WIP H7N6 build

Snakefile

@@ -591,6 +591,7 @@ rule refine:
     params:
         coalescent = config['refine']['coalescent'],
         date_inference = config['refine']['date_inference'],
+        timetree = lambda w: "--timetree" if resolve_config_value(['refine', 'timetree'], w) else "",
         clock_rates = refine_clock_rates,
         clock_filter = refine_clock_filter,
         root = lambda w: f"--root {resolve_config_value(['refine', 'root'], w)}" if resolve_config_value(['refine', 'root'], w) else ''
@@ -602,7 +603,7 @@ rule refine:
             --metadata {input.metadata} \
             --output-tree {output.tree} \
             --output-node-data {output.node_data} \
-            --timetree \
+            {params.timetree} \
             {params.root} \
             --coalescent {params.coalescent} \
             --date-confidence \

config/h7n6.yaml

@@ -0,0 +1,27 @@
+inputs:
+  - name: gisaid
+    metadata: ingest/fauna/results/metadata.tsv
+    sequences: ingest/fauna/results/sequences_{segment}.fasta
+
+builds:
+  - subtype: h7n6
+    segment: ['pb2', 'pb1', 'pa', 'ha', 'np', 'na', 'mp', 'ns']
+    time: all-time
+
+subtype_lookup:
+  h7n6: ['h7n6']
+
+filter: 
+  min_date:
+    "h7n6/*/all-time": 1900
+  group_by:
+    "h7n6/*/*": subtype
+  exclude_where:
+    host=laboratoryderived # can't use an empty string...
+
+refine:
+  clock_filter_iqd:
+    "h7n6/*/*": ""
+traits:
+  columns:
+    "h7n6/*/*": region

config/h7n6/auspice_config_h7n6.json

@@ -0,0 +1,87 @@
+{
+  "title": "Real-time tracking of influenza A/H7N6 evolution",
+  "maintainers": [
+    {"name": "James Hadfield"},
+    {"name": "Nextstrain"}
+  ],
+  "build_url": "https://github.com/nextstrain/avian-flu",
+  "data_provenance": [
+    {
+      "name": "GISAID"
+    }
+  ],
+  "colorings": [
+    {
+      "key": "gt",
+      "title": "Genotype",
+      "type": "categorical"
+    },
+    {
+      "key": "num_date",
+      "title": "Date",
+      "type": "continuous"
+    },
+    {
+      "key": "pathogenicity",
+      "title": "Pathogenicity",
+      "type": "categorical"
+    },
+    {
+      "key": "region",
+      "title": "Region",
+      "type": "categorical"
+    },
+    {
+      "key": "country",
+      "title": "Country",
+      "type": "categorical"
+    },
+    {
+      "key": "division",
+      "title": "Admin Division",
+      "type": "categorical"
+    },
+    {
+      "key": "host",
+      "title": "Host",
+      "type": "categorical"
+    },
+    {
+      "key": "furin_cleavage_motif",
+      "title": "Furin Cleavage Motif",
+      "type": "categorical"
+    },
+    {
+      "key": "cleavage_site_sequence",
+      "title": "Cleavage Site Sequence",
+      "type": "categorical"
+    },
+    {
+      "key": "originating_lab",
+      "title": "Originating Lab",
+      "type": "categorical"
+    },
+    {
+      "key": "submitting_lab",
+      "title": "Submitting Lab",
+      "type": "categorical"
+    }
+  ],
+  "geo_resolutions": [
+    "region",
+    "country",
+    "division"
+  ],
+  "display_defaults": {
+    "map_triplicate": true,
+    "color_by": "pathogenicity",
+    "geo_resolution": "region"
+  },
+  "filters": [
+    "host",
+    "country",
+    "division",
+    "originating_lab",
+    "submitting_lab"
+  ]
+}

config/h7n6/colors_h7n6.tsv

@@ -0,0 +1,2 @@
+pathogenicity	LPAI	#2b8cbe
+pathogenicity	HPAI	#f03b20

config/h7n6/reference_h7n6_ha.gb

@@ -0,0 +1,103 @@
+LOCUS       KJ411975                1710 bp    cRNA    linear   VRL 24-JUN-2014
+DEFINITION  Influenza A virus (A/Shanghai/01/2014(H7N9)) segment 4
+            hemagglutinin (HA) gene, complete cds.
+ACCESSION   KJ411975
+VERSION     KJ411975.1
+KEYWORDS    .
+SOURCE      Influenza A virus (A/Shanghai/01/2014(H7N9))
+  ORGANISM  Influenza A virus (A/Shanghai/01/2014(H7N9))
+            Viruses; ssRNA viruses; ssRNA negative-strand viruses;
+            Orthomyxoviridae; Influenzavirus A.
+REFERENCE   1  (bases 1 to 1710)
+  AUTHORS   Zhang,W., He,Y., Xu,L., Dai,F., Mei,Z., Qian,L., Xie,D., Shen,Y.,
+            Gu,Y., Zhang,Z., Yuan,Z., Jie,Z. and Hu,Y.
+  TITLE     Full-Genome Analysis of Influenza A(H7N9) Virus from Shanghai,
+            China, 2014
+  JOURNAL   Genome Announc 2 (3), e00578-14 (2014)
+   PUBMED   24948761
+  REMARK    Publication Status: Online-Only
+REFERENCE   2  (bases 1 to 1710)
+  AUTHORS   Zhang,W., Xu,L., Tian,D., Liu,Y. and Hu,Y.
+  TITLE     Direct Submission
+  JOURNAL   Submitted (07-FEB-2014) Pathogen Diagnosis and Biosafety
+            Department, Shanghai Public Health Clinical Center, Fudan
+            University, 2901 Caolang Road, Jin Shan District, Shanghai,
+            Shanghai 201508, P.R. China
+COMMENT     GenBank Accession Numbers KJ411975-KJ411982 represent sequences
+            from the 8 segments of Influenza A virus
+            (A/Shanghai/01/2014(H7N9)).
+
+            ##Assembly-Data-START##
+            Sequencing Technology :: Sanger dideoxy sequencing
+            ##Assembly-Data-END##
+FEATURES             Location/Qualifiers
+     source          1..1710
+                     /organism="Influenza A virus (A/Shanghai/01/2014(H7N9))"
+                     /mol_type="viral cRNA"
+                     /strain="A/Shanghai/01/2014"
+                     /serotype="H7N9"
+                     /isolation_source="sputum"
+                     /host="Homo sapiens"
+                     /db_xref="taxon:1460072"
+                     /segment="4"
+                     /country="China"
+                     /collection_date="03-Jan-2014"
+     gene            1..1683
+                     /gene="HA"
+     CDS             1..1683
+                     /gene="HA"
+                     /function="receptor binding and fusion protein"
+                     /codon_start=1
+                     /product="hemagglutinin"
+                     /protein_id="AHK10800.1"
+                     /translation="MNTQILVFALIAIIPTNADKICLGHHAVSNGTKVNTLTERGVEV
+                     VNATETVERTNIPRICSKGKRTVDLGQCGLLGTITGPPQCDQFLEFSADLIIERREGS
+                     DVCYPGKFVNEEALRQILRESGGIDKEAMGFTYSGIRTNGATSACRRSGSSFYAEMKW
+                     LLSNTDNAAFPQMTKSYKNTRKSPALIVWGIHHSVSTAEQTKLYGSGNKLVTVGSSNY
+                     QQSFVPSPGARPQVNGLSGRIDFHWLMLNPNDTVTFSFNGAFIAPDRASFLRGKSMGI
+                     QSGVQVDANCEGDCYHSGGTIISNLPFQNIDSRAVGKCPRYVKQRSLLLATGMKNVPE
+                     IPKGRGLFGAIAGFIENGWEGLIDGWYGFRHQNAQGEGTAADYKSTQSAIDQITGKLN
+                     RIIEKTNQQFELIDNEFNEVEKQIGNVINWTRDSITEVWSYNAELLVAMENQHTIDLA
+                     DSEMDKLYERVKRQLRENAEEDGTGCFEIFHKCDDDCMASIRNNTYDHSKYREEAMQN
+                     RIQIDPVKLSSGYKDVILWFSFGASCFILLAIVMGLVFICVKNGNMRCTICI"
+     CDS             1..54
+                     /gene="SigPep"       
+                     /product="Signal peptide"                   
+     CDS             55..1017
+                     /gene="HA1"
+                     /product="HA1"
+     CDS             1018..1683
+                     /gene="HA2"
+                     /product="HA2"
+ORIGIN      
+        1 atgaacactc aaatcctggt attcgctctg attgcgatca ttccaacaaa tgcagacaaa
+       61 atctgcctcg gacatcatgc cgtgtcaaac ggaaccaaag taaacacatt aactgaaaga
+      121 ggagtggaag tcgtcaatgc aactgaaaca gtggaacgaa caaacatccc caggatctgc
+      181 tcaaaaggga aaaggacagt tgacctcggt caatgtggac tcctggggac aatcactgga
+      241 ccacctcaat gtgaccaatt cctagaattt tcagccgatt taattattga gaggcgagaa
+      301 ggaagtgatg tctgttatcc tgggaaattc gtgaatgaag aagctctgag gcaaattctc
+      361 agagaatcag gcggaattga caaggaagca atgggattca catacagtgg aataagaact
+      421 aatggagcaa ccagtgcatg taggagatca ggatcttcat tctatgcaga aatgaaatgg
+      481 ctcctgtcaa acacagataa tgctgcattc ccgcagatga ctaagtcata taaaaataca
+      541 agaaaaagcc cagctctaat agtatgggga atccatcatt ccgtgtcaac tgcagagcaa
+      601 accaagctat atgggagtgg aaacaaactg gtgacagtcg ggagttctaa ttatcaacaa
+      661 tcttttgtac cgagtccagg agcgagacca caagttaatg gtctatctgg aagaattgac
+      721 tttcattggc taatgctaaa tcccaatgat acagtcactt tcagtttcaa tggggctttc
+      781 atagctccag accgtgcaag cttcctgaga ggaaaatcta tgggaatcca gagtggagta
+      841 caggttgatg ccaattgtga aggggactgc tatcatagtg gagggacaat aataagtaac
+      901 ttgccatttc agaacataga tagcagagca gttggaaaat gtccgagata tgttaagcaa
+      961 aggagtctgc tgctagcaac agggatgaag aatgttcctg agattccaaa gggaagaggc
+     1021 ctatttggtg ctatagcggg tttcattgaa aatggatggg aaggcctaat tgatggttgg
+     1081 tatggtttca gacaccagaa tgcacaggga gagggaactg ctgcagatta caaaagcact
+     1141 caatcggcaa ttgatcaaat aacaggaaaa ttaaaccgga ttatagaaaa aaccaaccaa
+     1201 caatttgagt tgatagacaa tgaattcaat gaggtagaga agcaaatcgg taatgtgata
+     1261 aattggacca gagattctat aacagaagtg tggtcataca atgctgaact cttggtagca
+     1321 atggagaacc agcatacaat tgatctggct gattcagaaa tggacaaact gtacgaacga
+     1381 gtgaaaagac agctaagaga gaatgctgaa gaagatggca ctggttgctt tgaaatattt
+     1441 cacaagtgtg atgatgactg tatggccagt attagaaata acacctatga tcacagcaaa
+     1501 tacagggaag aggcaatgca aaatagaata cagattgacc cagtcaaact aagcagcggc
+     1561 tacaaagatg tgatactttg gtttagcttc ggggcatcat gtttcatact tctagccatt
+     1621 gtaatgggcc ttgtcttcat atgtgtaaag aatggaaaca tgcggtgcac tatttgtata
+     1681 taagtttgga aaaaacaccc ttgtttctac
+//
+

config/h7n6/reference_h7n6_mp.gb

@@ -0,0 +1,107 @@
+LOCUS       NC_026427                985 bp    cRNA    linear   VRL 06-FEB-2015
+DEFINITION  Influenza A virus (A/Shanghai/02/2013(H7N9)) segment 7 matrix
+      protein 2 (M2) and matrix protein 1 (M1) genes, complete cds.
+ACCESSION   NC_026427
+VERSION     NC_026427.1
+DBLINK      BioProject: PRJNA274585
+KEYWORDS    RefSeq.
+SOURCE      Influenza A virus (A/Shanghai/02/2013(H7N9))
+  ORGANISM  Influenza A virus (A/Shanghai/02/2013(H7N9))
+            Viruses; ssRNA viruses; ssRNA negative-strand viruses;
+            Orthomyxoviridae; Influenzavirus A.
+REFERENCE   1  (bases 1 to 985)
+  AUTHORS   Zhu,H., Wang,D., Kelvin,D.J., Li,L., Zheng,Z., Yoon,S.W.,
+            Wong,S.S., Farooqui,A., Wang,J., Banner,D., Chen,R., Zheng,R.,
+            Zhou,J., Zhang,Y., Hong,W., Dong,W., Cai,Q., Roehrl,M.H.,
+            Huang,S.S., Kelvin,A.A., Yao,T., Zhou,B., Chen,X., Leung,G.M.,
+            Poon,L.L., Webster,R.G., Webby,R.J., Peiris,J.S., Guan,Y. and
+            Shu,Y.
+  TITLE     Infectivity, transmission, and pathology of human-isolated H7N9
+            influenza virus in ferrets and pigs
+  JOURNAL   Science 341 (6142), 183-186 (2013)
+   PUBMED   23704376
+  REMARK    Erratum:[Science. 2013 Aug 30;341(6149):959]
+REFERENCE   2  (bases 1 to 985)
+  CONSRTM   NCBI Genome Project
+  TITLE     Direct Submission
+  JOURNAL   Submitted (04-FEB-2015) National Center for Biotechnology
+            Information, NIH, Bethesda, MD 20894, USA
+REFERENCE   3  (bases 1 to 985)
+  AUTHORS   Zhu,H., Wang,D., Kelvin,D.J., Li,L., Zheng,Z., Yoon,S.W.,
+            Wong,S.S., Farooqui,A., Wang,J., Banner,D., Chen,R., Zheng,R.,
+            Zhou,J., Zhang,Y., Hong,W., Dong,W., Cai,Q., Roehrl,M.A.,
+            Huang,S.H., Calvin,A.A., Yao,T., Zhou,B., Chen,X., Leung,G.M.,
+            Poon,L.L., Webster,R.G., Webby,R.J., Peiris,J.S., Guan,Y. and
+            Shu,Y.
+  TITLE     Direct Submission
+  JOURNAL   Submitted (10-MAY-2013) Centre of Influenza Research, School of
+            Public Health, The University of Hong Kong, 5/F, Laboratory Block,
+            LKS Faculty of Medicine Building, 21 Sasson Road, Pokfulm, Hong
+            Kong SAR, China
+COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
+            reference sequence is identical to KF021600.
+            GenBank Accession Numbers KF021594-KF021601 represent sequences
+            from the 8 segments of Influenza A virus
+            (A/Shanghai/02/2013(H7N9)).
+
+            ##Assembly-Data-START##
+            Assembly Method       :: Lasergene v. 8.0
+            Sequencing Technology :: 454
+            ##Assembly-Data-END##
+            COMPLETENESS: full length.
+FEATURES             Location/Qualifiers
+     source          1..985
+                     /organism="Influenza A virus (A/Shanghai/02/2013(H7N9))"
+                     /mol_type="viral cRNA"
+                     /strain="A/Shanghai/02/2013"
+                     /serotype="H7N9"
+                     /host="Homo sapiens"
+                     /db_xref="taxon:1332244"
+                     /segment="7"
+                     /country="China"
+                     /collection_date="05-Mar-2013"
+                     /note="passage details: E1"
+     gene            1..982
+                     /gene="M2"
+                     /db_xref="GeneID:23104232"
+     CDS             join(1..26,715..982)
+                     /gene="M2"
+                     /codon_start=1
+                     /product="matrix protein 2"
+                     /protein_id="YP_009118477.1"
+                     /db_xref="GeneID:23104232"
+                     /translation="MSLLTEVETPTRTGWECNCSGSSEPLVVAANIIGILHLILWILD
+                     RLFFKCIYRRFKYGLKRGPSTEGMPESMREEYRQEQQNAVDVDDGHFVNIELK"
+     gene            1..759
+                     /gene="M1"
+                     /db_xref="GeneID:23104231"
+     CDS             1..759
+                     /gene="M1"
+                     /codon_start=1
+                     /product="matrix protein 1"
+                     /protein_id="YP_009118478.1"
+                     /db_xref="GeneID:23104231"
+                     /translation="MSLLTEVETYVLSIIPSGPLKAEIAQRLEDVFAGKNADLEALME
+                     WIKTRPILSPLTKGILGFVFTLTVPSERGLQRRRFVQNALNGNGDPNNMDKAVKLYKK
+                     LKREMTFHGAKEVALSYSTGALASCMGLIYNRMGTVTAEGALGLVCATCEQIADAQHR
+                     SHRQMATTTNPLIRHENRMVLASTTAKAMEQMAGSSEQAAEAMEVASQARQMVQAMRT
+                     VGTHPNSSTGLKDDLIENLQAYQNRMGVQLQRFK"
+ORIGIN
+        1 atgagtcttc taaccgaggt cgaaacgtac gttctctcta tcattccatc aggccccctc
+       61 aaagccgaga tcgcacagag acttgaggat gtttttgcag ggaagaacgc agatctcgag
+      121 gctctcatgg agtggataaa gacaagacca atcctgtcac ctctgactaa ggggatttta
+      181 gggtttgtgt tcacgctcac cgtgcccagt gagcgaggac tgcagcgtag acggtttgtc
+      241 caaaacgccc taaatgggaa tggagaccca aacaacatgg acaaggcggt taaattatac
+      301 aagaaactga agagggaaat gacatttcat ggagcaaagg aagttgcact cagttactca
+      361 actggtgcgc ttgccagctg catgggtctc atatacaaca gaatggggac tgtgaccgca
+      421 gaaggggctc ttggactagt atgtgccact tgtgagcaga ttgctgacgc acaacatcgg
+      481 tcccacaggc agatggcgac tactactaac ccactaatta ggcatgagaa tagaatggta
+      541 ctagccagca ctacggctaa ggctatggag cagatggctg gatcaagtga acaggcagcg
+      601 gaagccatgg aagttgcaag tcaggctagg caaatggtgc aggctatgag aacagttggg
+      661 actcacccta actccagtac aggtctaaaa gatgatctta ttgaaaattt gcaggcctac
+      721 cagaaccgga tgggagtgca actgcagcgg ttcaagtgag cctctagtcg ttgcagctaa
+      781 cattattggg atattgcact tgatattgtg gattcttgat cgtcttttct tcaaatgcat
+      841 ttatcgtcgt tttaaatacg gtttgaaaag agggccttct acggaaggaa tgcctgagtc
+      901 tatgagggaa gaatatcggc aggaacagca gaatgctgtg gatgttgacg atggtcattt
+      961 tgtcaacata gagctgaagt aaaaa
+//