHHH9N2s4gp1;Dbxref=GOA:Q9ICY5,InterPro:IPR000149,InterPro:IPR001364,InterPro:IPR008980,InterPro:IPR013827,InterPro:IPR013828,InterPro:IPR013829,UniProtKB/TrEMBL:Q9ICY5,GenBank:NP_859037.1,GeneID:1460996;Name=NP_859037.1;gbkey=CDS;gene=ha;locus_tag=FLUAVAHHH9N2s4gp1;product=Hemagglutinin;protein_id=NP_859037.1 - +NC_004908.1 RefSeq CDS 32 1714 . + 0 ID=cds-NP_859037.1;Parent=gene-FLUAVAHHH9N2s4gp1;Dbxref=GOA:Q9ICY5,InterPro:IPR000149,InterPro:IPR001364,InterPro:IPR008980,InterPro:IPR013827,InterPro:IPR013828,InterPro:IPR013829,UniProtKB/TrEMBL:Q9ICY5,GenBank:NP_859037.1,GeneID:1460996;Name=ha;gbkey=CDS;locus_tag=FLUAVAHHH9N2s4gp1;product=Hemagglutinin;protein_id=NP_859037.1 diff --git a/data/flu/NA/na_n10_h17n10/CY103878/unreleased/dataset.zip b/data/flu/NA/na_n10_h17n10/CY103878/unreleased/dataset.zip index 3ffcdc69a72505964dc48535df9f26f33c729a1f..4fd1e37a28fa39702d11128b4bf54c9ee0a3b9e6 100644 GIT binary patch delta 634 zcmV-=0)_qf4f72QP)h>@6aWAK2mlFvu?#^04G4WYTsO;XGW!7l05X$W0Uv+MZrd;r zJj-9f!pN!6J8lvaMBylDngTHbyO*8}idxG=DAFaV$ol&(orfDBAOu3QyED7Pole{B zHhu={q|v0DOuvMGw+HbK=1GwwzPCnzbH$n&;nc{|fU=MtZi!8gsK(DAVJlv=6bEf&MOoIiVnT|a|RGg#dv*P4=Kx3Tl=qcVW z24M}*5IRD5Z)*9{7_OEFsW-wjQn#P!R5$AnGFgxjjf)pQs&aN-WJyjRxeWuqiNC&b zSk}$ms4fqWVP)h>@6aWAK2mkHyxOrk<`FMFyS=Qg!)?9O%w`S-hSfiek2mgRFl&bcRdI&HVx z_!+E|Mw4W*-&jUTM^U?InP24HkIJW&ijA8TcqhQ42c%COtk6}Eq6(4p3~p_#c0!w>6JBu0~@kD ze@R3uzsrW@c`+}~XOmO^=oWO%^;2|Yj`AqbMM?A(&)qdUWiIk02{C$IzgXBZAE*|u z9qEd9z`jvolmg+gQ`~S5?4FNtk!5oX^xE5z-S!A~T=50DQRJ7Y4Q+qxCm7k<3M!pZ z{7~#nZv`-my|^N7;5F@x+W2t~>{(jG#N%p7HTUt(IM3F;w;FMxq>_DiR$h@7bOV;$ zQ#2Y_WxBlr59H12v!WuH;fOGLD{Ti2sYmj-tZw3m>XABVJJ23SLKn?}_h){w$}{S` zwleYj8G=S=finFb3!GaWTTRGg#dv*P4=Kx3Tl;3?im zgRll@2pu52H?=$p!`1R2^+uRR>h?39>U#YjO%`ZGVeujHAnU{XC=V&#)uEuK7oKV8E$^h34R=7_Wa1v4swWPUe^5&U1QY-O00;p6 zd$WE6uL1%9e3LH*ISl}OI$RWEPTc?k002Xibp|&A{d<$H1{?u*lgkDo1||jo0000l C4IL@~ diff --git a/data/flu/NA/na_n10_h17n10/CY103878/unreleased/genome_annotation.gff3 b/data/flu/NA/na_n10_h17n10/CY103878/unreleased/genome_annotation.gff3 index 8e396d5..493c7b9 100644 --- a/data/flu/NA/na_n10_h17n10/CY103878/unreleased/genome_annotation.gff3 +++ b/data/flu/NA/na_n10_h17n10/CY103878/unreleased/genome_annotation.gff3 @@ -5,5 +5,4 @@ ##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1129345 CY103878.1 Genbank region 1 1390 . + . ID=CY103878.1:1..1390;Dbxref=taxon:1129345;Name=6;collection-date=May-2009;country=Guatemala: El Jobo;gbkey=Src;isolation-source=rectal swab;mol_type=viral cRNA;nat-host=Sturnira lilium%3B gender M;note=Complete sequence%2C ends confirmed by RACE-PCR;segment=6;serotype=H17N10;strain=A/little yellow-shouldered bat/Guatemala/153/2009 CY103878.1 Genbank gene 24 1352 . + . 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ID=NC_004909.1:1..1418;Dbxref=taxon:130760;Name=6;gbkey=Src;genome=genomic;mol_type=genomic RNA;note=subtype H9N2;segment=6;strain=A/Hong Kong/1073/99 NC_004909.1 RefSeq gene 1 1404 . + . ID=gene-FLUAVAHHH9N2s6gp1;Dbxref=GeneID:1460997;Name=na;gbkey=Gene;gene=na;gene_biotype=protein_coding;locus_tag=FLUAVAHHH9N2s6gp1 -NC_004909.1 RefSeq CDS 1 1404 . + 0 ID=cds-NP_859038.1;Parent=gene-FLUAVAHHH9N2s6gp1;Dbxref=GOA:Q9ICY2,InterPro:IPR001860,InterPro:IPR011040,UniProtKB/TrEMBL:Q9ICY2,GenBank:NP_859038.1,GeneID:1460997;Name=NP_859038.1;gbkey=CDS;gene=na;locus_tag=FLUAVAHHH9N2s6gp1;product=neuraminidase;protein_id=NP_859038.1 - +NC_004909.1 RefSeq CDS 1 1404 . + 0 ID=cds-NP_859038.1;Parent=gene-FLUAVAHHH9N2s6gp1;Dbxref=GOA:Q9ICY2,InterPro:IPR001860,InterPro:IPR011040,UniProtKB/TrEMBL:Q9ICY2,GenBank:NP_859038.1,GeneID:1460997;Name=na;gbkey=CDS;locus_tag=FLUAVAHHH9N2s6gp1;product=neuraminidase;protein_id=NP_859038.1 diff --git a/data/flu/NA/na_n3_h16n3/CY136632/unreleased/dataset.zip b/data/flu/NA/na_n3_h16n3/CY136632/unreleased/dataset.zip index c192d648951aa4d3887a757049d9b252fbaf562c..c180147a00a5680b3a50cec6adc8457b233932a9 100644 GIT binary patch delta 609 zcmV-n0-pVa4uB2}P)h>@6aWAK2mt+ju?#o?4gGvNT#wH`zX<{W0DO~C0WW_Gv7(C0 zie;rD1nongBF7nmwTVq_hs)o00?V?iQbmcC@tHYi&Wz`kn~lE*ZG@6;x8r?k|IH5g zTaW}X!T3%q4#p_$E+*r-%cNBHpoIn9@jL^68ju`(4P~1%`Axe0em4$?i%&0(TMQNz zVBD>>JClUr;cy5f&qW}sI*@;28En;HCI3ij>5IZto%P z-0C|skU5ht&V|__PD|$m&R2Zr)AWW+ND#DlbebPEY*O1&C9f6fg4K}rX)cssGi*w* zDxEyeS8I>-dcCOcQLd^AxJ44bKtxK0{ttHY$#C$1ca60Al>SVA6`YcV|EI$$6?qCy=UBYcG(7)Z8ZF2p(y zlf`_tUS?;vvi0*Mib#L@6aWAK2mthZu?#o?4fK0DTmg1Sz77Ha0F9GT0WW{M5Lp$3 z6=kI&1nongBI69f+Qg=|!{zTg3CpD_Rg^>?pP6&!%y?e0+4y_VMkwiaJKl%pY<9q} zK@!9S<2$W57^Ad1PscNtNvZ5X3k$mAc?N#hAUXINiY6!hMY{cdHx7u4PcM!e3>Fn& z+^w}cGYrGS;Sfl^7J)3QK#G5DP^f+QgB_Jr)hQfnbugeClx4?&7vihPDT$xEy{EWy ztM5!fu9M0{f}pueChMby4Ydu`@V#O(XBE(XvKGp(7&awX zNz<3va^;a;uNU>bgsZXyZjr>#5kbko|ISW689YDXT`jFX(Vwf)(4Buk$qr0IQmo(L zL|2+8C0qMjWh{Lm?v5G53ixO~C6y{Od)fir3(ZQGFXy8~GJA%WtS+`f7H(0OWn!SH zKw6ZDuBbNY8|lxxiLsgqNk`#d`0yga9kWx2Jr2S~=p*AUv&%NXY^~uR3q|h#-^JN- zGMvw*t3}qjm91XWC?bE^>p0D#=u7k*U`uBoDq;AAXIqi@-r&L0d=O9KQH000080Q7sa zg9En$0`z;6JO()p^m{s70d`2f4gvrGjgx`~Hv;r~le-2S0eq9#1|kMC1^@s605>)i AqyPW_ diff --git a/data/flu/NA/na_n3_h16n3/CY136632/unreleased/genome_annotation.gff3 b/data/flu/NA/na_n3_h16n3/CY136632/unreleased/genome_annotation.gff3 index 9c6397b..c12ff23 100644 --- a/data/flu/NA/na_n3_h16n3/CY136632/unreleased/genome_annotation.gff3 +++ b/data/flu/NA/na_n3_h16n3/CY136632/unreleased/genome_annotation.gff3 @@ -6,5 +6,4 @@ CY136632.1 Genbank region 1 1422 . + . ID=CY136632.1:1..1422;Dbxref=taxon:1283472;Name=6;bio-material=CEIRS#144406#;collection-date=19-May-1987;country=USA: Delaware;gbkey=Src;lab-host=E1 passage(s);mol_type=viral cRNA;nat-host=laughing gull;segment=6;serotype=H16N3;strain=A/laughing gull/Delaware Bay/2839/1987 CY136632.1 Genbank sequence_feature 1 1422 . + . ID=id-CY136632.1:1..1422;Dbxref=IRD:NIGSP_CEIRS_SJC001_JBC_00508.NA;gbkey=misc_feature CY136632.1 Genbank gene 4 1413 . + . ID=gene-NA;Name=NA;gbkey=Gene;gene=NA;gene_biotype=protein_coding -CY136632.1 Genbank CDS 4 1413 . + 0 ID=cds-AGG26999.1;Parent=gene-NA;Dbxref=NCBI_GP:AGG26999.1;Name=AGG26999.1;gbkey=CDS;gene=NA;product=neuraminidase;protein_id=AGG26999.1 - +CY136632.1 Genbank CDS 4 1413 . + 0 ID=cds-AGG26999.1;Parent=gene-NA;Dbxref=NCBI_GP:AGG26999.1;Name=NA;gbkey=CDS;product=neuraminidase;protein_id=AGG26999.1 diff --git a/data/flu/NA/na_n4_h8n4/CY136133/unreleased/dataset.zip b/data/flu/NA/na_n4_h8n4/CY136133/unreleased/dataset.zip index a261e8c19102495890e2d4c1b8adaa8e274ac70c..d208dcb44db6ed35d05728f856df770ac7cd69a8 100644 GIT binary patch delta 694 zcmV;n0!jVM4#f@(P)h>@6aWAK2mkup{>@n8u|Y5c=R~Un8(Y?<812{;^6-vC&5M4 z_!B9P3Z(7QzD^aGpsUbcvNlHXli!tUzUs}14dJB@HnsH57 z`Mxtj1@IgsdbVSOfwn}`Eoy*BY#fJpO{%&CWa2om9CDO3=!LU$Sh_)Cb5(}E5+(u_28iBE z_$LRJyZ?_OS`x?+mnI3DRR?iudDkVny- z+*VzKaSr(v%d7!xr_LqwO-=e|dyKgn7*DCl88063OlRviG=Zg|xpK!q^Lf;ddQV=6 zmqc3IZ{*j#+S`-Pm!m%#-^w!3*a*n?)Ep4lOHwh;a-sm=WSNU_U)}x@6aWAK z2mk@6aWAK2mtkau?#%{4fT6ET$Az|Q#S$t0MwIK0Uv+cj@mF3 ze1@-Z6;*0gqbp{|9CuloaW5qRqb)M^Gb2>e~^>lqHg_}6h{Tp zc4>0*XvsdaA`YWyJRXkvH~iibcux3p@66l_dzP-}^*)(5S;V)_N$7cY4lnYPgl()X z)#QSRSEPn`gmWg`nwU*7QpNKx$tHCkW{=}AcyKTkd#+_0Kc&+NnpS^AJri8!&(OxH zq_`rvyAw*sn*cRLDN@1*^%2*i%5>X6d|;APh;CL>%!xj?av}8&Bu5S7ny~8qV1`QI z1xWO0{|yG(5lwff1tPI=9O9JJO$ErrabN`$C~wgdXI)sjMPhqVhQ1OetuYEKC~M%_ z?9Lb}Ix*kIt07ie62^byssFbOKjGE^6ZIL(zgVyd{3r+>-g5tX0J1F*y_fJ$4yY!-y%4X7w6@6aWAK z2mtkav#$ft0s{4WlYs^~4fT6ET$Az|Q#S$t0MwJm1~&rrdy)qn0jiT72O@6aWAK2mk?nu?#B#e*t|uT&`GW8RP)~07L@-02TlM0B2=x zZ*65?VQy}3bYXO9Z*DGUW@a;Wl3$OaFcig~@l&wjaYF&ce>BZTapJlU#^@%SeIlh? zu@PFgtvY`DX>}ZDvu+3hE~n>r?`eae-fqJaD9xqtd!68m`_>0wAH@W96I(wh$v|tV zfBa=WUHDW8Y0iopP@N#q@aG7EL8zd1Yx3VoFOEksN_=~zY3elAl!Nwn#vF7OMd$Mw z3086>nidJZL$y3bKk2I!vb{u8CC?g^QyKb-Sk1rjiu6YP{;1n|*n4vjB^7(`2KExq z(LCgRwfAC19?C31$o<2!@>Ri>7)Q!(e};HTTOb2mav8SNj>Kt0@|VSW6C~-dHx4k9 zO#{qWL|9n?Nyfv0EgpqY7m`y!E1LO}rUYduuFE}K$VM^T%BC=v1CSF}wDH+`Il+RO za3{4P)sgM7hPnk|EZj~juiEcPciG3@6aWAK2mtnbu?#B#fA)JiT=I7@lj#8f096A302TlM0B2=x zZ*65?VQy}3bYXO9Z*DGUW@a;Wl3UNBFc5~X@mH|nazg>d6QtQFesSFkV|0_vUXfBp zY=qWr>*?Qbi=T&N-4FtuzMbct>3CkX-TEhxiV5!aI^Gw%RtKPuV1&Ani65k(pp=mA ze=?gcT*A4~XUR0kj^`=(a|BMomr&U=+3%UN&#ojLG=@V#>bJCS2) z4syPlcQM0HWfCD|_tIH$k+8+ul9F4(e{@M2z=O14!f%KviIEy-AB*+Ii{fE#?4?xH zHBfC3erW_a8V?61c;s4MaYi^PN#aiG0;DEsRqWx4H=nuq2mM#lNAu7)XkXT0-K0S9Mn*uC({wn5*d zXdC@VWsX2?49++v@6aWAK z2mtnbvrz-60s{7XlluiZ4fcCFT=I7@lj#8f09BJg1~&rsdy{$w905v`mj)sR@&y0@ F005Qa74X3oO3JIK2@#pvd zv}3|7SIeaLHJUkj?!V4yw`1!~=6e2Rf#yel#A)*#(|D`Dd~)mgB_ZDyw6fmiWMbYQ zH9^LScdE7V-p=Yv>+J7p-H#7H6!6?9IC0HvkFMB|mD_(v zTWhVH6>M|yRf2={)YRi0;g2?JWai&^-|see_Fi-Lor#~W?rzw7rPxIOlij1;GcL|H z@?L!6?ZlhURwR0_RZbOm-ju?7!9PVgOWdmj~E9_RbJg890&#oEFL zZ!PvZa$C%q&!L6ucAtn}<~d2sexAB(lfA#-v$~aQ1l!^z>-#^gaA-1jDEr>`wn;H+ zj`ZKWR`-S-Yl}Jdv)((fliMO!tVL&sR_hwM#ATcR%$sDvrSEGo&wt(}Ikh>HL@%$~ z8UAg)*WDjtpF_*k|5$66sGZP{&Rf|Mw%N@i(1`iTEK$ElZ%dw=BT@qsFd1;IUbwoJ ziGe|mjbU>N^IRq-=Gw{3Y?izzNo2Aoo4GuiY6gB_ih_Y9jjogDvnjE?X9bA>02oLO AO8@`> delta 578 zcmV-I0=@mg4aW@(P)h>@6aWAK2mttdu?#E$4fuOHT)S}-qv-(v09BJk0WE)I3na2C z4l7EfB1BqMy^4%81ZxwU+Rg%R-*G4hsZ>#vc>H_5f5zi^)o$m%gVJ0IchK`b*tI?Y zy9MK*A7lKWBm=Fba#yqI(xpO3b5z`b>Uo}q-z^9RzJki0nf;0fQ8XF_v5QZV^sNSy za?tMHn1fEk@OV51f^B&q>Lz~>d>>TuJ^W5jQpn~UPL(`rP*!E=DPR@<%u6yDCCPZ) zyQg;+AhuMzITx@KJC^1I&PRNgb8=UvaS+(OY`#4y*b!q%=_O&dq79Hw*_KPcp;!{9 zHJQCGH@P>8M&rcGn5=7H1`&RV0uqmhLkzaUs5AMIPg3_ARp*+DGOK^KZ*V5LVp${W z!kiC4-npW+%QmY?CaCfEQX5jWb)9Lb8W0B2SgY)`U*f?Emqt-8$RxC~@R~auMoDPV z&pL3ugJK8Nvo^6Ul(27MgDabMRD=-by`ID^Ae!n2Y{gf>;L_n)(!v!y?hV1GRC-Z)~ z*ZTudO9KQH000080Qh^eQ3I+10{DBA{RKG<_Y%$Rg*&oHv;&3lY9mo Q0ZWsa1|kOa1poj50OA1!xBvhE diff --git a/data/flu/NA/na_n6_h13n6/CY130088/unreleased/genome_annotation.gff3 b/data/flu/NA/na_n6_h13n6/CY130088/unreleased/genome_annotation.gff3 index d34b704..a997f94 100644 --- a/data/flu/NA/na_n6_h13n6/CY130088/unreleased/genome_annotation.gff3 +++ b/data/flu/NA/na_n6_h13n6/CY130088/unreleased/genome_annotation.gff3 @@ -6,5 +6,4 @@ CY130088.1 Genbank region 1 1442 . + . ID=CY130088.1:1..1442;Dbxref=taxon:384499;Name=6;bio-material=CEIRS#80894#;collection-date=1977;country=USA: Maryland;gbkey=Src;mol_type=viral cRNA;nat-host=gull;segment=6;serotype=H13N6;strain=A/gull/Maryland/704/1977 CY130088.1 Genbank sequence_feature 1 1442 . + . ID=id-CY130088.1:1..1442;Dbxref=IRD:NIGSP_CEIRS_SJC001_WEB_00015.NA;gbkey=misc_feature CY130088.1 Genbank gene 7 1422 . + . ID=gene-NA;Name=NA;gbkey=Gene;gene=NA;gene_biotype=protein_coding -CY130088.1 Genbank CDS 7 1422 . + 0 ID=cds-AGB51315.1;Parent=gene-NA;Dbxref=NCBI_GP:AGB51315.1;Name=AGB51315.1;gbkey=CDS;gene=NA;product=neuraminidase;protein_id=AGB51315.1 - +CY130088.1 Genbank CDS 7 1422 . + 0 ID=cds-AGB51315.1;Parent=gene-NA;Dbxref=NCBI_GP:AGB51315.1;Name=NA;gbkey=CDS;product=neuraminidase;protein_id=AGB51315.1 diff --git a/data/flu/NA/na_n6_h14n6/KC110598/unreleased/dataset.zip b/data/flu/NA/na_n6_h14n6/KC110598/unreleased/dataset.zip index da3b6985eacb607a55ca95e679d38dd940570018..257da3da661ed737a787873e3ed3fdb5c50e2b2f 100644 GIT binary patch delta 601 zcmV-f0;c`)4eJdIP)h>@6aWAK2ml0qu?#=~4Fr8UTz?JnHroLJ03efD0UdvZl3{P! zFc5}6hhLG2FPpYFF?20pSrY}Vt0u8(Y}&pd;~c@lIWyY<^6zJ-Y^+tKDY7h|&+k3= z=KB3=v&jx%oidmXd;M4O?Dio41}PcP5Z_xP!8v2o#q9Pz6^O5x7ACCx4!*?|p#+-j3s=%dN@Aqz!=f~rbpj<10x+bW$q%w#6n>ZOXb(`N> zb97*1mKP@?EA>H@oED?eO+kAX{p1dCEpV4SR!(RV%Oxav8`k}tUot0@ka)-D>yw2I z_p#LEtjHFk27b+?(Hf)=N?9p9aC)6B%pn^Tv})fl!h`b8@YSK98@)+ z4=|yB(`kL8SBr4;Rw(4t{P~;whjP-OQ<&4@%W^oTgFF(yWK-aTgpQxN6r))n?OX^u zV7an^H5d@`-jQ>^K?Hwd!(C3?S8Mf17^cI6!j&|o!iw#M^-5^&Z38b+%;w7{5JiNL zrOT!te~#$rW=JS|5H{NI2krdV;_$8R9wz@J{s%hLdcwm3YjDkTgvN?mp(=&zqFo1J z$}ZZy-%v{f1QY-O00;mBeL7qbx3Hs|0ssIe1^@sL0001TWoEN^1G54G1bve(200A` neL7r!4e~bI0RR9XlXM0*0t0=Mtp*$cQIpCBA_f@-00000|1A$y delta 629 zcmaFO`-zt)z?+#xgn@y9gW+fOMji)7p`X=OF|xfUm3Fo-csZeWwBFP)T| zf6GANcznD6#7^_s+bj%AbQ2z?9cnS+Ncjc-4Ec>BCxWMb&@6IOSB z{@H&&cHQl@VXJf4uW2@C?!R0sT)Un1r_7Qi?#?yYy)4greA6f2ZVyqA+Q0o&^V^c$ ze0AmxLPp%7HJ?+RGCvktD46ix4_z-`+*H4UY5Kao_jd)(d;h(HVXG3s;W+xi)Jrv-IXY76Oqg{Z~ENBEgf#b<6U#dU=C)jA=RovgmDRm*KOT$y@QYj+{4>`qO`~R;*}2c1ViBfMOI|Bqanhc? z?<(8sGu%rT`kZ#lyJyHA%KL)Z=f(XkQQyC0iN)l%I@z6z-*>WJOP$xM)lzrgx!=yW zPAh-RPUf03;ljgi&7&D&9=A1FxFhs(5_p+8D&yJL^zLRqo z@6`R$`d|J>z~`BNC-t*_GjKgGD5ag%x=LhS?>5=iwbt3?R`m>s#P9={3Iw-rSUj7F zfkBOpfnjqt^DZW)pVgDq*(`ZclE~y-HgkD&<@~@D1p`YOBPJhaQ({v98pFT<0O7(C A(EtDd diff --git a/data/flu/NA/na_n6_h14n6/KC110598/unreleased/genome_annotation.gff3 b/data/flu/NA/na_n6_h14n6/KC110598/unreleased/genome_annotation.gff3 index 1810c47..f13b96b 100644 --- a/data/flu/NA/na_n6_h14n6/KC110598/unreleased/genome_annotation.gff3 +++ b/data/flu/NA/na_n6_h14n6/KC110598/unreleased/genome_annotation.gff3 @@ -5,5 +5,4 @@ ##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1088701 KC110598.1 Genbank region 1 1423 . + . ID=KC110598.1:1..1423;Dbxref=taxon:1088701;Name=6;collection-date=16-Nov-2010;country=USA;gbkey=Src;genome=genomic;mol_type=viral cRNA;nat-host=Clangula hyemalis (long-tailed duck);segment=6;serotype=H14N6;strain=A/long-tailed duck/Wisconsin/10OS3912/2010 KC110598.1 Genbank gene 19 1423 . + . ID=gene-NA;Name=NA;end_range=1423,.;gbkey=Gene;gene=NA;gene_biotype=protein_coding;partial=true -KC110598.1 Genbank CDS 19 1423 . + 0 ID=cds-AFX81873.1;Parent=gene-NA;Dbxref=NCBI_GP:AFX81873.1;Name=AFX81873.1;end_range=1423,.;gbkey=CDS;gene=NA;partial=true;product=neuraminidase;protein_id=AFX81873.1 - +KC110598.1 Genbank CDS 19 1423 . + 0 ID=cds-AFX81873.1;Parent=gene-NA;Dbxref=NCBI_GP:AFX81873.1;Name=NA;end_range=1423,.;gbkey=CDS;partial=true;product=neuraminidase;protein_id=AFX81873.1 diff --git a/data/flu/NA/na_n6_h4n6/CY181243/unreleased/dataset.zip b/data/flu/NA/na_n6_h4n6/CY181243/unreleased/dataset.zip index d59d8a38121f97f14840f29501758d41aea9c8c8..8c0ae1bc9839ede9647c44564a2ab34eb2d559a3 100644 GIT binary patch delta 600 zcmdnNyP20Kz?+#xgn@y9gMq1bBab$t5L2yH%(}L+b(a|#7<8E#7{nMR`?5*YmrlBy z_sBq?b^YPsB~H~_yP6esb9J&^9T(kkS#eYJRcOi_#R%V=Yi2C>>T>J2R;P+aPCTA| z&fIub-u9@qi)1sDr|_`Peb>ByHt&b^3U0M;9!amYkXT$Yqc=WXadObjFmCQ$m)}bL z*vooS@lwFgIUm{Uj{Qw(D0s0i<-;S>b0PH&oY$}A`A8kly{&X|I@8HrjzMbzmzI6> z-xeNZ+WsSS^|gj?TBpBtggzn}sb8G#+Qw`0?&sj??;6 zBFazhpGetxeZ!(_i!W_fJ{iIMrL!RP`hm5@U0!L8kESO+YKqSM+W7C3d!|KWOr)sZ zfgAaM3+s2xn3(mGlYLgUpH!&$w+)QDglAnc%aJrDsb#c|v$SUMH-x zFP*Yqb>{BKvn@*&|Iq0XKUARFJHgN|DgMOXZTge-!w$R&J8aJ^kox7no0aip+Sf@BFDoBPIk#p0i`Lq_bMG?^=Poxtw10Kc zxg#G>>uwJ@6t>yTBhZNXNzl~jo!Mp2`4O?tSi9Mkc`XwYQ|;t0td_hesbI1do4GtA kFkS44Nf&BhVqlPEV_@J1CK?!6(r7Yy0-F-sLspOo05#?d4FCWD delta 602 zcmV-g0;T=44Y&;qP)h>@6aWAK2mtqcu?#B#fA@PjT+!$MNZ0`Y06qf%02TlM0B2=x zZ*65?VQy}3bYXO9Z*DGUW@a;Wl5dORFc8LH*H6)-+^eIhsoizAB^<7T>zg9mJLF!K zn2t4Un|MjI`t3LIKb%JiWhOJv@0lS%P_I_u4wU9n_=8^X&Bb~H?3%3dd7e73yzZk!oK~I!Kz z4(B27hdr|ixmBhZA$ONemU{&&VjLi|iwG4FbHO#o;@gONLhBxX-JUZGp^P9aHvSF8OJ6 z`>YIbQ8HO^Q9r_rC&fLb? z;cCwMskY1z0b4~|E_g*XWEYqA5((bAd%Z7EO9KQH000080QP&cKm)A;0{459?*%yx o_j@{A(dYk2*Z}|lK9e;DHv;y1lWqna0XdV41|kOL1poj501IpvhyVZp diff --git a/data/flu/NA/na_n6_h4n6/CY181243/unreleased/genome_annotation.gff3 b/data/flu/NA/na_n6_h4n6/CY181243/unreleased/genome_annotation.gff3 index 64c8564..9593a30 100644 --- a/data/flu/NA/na_n6_h4n6/CY181243/unreleased/genome_annotation.gff3 +++ b/data/flu/NA/na_n6_h4n6/CY181243/unreleased/genome_annotation.gff3 @@ -6,5 +6,4 @@ CY181243.1 Genbank region 1 1439 . + . ID=CY181243.1:1..1439;Dbxref=taxon:1445223;Name=6;collection-date=1974;country=USA: DeSoto West%2C WI;gbkey=Src;mol_type=viral cRNA;nat-host=mallard;segment=6;serotype=H4N6;strain=A/mallard/Wisconsin/14/1974 CY181243.1 Genbank sequence_feature 1 1439 . + . ID=id-CY181243.1:1..1439;Dbxref=IRD:NIGSP_SSC_00484.NA;gbkey=misc_feature CY181243.1 Genbank gene 7 1419 . + . ID=gene-NA;Name=NA;gbkey=Gene;gene=NA;gene_biotype=protein_coding -CY181243.1 Genbank CDS 7 1419 . + 0 ID=cds-AHN04765.1;Parent=gene-NA;Dbxref=NCBI_GP:AHN04765.1;Name=AHN04765.1;gbkey=CDS;gene=NA;product=neuraminidase;protein_id=AHN04765.1 - +CY181243.1 Genbank CDS 7 1419 . + 0 ID=cds-AHN04765.1;Parent=gene-NA;Dbxref=NCBI_GP:AHN04765.1;Name=NA;gbkey=CDS;product=neuraminidase;protein_id=AHN04765.1 diff --git a/data/flu/NA/na_n7_h10n7/CY136096/unreleased/dataset.zip b/data/flu/NA/na_n7_h10n7/CY136096/unreleased/dataset.zip index c7ff141ec763af1e4d1a5a37555e4190334e3333..de86ba0267a9998e63d86a7c09eafc2491d0487f 100644 GIT binary patch delta 664 zcmV;J0%!fg4!jNwP)h>@6aWAK2ml3ru?#-}4Fr8UTy&tyK{5gW0LGJ80U>|dFcf`; zU*Rd5v}wwRlNJhAH1V;rXc|JWKI|!SoJ+8p*qLph`S-J-ly&PAMRBgL&pAHF_PlDl z^$(ylmjWey@16VCEwGm&4q|NUt&$A1mI^Ir(+p7|q&X^XK=nOO!>>IE2EKyIt(pDA z$sigH0*vf)lMG#t1?8a8&X|8zkHheIJO+XlJP>sg2)+v{c?f^dCn;ppg;OPu8kFlY z^eJE!|IEu2$MM}wob<2wy#t{3z^**BY~*Um8x0yjtI#gl?1^Qo8q)iXJ4}Q#v4t)W1QR#J;LN(7}cc@o5>hWYN~%9DXEG_=+cd1 zq^59GD;Zbu#`S8`YNEygM5 z7c9F5h?_c<>^HXu;AD`s*8mqelO-3`TRgM*<`qrkXjrNJ$znbc58?<1n5?LB#$U*v z_v$WCzF3X_XnZZpLK7>X+%tPbV6SMy1uv-va*<{4!gY23H&9Ch1QY-O00;mCeY3d( y!vX>YeUp9$ISmATI$U(1%0V&$00735#0ED41bvhJ1{?vWlNtvi25JTX0001R0V@Ll delta 702 zcmV;v0zv(}4#Ex$P)h>@6aWAK2mtzfu?#-}68d{OTuyV%qBsHo0M`Qm02Tm~(FPcQ zbyHn$n=ll8PJV?aG-=bshoMc|SZK<}nxSb?l&lYXLdM(>t6($RNy@*UO`4|LIw1tU zzCP#p9NY7%?bbhl(p(CZ483=5tXp6&MI6M~)>|bRXe||5&ZZfnLP&E|+<+Q-o`zq0 z5Da_;m0L6WiIY)uHwrMa&sB2cdMqe^2aR^dw0azd$Kx>&tl)vDn?UegP{~91gFZm!VGqtN3SLrZ|poui|8Q!5=I@6jVG8PRs*5aCC!U@X5Z}JiT;|aS*sU zGB2JKY*XW?#?OdkNgGHQG!DE?%!gd9W`u+I-rVJ%OTy+rmX?lJPy2s5)~bK5WG*zbVzQWm7#me zm2*ZD4OIie*zH+IWiRF{j+QrnL>oo9NGIXnI>Jmi4{X>cu<&fcItt?`x_c{t^BKsu zK+RskKT+_~|9=|UdOluei_I$UUC(FPD!RVTC*R^ciefwptZgT+8?M=z<1HQ5Kg;dN zQXDMFPSwZEV*&_pcMH?=7Ni~qOOnWyjtB1qi zP)h>@6aWAK2mtwev$F%k0s{JblXwO>4f=aJTuyV%qBsHo0N0bg1~(u1dpcaGpySw< k0ssIr1^@sL00000000000001_fvuAi2O@6aWAK2ml3ru?!&r4F!EVT;7urot*&y0H2dO0Uv)|Z<{a_ zhOf!5VB&JZ)X;Sl%bN1Bb-h?rE!#z}B4bX7RX9#aGLnyiwW+2b|vD6}~v2GbjFgHLc=roi?fwtgT<*#8*bLUUz?MciI8pDS0%sL|!@@WR6F8iTGuQHki?t39yKo}#^ ztB9ePdgz$JujkQx3$U;?mi)S|)tT%s(t*OY)Q!USJ`9mq=#BmNOv9hCet0UXu7v+j<(--5H-mH>VK6=}`s1{~-lp=GeCeM20Z>Z=1QY-O z00;mDeX|7vq5=X1eUqsLISmDUI$Yk95uKd@005tp?*%sk1$~n!1{?wOlSKw129^Z? 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ID=CY130072.1:1..1435;Dbxref=taxon:402474;Name=6;bio-material=CEIRS#162855#;collection-date=1974;country=USA: Memphis;gbkey=Src;mol_type=viral cRNA;nat-host=duck;segment=6;serotype=H11N9;strain=A/duck/Memphis/546/1974 CY130072.1 Genbank sequence_feature 1 1435 . + . ID=id-CY130072.1:1..1435;Dbxref=IRD:NIGSP_CEIRS_SJC001_WEB_00013.NA;gbkey=misc_feature CY130072.1 Genbank gene 7 1419 . + . 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ID=CY005407.1:1..1459;Dbxref=taxon:352560;Name=6;collection-date=1979;country=Australia: Western Australia;gbkey=Src;mol_type=viral cRNA;nat-host=Avian;segment=6;serotype=H15N9;strain=A/wedge-tailed shearwater/Western Australia/2576/1979 CY005407.1 Genbank primer_binding_site 1 15 . + . ID=id-CY005407.1:1..15;Note=PCR amplification primer sequence;gbkey=primer_bind CY005407.1 Genbank gene 19 1431 . + . ID=gene-NA;Name=NA;gbkey=Gene;gene=NA;gene_biotype=protein_coding -CY005407.1 Genbank CDS 19 1431 . + 0 ID=cds-ABB88141.1;Parent=gene-NA;Dbxref=NCBI_GP:ABB88141.1;Name=ABB88141.1;gbkey=CDS;gene=NA;product=neuraminidase;protein_id=ABB88141.1 +CY005407.1 Genbank CDS 19 1431 . + 0 ID=cds-ABB88141.1;Parent=gene-NA;Dbxref=NCBI_GP:ABB88141.1;Name=NA;gbkey=CDS;product=neuraminidase;protein_id=ABB88141.1 CY005407.1 Genbank primer_binding_site 1439 1459 . - . ID=id-CY005407.1:1439..1459;Note=PCR amplification primer sequence;gbkey=primer_bind - diff --git a/data/flu/NA/na_n9_h7n9/NC_026429.1/unreleased/dataset.zip b/data/flu/NA/na_n9_h7n9/NC_026429.1/unreleased/dataset.zip index a31fbc9837c81bd0d0341fa4f26449554e907fa3..8ef027b655dce3d40cda669fbe68d1d4912a221f 100644 GIT binary patch delta 607 zcmdnRyM>o0z?+#xgn@y9gMqDfBab$t5L>NPj76`|zFUk84A#sH3}OtE{n;eyYbV9# z-&PQ5TR%7cq2~128#it?F?0%^?31l07V4W{mMU1&6qsAkSo8O{)8=(6r}=Uyp0k|u z-EzGI-_f$!Zw^MR42|Jwn}6u;w*&uK3{P$B|L#`2A#8Sq>3rSfWmC%7m1SofEXa6R z$=>Ch zeNivpO*z+N7h$mQ)JEk;PIZ$_kGf8LzWCw;Cxxnpw^H*KZ!T$BtRTMd#pe5`S@*8c zF?3S&6q~)cQMc4_^`E*{&cnQV+MTz4+I^m1F#a=90AQrC|CNi6jiDfV2vc5(Tx%NtYovZQu?7sxoj zCY9-tl+5I{x{u$_h!Bv~cwV`O{nyr;ch6>dtugk|s+zq{dYQ}Nlvz(R6LvrAc;2}G z568hLg|>3xWja-Vo*m_vkJCG~=fF)3eYJFRo9~q;Ch!K&%XI#?#_W^N)BUZ?E49{T zuVl$Iy?^tRq2qnkbqmjmzxLjwGvVVcwf*l_>&#BFk@Ph<^km-52Z#30O!u*!DlcFA z^S?&iPc7Atldo96ThTN(ac;<_G_e!6YyQ2jog%r10XY$D_GMnq#KcxR`5UVxFG^yV pY{OCm4SgDn08=bNu%}TNo-1NkAUI~3;+r04CDX+ delta 610 zcmV-o0-gP|4Y~~sP)h>@6aWAK2mt(hu?#B#fBSnnTowpYy5Io-08j$}02TlM0B2=x zZ*65?VQy}3bYXO9Z*DGUW@a;Wl3#DzAQZ))oloH@kDIZvvn(+}Qj+A?$4r{H=&lj(xp1nuE34 zf5hwM;x1-NX?HZzfft>RmF~{z!sw#~6S^EbAui-sSyNmTc|MtpE(Syou-m|MG>ndL z6vjm;`sn|=6}{*zF+$;xthOfuJL{RslHH+`Qe77p|0%w!Fm6lWztb0YQ_D1|kON1poj506xVZpa1{> diff --git a/data/flu/NA/na_n9_h7n9/NC_026429.1/unreleased/genome_annotation.gff3 b/data/flu/NA/na_n9_h7n9/NC_026429.1/unreleased/genome_annotation.gff3 index 1252237..5723836 100644 --- a/data/flu/NA/na_n9_h7n9/NC_026429.1/unreleased/genome_annotation.gff3 +++ b/data/flu/NA/na_n9_h7n9/NC_026429.1/unreleased/genome_annotation.gff3 @@ -5,5 +5,4 @@ ##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1332244 NC_026429.1 RefSeq region 1 1398 . + . ID=NC_026429.1:1..1398;Dbxref=taxon:1332244;Name=6;collection-date=05-Mar-2013;country=China;gbkey=Src;genome=genomic;mol_type=viral cRNA;nat-host=Homo sapiens;note=passage details: E1;segment=6;serotype=H7N9;strain=A/Shanghai/02/2013 NC_026429.1 RefSeq gene 1 1398 . + . ID=gene-TS66_s6gp1;Dbxref=GeneID:23104238;Name=NA;gbkey=Gene;gene=NA;gene_biotype=protein_coding;locus_tag=TS66_s6gp1 -NC_026429.1 RefSeq CDS 1 1398 . + 0 ID=cds-YP_009118481.1;Parent=gene-TS66_s6gp1;Dbxref=GenBank:YP_009118481.1,GeneID:23104238;Name=YP_009118481.1;gbkey=CDS;gene=NA;locus_tag=TS66_s6gp1;product=neuraminidase;protein_id=YP_009118481.1 - +NC_026429.1 RefSeq CDS 1 1398 . + 0 ID=cds-YP_009118481.1;Parent=gene-TS66_s6gp1;Dbxref=GenBank:YP_009118481.1,GeneID:23104238;Name=NA;gbkey=CDS;locus_tag=TS66_s6gp1;product=neuraminidase;protein_id=YP_009118481.1 diff --git a/data/index.json b/data/index.json index 3302303..2a0d46e 100644 --- a/data/index.json +++ b/data/index.json @@ -871,7 +871,7 @@ } }, { - "path": "flu/NA/na_n6_h13n6/CY130088/unreleased", + "path": "flu/NA/na_n6_h13n6/CY130088", "enabled": true, "attributes": { "name": "na_n6_h13n6", @@ -893,7 +893,7 @@ } }, { - "path": "flu/NA/na_n6_h14n6/KC110598/unreleased", + "path": "flu/NA/na_n6_h14n6/KC110598", "enabled": true, "attributes": { "name": "na_n6_h14n6", @@ -915,7 +915,7 @@ } }, { - "path": "flu/NA/na_n7_h10n7/CY136096/unreleased", + "path": "flu/NA/na_n7_h10n7/CY136096", "enabled": true, "attributes": { "name": "na_n7_h10n7", @@ -937,7 +937,7 @@ } }, { - "path": "flu/NA/na_n8_h3n8/CY028838/unreleased", + "path": "flu/NA/na_n8_h3n8/CY028838", "enabled": true, "attributes": { "name": "na_n8_h3n8", @@ -959,7 +959,7 @@ } }, { - "path": "flu/NA/na_n9_h7n9/NC_026429.1/unreleased", + "path": "flu/NA/na_n9_h7n9/NC_026429.1", "enabled": true, "attributes": { "name": "na_n9_h7n9", @@ -981,7 +981,7 @@ } }, { - "path": "flu/NA/na_n9_h11n9/CY130072/unreleased", + "path": "flu/NA/na_n9_h11n9/CY130072", "enabled": true, "attributes": { "name": "na_n9_h11n9", @@ -1003,7 +1003,7 @@ } }, { - "path": "flu/NA/na_n9_h15n9/CY005407/unreleased", + "path": "flu/NA/na_n9_h15n9/CY005407", "enabled": true, "attributes": { "name": "na_n9_h15n9", @@ -1025,7 +1025,7 @@ } }, { - "path": "flu/NA/na_n10_h17n10/CY103878/unreleased", + "path": "flu/NA/na_n10_h17n10/CY103878", "enabled": true, "attributes": { "name": "na_n10_h17n10", @@ -1047,7 +1047,7 @@ } }, { - "path": "flu/NA/na_n11_h18n11/CY125947/unreleased", + "path": "flu/NA/na_n11_h18n11/CY125947", "enabled": true, "attributes": { "name": "na_n11_h18n11", diff --git a/flu-dataset-generator/generator.py b/flu-dataset-generator/generator.py index cd96494..9ed67ef 100644 --- a/flu-dataset-generator/generator.py +++ b/flu-dataset-generator/generator.py @@ -75,6 +75,29 @@ def update_index(pathogen_json, path, output_dir): json.dumps(index, indent=2, ensure_ascii=False) + "\n" ) +def rename_cds_to_gene_names(gff_content: str) -> str: + lines = gff_content.splitlines() + updated_lines = [] + for line in lines: + if line.startswith("#") or not line.strip(): + updated_lines.append(line) + continue + parts = line.split("\t") + if len(parts) < 9: + updated_lines.append(line) + continue + attributes = parts[8] + attr_dict = dict(item.split("=") for item in attributes.split(";") if "=" in item) + if parts[2] == "CDS" and "gene" in attr_dict: + attr_dict["Name"] = attr_dict["gene"] + del attr_dict["gene"] + parts[8] = ";".join(f"{k}={v}" for k, v in attr_dict.items()) + updated_line = "\t".join(parts) + updated_lines.append(updated_line) + else: + updated_lines.append(line) + return "\n".join(updated_lines) + def generate_dataset(dataset_dir: Path, ref_name: str, accession: str, output_dir: str): dataset_dir.mkdir(parents=True, exist_ok=True) @@ -92,7 +115,8 @@ def generate_dataset(dataset_dir: Path, ref_name: str, accession: str, output_di gff3 = Entrez.efetch( db="nucleotide", id=accession, rettype="gff3", retmode="text" ) - gff_path.write_text(gff3.read()) + gff_content = gff3.read() + gff_path.write_text(rename_cds_to_gene_names(gff_content)) pathogen_json = PATHOGEN_TEMPLATE.copy() pathogen_json["attributes"]["name"] = ref_name From 2e7b13a3a173704fe66d82b19e8af1ffbc8537d3 Mon Sep 17 00:00:00 2001 From: anna-parker <50943381+anna-parker@users.noreply.github.com> Date: Mon, 26 Jan 2026 15:56:11 +0100 Subject: [PATCH 4/5] delete weird NA sequence --- .../KC110598/unreleased/dataset.zip | Bin 1771 -> 0 bytes .../unreleased/genome_annotation.gff3 | 8 ------ .../KC110598/unreleased/pathogen.json | 16 ------------ .../KC110598/unreleased/reference.fasta | 23 ------------------ data/index.json | 22 ----------------- flu-dataset-generator/config.yml | 1 - 6 files changed, 70 deletions(-) delete mode 100644 data/flu/NA/na_n6_h14n6/KC110598/unreleased/dataset.zip delete mode 100644 data/flu/NA/na_n6_h14n6/KC110598/unreleased/genome_annotation.gff3 delete mode 100644 data/flu/NA/na_n6_h14n6/KC110598/unreleased/pathogen.json delete mode 100644 data/flu/NA/na_n6_h14n6/KC110598/unreleased/reference.fasta diff --git a/data/flu/NA/na_n6_h14n6/KC110598/unreleased/dataset.zip b/data/flu/NA/na_n6_h14n6/KC110598/unreleased/dataset.zip deleted file mode 100644 index 257da3da661ed737a787873e3ed3fdb5c50e2b2f..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 1771 zcmZ`)c{JN;7ygk7+NMZ}olv#4q=Ht-OvPHFN=vC_B8Ub}f~3}>KCzUJJ$8zO8ls!F zLrJTQw3F1dq=OM##b8E5DK%{^lj--zeA6@Eea}7jy!V`Y|9H;xJl6vQ+NB5pfDEuJ z**ak0P^7=I1ORZv2@!Xra8v^M0-j_VK_Qdy9;YJHZROeXK6`6*nZI+qDkt^IQf&QX z?m1W7WRP0had89nIy>x0=)sr5PvsRGb5dA27 zFM6&tW%pd%Gj68!COm{5h5(1pu1~Y-DNf1jd8AmgSc_4WJwN3*v8-&W*rCn3_J?Ji z_~t&u)0?>kedvnGUR1vSz7EE{gcefv0e%In?L&zf(xtX1P( zj2;{W05CCvV(`dBJQhbHk*PRpIGJR6AuP;1qXK&7bc7mDdXJk6BvzL%+_=c{ZZx`k`1*_GuQujBZbh{JxG$&%S-vl6%V*`y zd-x96NcE-sl>dPz$3yu2Z{B~cl+Dp@TMbIudX$cZ)X|>XDNS9j_4Mo3&X+mW7iX!$ zsfM@oH2N=Zkc#G?3JdE34*ln$e)9t+GHbKSO4Z_0)s!EF8Wd8hY@mB+9Zj!>F$Pbe zla#k+_eGgRm7&hL6QI0oTh&;kK}kXU)49ds49LcvSF@~Vum*6-0CP}{Dd&3L z2o;rBWAa=_UGbhw93)Y&y38|b9kwBS7;-&_o|c*|eLH zMc2N#*V8hnJMq9{Pg}r8KXn!oQId%?QSVIZ)9|valRHwM$`4O&@X3u@J7+k{-~3Ru znH4isceb2A!;7(MN=HE-hn}6L(ekc$Dl*Q)MFBE4L7jKgELG%JCkrW$(Yu2C0^P@b zBG*rZ<&RA>+l*VyQ$JkSU(*YzFl*0G78C8-1pbrKB zIWZk#@L~8EJShZk8iu1#agJWRy#46C-5Wk@W`$QmVZL{i^?1_h1*M=;tNbDzwL+0& z1r3DFZyj$}cN}C2@>^mOzE0)iMpG~Uu|{gf3U0k4M(l8m*OxDMnp`^2^^Ri0X6L<2 zupSnQ-X?8OzS;MJSRo*drtYk4<2nQrqO7es-rLtJDP3(mYGUQs{mGG|6Q)A`_?)oA z?b16#fw;HUw5^I5NkEPCMH>YhuUy5NQ~JzP0;As~7-;23vu3oMVR14SLQx#=!IPzb z%pfH-k6(*&IDp_j^)AUZR?rO3No@X>bMYIEbw$k;WeDBY0^P50voN=P`{2V7gP-k2 zO=Zg*Y^5fWFi6KU)hgu}XnuS!^@t%ssV=%C{#vpI!OcZ4UP?WOwp|MM9lvtUmRl}K zSa5S7gtPXteGRxB?=ggIN!uT&-`hsvjw8f_I}HG0l)LOI3WegrC4*PG@+ z05Lm2)mk+HDCgn~`ZY;sr!pp4z;gm&=>q|wvXk&tzWnnW$5Jls1oW@&+iH|CF9U} zs$+70|D%sB1IAKaL-sCdj2?Mk>&9QZyRM@Am7Mr4LrT#vek(dwMjtvW)mU5)_EabC z*LjsWob`l&m}gnGS1hjO6+GAT@sdDHx@|UClv^Czu*@dQ5;N68VW88; zJGV-Qd!WA96Ub%EPJ^sw?UfIeIglIkmQ%1mHGk~x@olOxq@cCe$)W%KUc<%B3|dJa zc>hw({FuLAaNw~!BkPxoYo%ctyU6(U(?QqL zRc#N9grp+q|DOginLh_J?XU8WL-FP4m!A0FK>%Q;*@>O<-yQOQcl?`>{@&p!cG@pw U<$;kB>kR-v;@2&%s-J&<0vpH(WB>pF diff --git a/data/flu/NA/na_n6_h14n6/KC110598/unreleased/genome_annotation.gff3 b/data/flu/NA/na_n6_h14n6/KC110598/unreleased/genome_annotation.gff3 deleted file mode 100644 index f13b96b..0000000 --- a/data/flu/NA/na_n6_h14n6/KC110598/unreleased/genome_annotation.gff3 +++ /dev/null @@ -1,8 +0,0 @@ -##gff-version 3 -#!gff-spec-version 1.21 -#!processor NCBI annotwriter -##sequence-region KC110598.1 1 1423 -##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1088701 -KC110598.1 Genbank region 1 1423 . + . ID=KC110598.1:1..1423;Dbxref=taxon:1088701;Name=6;collection-date=16-Nov-2010;country=USA;gbkey=Src;genome=genomic;mol_type=viral cRNA;nat-host=Clangula hyemalis (long-tailed duck);segment=6;serotype=H14N6;strain=A/long-tailed duck/Wisconsin/10OS3912/2010 -KC110598.1 Genbank gene 19 1423 . + . ID=gene-NA;Name=NA;end_range=1423,.;gbkey=Gene;gene=NA;gene_biotype=protein_coding;partial=true -KC110598.1 Genbank CDS 19 1423 . + 0 ID=cds-AFX81873.1;Parent=gene-NA;Dbxref=NCBI_GP:AFX81873.1;Name=NA;end_range=1423,.;gbkey=CDS;partial=true;product=neuraminidase;protein_id=AFX81873.1 diff --git a/data/flu/NA/na_n6_h14n6/KC110598/unreleased/pathogen.json b/data/flu/NA/na_n6_h14n6/KC110598/unreleased/pathogen.json deleted file mode 100644 index 3015f1b..0000000 --- a/data/flu/NA/na_n6_h14n6/KC110598/unreleased/pathogen.json +++ /dev/null @@ -1,16 +0,0 @@ -{ - "alignmentParams": { - "minSeedCover": 0.01 - }, - "schemaVersion": "3.0.0", - "attributes": { - "name": "na_n6_h14n6", - "reference name": "Influenza A virus (A/long-tailed duck/Wisconsin/10OS3912/2010(H14N6)) segment 6 neuraminidase (NA) gene, partial cds", - "reference accession": "KC110598" - }, - "files": { - "reference": "reference.fasta", - "pathogenJson": "pathogen.json", - "genomeAnnotation": "genome_annotation.gff3" - } -} diff --git a/data/flu/NA/na_n6_h14n6/KC110598/unreleased/reference.fasta b/data/flu/NA/na_n6_h14n6/KC110598/unreleased/reference.fasta deleted file mode 100644 index 805091a..0000000 --- a/data/flu/NA/na_n6_h14n6/KC110598/unreleased/reference.fasta +++ /dev/null @@ -1,23 +0,0 @@ ->KC110598.1 Influenza A virus (A/long-tailed duck/Wisconsin/10OS3912/2010(H14N6)) segment 6 neuraminidase (NA) gene, partial cds -AGCAAAAGCAGGGTGAAAATGAATCCAAATCAAAAGATAATATGCATTTCAGCCACAGGAATGACACTAT -CGGTAGTAAGCCTGCTGATAGGAATTGCCAATTTGGGCCTAAACATCGGACTCCATTATAAGGTGGGTGA -TACACCAGATGTGAGCATCCCAAACATGAATGAGACCAACTCAACAACAACAATAATAAACAATAATACC -CAAAATAATTTCACAAATATCACTAACATTATAGTGAATAAAAACGAGGGAAAAATGTTCCTAAATCTGA -CCAAGCCCCTATGTGAGGTAAACTCATGGCACATCTTGTCGAAAGACAATGCAATAAGAATAGGAGAAGA -TGCTCATATACTAGTCACAAGGGAGCCCTACCTGTCTTGCGATCCACAAGGCTGCAGGATGTTTGCTCTG -AGCCAAGGAACAACACTCAGAGGGCGACATGCGAATGGGACTATACATGATAGAAGTCCATTTCGAGCTC -TCGTGAGTTGGGAGATGGGTCAAGCGCCCAGTCCATACAATGTTAAGGTCGAATGCATAGGCTGGTCAAG -CACATCGTGCCATGATGGCATATCAAGAATGTCAATATGCATGTCGGGACCGAACAACAATGCATCAGCA -GTGGTCTGGTACGGGGGGAGGCCAGTAACAGAAATTCCATCATGGGCAGGAAATATTCTCAGAACCCAAG -AGTCAGAATGTGTGTGCCATAAAGGGATCTGTCCAGTAGTCATGACGGATGGCCCAGCAAACAACAGAGC -AGCAACTAAGATAATCTATTTCAAAGAGGGAAAGGTACAGAAAATTGAAGAACTGGCAGGAAGTGCCCAG -CACATCGAAGAATGTTCATGCTATGGGGCAGTCGAGGTGATCAAATGCATATGCAGAGACAATTGGAAAG -GGGCAAATAGACCAGTAATTACTATAAACCCTGAAATGATGACCCACACGAGCAAGTATTTGTGCTCGAA -AGTCCTAACCGATACAAGTCGCCCCAATGATCCCACTAATGGTAACTGTGATGCGCCAATAACAGGAGGG -AGCCCTGATCCTGGAGTGAAGGGGTTTGCGTTCCTAGATGGGGAGAATTCATGGCTGGGAAGGACAATTA -GCAAAGACTCCAGGTCGGGCTACGAAATGTTGAAAGTCCCAAATGCAGAGACCGACACCCAATCAGGGCC -GACATCACACCAAGTAATTGTCAACAACCAAAACTGGTCGGGATACTCAGGGGCTTTCATAGACTACTGG -GCAAACAAAGAGTGCTTCAATCCTTGTTTTTATGTGGAACTAATCAGAGGGAGACCCAAGGAGAGTAGTG -TACTGTGGACTTCAAATAGCATTGTGGCTCTCTGTGGATCCAAAGAGCGATTGGGATCATGGTCCTGGCA -TGATGGTGCTGAAATCATCTACT - diff --git a/data/index.json b/data/index.json index 2a0d46e..462aa6e 100644 --- a/data/index.json +++ b/data/index.json @@ -892,28 +892,6 @@ "tag": "unreleased" } }, - { - "path": "flu/NA/na_n6_h14n6/KC110598", - "enabled": true, - "attributes": { - "name": "na_n6_h14n6", - "reference name": "Influenza A virus (A/long-tailed duck/Wisconsin/10OS3912/2010(H14N6)) segment 6 neuraminidase (NA) gene, partial cds", - "reference accession": "KC110598" - }, - "files": { - "reference": "reference.fasta", - "pathogenJson": "pathogen.json", - "genomeAnnotation": "genome_annotation.gff3" - }, - "versions": [ - { - "tag": "unreleased" - } - ], - "version": { - "tag": "unreleased" - } - }, { "path": "flu/NA/na_n7_h10n7/CY136096", "enabled": true, diff --git a/flu-dataset-generator/config.yml b/flu-dataset-generator/config.yml index e94457f..17acab4 100644 --- a/flu-dataset-generator/config.yml +++ b/flu-dataset-generator/config.yml @@ -27,7 +27,6 @@ NA: na_n5_h12n5: CY130080 na_n6_h4n6: CY181243 na_n6_h13n6: CY130088 - na_n6_h14n6: KC110598 na_n7_h10n7: CY136096 na_n8_h3n8: CY028838 na_n9_h7n9: 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.../KU143256/unreleased/dataset.zip | Bin 1895 -> 1895 bytes .../CY130030/unreleased/dataset.zip | Bin 1931 -> 1931 bytes .../NC_026425.1/unreleased/dataset.zip | Bin 1924 -> 1924 bytes .../CY136131/unreleased/dataset.zip | Bin 2029 -> 2029 bytes .../NC_004908.1/unreleased/dataset.zip | Bin 1825 -> 1829 bytes .../unreleased/genome_annotation.gff3 | 2 +- .../CY103878/unreleased/dataset.zip | Bin 1779 -> 1779 bytes .../CY125947/unreleased/dataset.zip | Bin 1782 -> 1782 bytes .../NC_007361.1/unreleased/dataset.zip | Bin 1693 -> 1693 bytes .../KU143347/unreleased/dataset.zip | Bin 1711 -> 1711 bytes .../CY130032/unreleased/dataset.zip | Bin 1748 -> 1748 bytes .../NC_004909.1/unreleased/dataset.zip | Bin 1708 -> 1712 bytes .../unreleased/genome_annotation.gff3 | 2 +- .../CY136632/unreleased/dataset.zip | Bin 1792 -> 1792 bytes .../CY136133/unreleased/dataset.zip | Bin 1861 -> 1861 bytes .../CY130080/unreleased/dataset.zip | Bin 1727 -> 1727 bytes .../CY130088/unreleased/dataset.zip | Bin 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ID=NC_004908.1:1..1714;Dbxref=taxon:130760;Name=4;gbkey=Src;genome=genomic;mol_type=genomic RNA;note=subtype H9N2;segment=4;strain=A/Hong Kong/1073/99 NC_004908.1 RefSeq gene 32 1714 . + . 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JPF7}f1pvA35MuxU delta 57 zcmaFC^MZ#bz?+#xgn@y9gMqbnBab2@6Km~eea7=3dK2>^CLlF=39BWDy3gtaqLkTO E0e>P5;{X5v diff --git a/data/flu/NA/na_n9_h11n9/CY130072/unreleased/dataset.zip b/data/flu/NA/na_n9_h11n9/CY130072/unreleased/dataset.zip index d7b8e28fa078a757f88aa07930097fa74420da75..df36365d47cdb3fa999fe7806c066d156d30935f 100644 GIT binary patch delta 58 zcmX@cdyJPSz?+#xgn@y9gTZg%MjjnTCf|jdtr*3aKy(oEIwmH+g_D`sEP>p~wroxy Is*%kV0GkRA1ONa4 delta 58 zcmX@cdyJPSz?+#xgn@y9gMqzvBaaRv6MOAuD@HLU5FNz44n$98VzUHMwroxys*%kV E0ADW*h5!Hn diff --git a/data/flu/NA/na_n9_h15n9/CY005407/unreleased/dataset.zip b/data/flu/NA/na_n9_h15n9/CY005407/unreleased/dataset.zip index fad3cfd657fb4c5757288c9cb0581bdb5c1767b1..e0c5e89a8abe3c9b512cd0f4926b1ccc4cd34877 100644 GIT binary patch delta 58 zcmZqVYvkhz@MdNaVPIh3VDMYGk;jse$#3CicSbEH5M9iC0z^-?WwQiP6>Lr*Y7d($ E0FR&#ng9R* delta 58 zcmZqVYvkhz@MdNaVPIh3VBo0T$YaUK#8JE1ol%R4iM@7nG4lx~Ab+wgnYB JPTs@j3IJ2$4IBUf diff --git a/data/flu/NA/na_n9_h7n9/NC_026429.1/unreleased/dataset.zip b/data/flu/NA/na_n9_h7n9/NC_026429.1/unreleased/dataset.zip index 8ef027b655dce3d40cda669fbe68d1d4912a221f..6fe0ae42043ee9082e4da25f9753214ca9603471 100644 GIT binary patch delta 58 zcmdnOyM>o0z?+#xgn@y9gTZ&o0z?+#xgn@y9gMqDfBab#C6I< str: attributes = parts[8] attr_dict = dict(item.split("=") for item in attributes.split(";") if "=" in item) if parts[2] == "CDS" and "gene" in attr_dict: - attr_dict["Name"] = attr_dict["gene"] + attr_dict["Name"] = attr_dict["gene"].upper() del attr_dict["gene"] parts[8] = ";".join(f"{k}={v}" for k, v in attr_dict.items()) updated_line = "\t".join(parts)