diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 66a4f62..c7f9160 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,7 +1,6 @@ default_language_version: python: python3 -# TODO remove _LEGACY once it's gone -exclude: '\.(tsv|fasta|gb)$|^ingest/vendored/|^_LEGACY' +exclude: '\.(tsv|fasta|gb)$|^ingest/vendored/|' repos: - repo: https://github.com/pre-commit/sync-pre-commit-deps rev: v0.0.1 diff --git a/_LEGACY/Snakefile b/_LEGACY/Snakefile deleted file mode 100644 index 960d9e4..0000000 --- a/_LEGACY/Snakefile +++ /dev/null @@ -1,172 +0,0 @@ -rule all: - input: - auspice_tree = "auspice/yellow-fever_tree.json", - auspice_meta = "auspice/yellow-fever_meta.json" - -rule files: - params: - input_sequences = ["data/genbankReleased.fasta", "data/newSequences.fasta"], - input_metadata = ["data/genbankReleased.csv", "data/newSequences.csv"], - reference = "config/YFV112.gb", - auspice_config = "config/auspice_config.json" - -files = rules.files.params - -rule parse: - """Parsing provided metadata & sequences into augur formats""" - input: - metadata = files.input_metadata, - sequences = files.input_sequences - output: - sequences = "results/sequences.fasta", - metadata = "results/metadata.tsv", - latlongs = "results/latlongs.tsv" - params: - fasta_fields = "strain virus accession date region country division city db segment authors url title journal paper_url" - shell: - """ - python scripts/parseMetadata.py \ - --metadataIn {input.metadata} \ - --metadataOut {output.metadata} \ - --latlongs {output.latlongs} \ - --sequencesIn {input.sequences} \ - --sequencesOut {output.sequences} - """ - -rule align: - """ - Aligning sequences to {input.reference} - - filling gaps with N - """ - input: - sequences = "results/sequences.fasta", - reference = files.reference - output: - alignment = "results/aligned.fasta" - shell: - """ - augur align \ - --sequences {input.sequences} \ - --reference-sequence {input.reference} \ - --output {output.alignment} \ - --fill-gaps \ - --remove-reference - """ - -rule tree: - """Building tree using IQ-TREE""" - input: - alignment = "results/aligned.fasta" - output: - tree = "results/tree_raw.nwk" - shell: - """ - augur tree \ - --alignment {input.alignment} \ - --output {output.tree} - """ - -rule refine: - """ - Refining tree to add names to internal nodes and inferring a timetree. - NOTE: this step can drop samples which are extreme outliers in the root-to-tip analysis - """ - input: - tree = "results/tree_raw.nwk", - alignment = "results/aligned.fasta", - metadata = "results/metadata.tsv" - output: - tree = "results/tree.nwk", - node_data = "results/branch_lengths.json" - params: - root="best", - coalescent = "opt", - clock_filter_iqd = 4, - date_inference = "marginal" - shell: - """ - augur refine \ - --tree {input.tree} \ - --alignment {input.alignment} \ - --metadata {input.metadata} \ - --output-tree {output.tree} \ - --output-node-data {output.node_data} \ - --timetree \ - --coalescent {params.coalescent} \ - --date-confidence \ - --date-inference {params.date_inference} \ - --clock-filter-iqd {params.clock_filter_iqd} \ - --root {params.root} - """ - -rule ancestral: - """Reconstructing ancestral sequences and mutations""" - input: - tree = "results/tree.nwk", - alignment = "results/aligned.fasta", - output: - node_data = "results/nt_muts.json" - params: - inference = "joint" - shell: - """ - augur ancestral \ - --tree {input.tree} \ - --alignment {input.alignment} \ - --output {output.node_data} \ - --inference {params.inference} - """ - -rule traits: - """Inferring ancestral traits for {params.columns!s}""" - input: - tree = "results/tree.nwk", - metadata = "results/metadata.tsv", - output: - node_data = "results/traits.json", - params: - columns = "country" - shell: - """ - augur traits \ - --tree {input.tree} \ - --metadata {input.metadata} \ - --output {output.node_data} \ - --columns {params.columns} \ - --confidence - """ - - -rule export: - """Exporting data files for for auspice""" - input: - tree = "results/tree.nwk", - metadata = "results/metadata.tsv", - branch_lengths = "results/branch_lengths.json", - traits = "results/traits.json", - nt_muts = "results/nt_muts.json", - auspice_config = files.auspice_config, - lat_longs = "results/latlongs.tsv", - annotation_file = "config/genome_annotation_file.json" - output: - auspice_tree = rules.all.input.auspice_tree, - auspice_meta = rules.all.input.auspice_meta - shell: - """ - augur export \ - --tree {input.tree} \ - --metadata {input.metadata} \ - --node-data {input.branch_lengths} {input.traits} {input.nt_muts} {input.annotation_file} \ - --lat-longs {input.lat_longs} \ - --auspice-config {input.auspice_config} \ - --output-tree {output.auspice_tree} \ - --output-meta {output.auspice_meta} - """ - -rule clean: - """Removing directories: {params}""" - params: - "results ", - "auspice" - shell: - "rm -rfv {params}" diff --git a/_LEGACY/auspice/yellow-fever_meta.json b/_LEGACY/auspice/yellow-fever_meta.json deleted file mode 100644 index d08a5a5..0000000 --- a/_LEGACY/auspice/yellow-fever_meta.json +++ /dev/null @@ -1,535 +0,0 @@ -{ - "annotations": { - "nuc": { - "end": 10948, - "start": 0, - "strand": 1 - } - }, - "author_info": {}, - "color_options": { - "collection_year": { - "key": "collection_year", - "legendTitle": "Collection Year", - "menuItem": "Collection Year", - "type": "continuous" - }, - "country": { - "key": "country", - "legendTitle": "country", - "menuItem": "country", - "type": "discrete" - }, - "gt": { - "key": "genotype", - "legendTitle": "Genotype", - "menuItem": "genotype", - "type": "discrete" - }, - "host": { - "key": "host", - "legendTitle": "host", - "menuItem": "host", - "type": "discrete" - }, - "host_genus": { - "key": "host_genus", - "legendTitle": "Host Genus", - "menuItem": "Host Genus", - "type": "discrete" - }, - "host_species": { - "key": "host_species", - "legendTitle": "Host Species", - "menuItem": "Host Species", - "type": "discrete" - }, - "municipality": { - "key": "municipality", - "legendTitle": "municipality", - "menuItem": "municipality", - "type": "discrete" - }, - "municipality_code": { - "key": "municipality_code", - "legendTitle": "Municipality Code", - "menuItem": "Municipality Code", - "type": "discrete" - }, - "num_date": { - "key": "num_date", - "legendTitle": "Sampling date", - "menuItem": "date", - "type": "continuous" - }, - "sample_type": { - "key": "sample_type", - "legendTitle": "Sample Type", - "menuItem": "Sample Type", - "type": "discrete" - }, - "source_file": { - "key": "source_file", - "legendTitle": "Source File", - "menuItem": "Source File", - "type": "discrete" - } - }, - "defaults": { - "colorBy": "source_file", - "distanceMeasure": "div", - "geoResolution": "strain", - "mapTriplicate": false - }, - "filters": [ - "country", - "collection_year", - "sample_type", - "municipality", - "municipality_code", - "host", - "host_genus", - "host_species", - "source_file" - ], - "geo": { - "strain": { - "JF912179": { - "latitude": -14.5238, - "longitude": -49.1396 - }, - "JF912180": { - "latitude": -8.26136, - "longitude": -49.2689 - }, - "JF912182": { - "latitude": -1.99768, - 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"latitude": -19.836, - "longitude": -42.3165 - } - } - }, - "maintainer": [ - "Sarah Hill", - "http://evolve.zoo.ox.ac.uk/Evolve/Sarah_Hill.html" - ], - "panels": [ - "tree", - "map", - "entropy" - ], - "title": "Yellow Fever Virus SA1", - "updated": "04 Jul 2019", - "virus_count": 115 -} \ No newline at end of file diff --git a/_LEGACY/auspice/yellow-fever_tree.json b/_LEGACY/auspice/yellow-fever_tree.json deleted file mode 100644 index bb3cff0..0000000 --- a/_LEGACY/auspice/yellow-fever_tree.json +++ /dev/null @@ -1,8064 +0,0 @@ -{ - "attr": { - "clock_length": 0.001, - "country": "Brazil", - "country_confidence": { - "Brazil": 0.9995141188964265 - }, - "country_entropy": 0.004528573290771894, - "date": "1939-11-06", - "div": 0, - "num_date": 1939.850605222006, - "num_date_confidence": [ - 1925.8145753329113, - 1946.1759317788888 - ], - "strain": "NODE_0000130" - }, - "branch_length": 0.001, - "children": [ - { - "attr": { - "clock_length": 0.00901458563639488, - "country": "Brazil", - "country_confidence": { - "Brazil": 0.9999854129126643 - }, - "country_entropy": 0.00018713030929855533, - "date": "1968-12-22", - "div": 0.009643917695351648, - "num_date": 1968.9770786883855, - "num_date_confidence": [ - 1963.4739612916223, - 1970.9017675275884 - ], - "strain": "NODE_0000004" - }, - "branch_length": 0.00901459, - "children": [ - { - "attr": { - "clock_length": 0.004650411640774113, - "collection_year": 1984, - "country": "Brazil", - "country_confidence": { - "Brazil": 0.9999999999999999 - }, - "country_entropy": -9.99866855976916e-13, - "date": "1984-01-01", - "div": 0.014256935676863064, - "host": "HU", - "host_genus": "Homo", - "host_species": "sapiens", - "municipality": "SaoDomingosDoCapim", - "municipality_code": 1507201.0, - "num_date": 1984.0, - "num_date_confidence": [ - 1984.002737850787, - 1984.8908204941606 - ], - "raw_date": "1984-XX-XX", - "source_file": "genbankReleased.csv", - "strain": "JF912183" - }, - "branch_length": 0.00465041, - "clade": 0, - "muts": [ - "G276A", - "T528G", - "C615T", - "T940C", - "G1014A", - "C1074T", - "C1089T", - "T1248C", - "C1722T", - "C2004T", - "C2085T", - "C2166T", - "C2191T", - "T2232C", - "T2403A", - "T2508C", - "G2655A", - "C2667T", - "C3306T", - "C3312T", - "C3345T", - "C3468T", - "C3507T", - "C4008T", - "T4032C", - "C4035T", - "C4105T", - "G4440A", - "A4884G", - "C4908T", - "T5025C", - "C5196T", - "C5283T", - "T5322C", - "T5791C", - "C6055T", - "C6060T", - "A6882G", - "C7125T", - "T7398C", - "A7905G", - "A8331G", - "C8595T", - "A8816G", - "T9156C", - "T9198C", - "C9369A", - "T9381C", - "C9951T", - "C10281T" - ], - "strain": "JF912183", - "yvalue": 115 - }, - { - "attr": { - "clock_length": 0.0006260875851779747, - "country": "Brazil", - "country_confidence": { - "Brazil": 0.9999935565096031 - }, - "country_entropy": 8.792518578984638e-05, - "date": "1970-12-31", - "div": 0.010675759548647924, - "num_date": 1970.9999917953055, - "num_date_confidence": [ - 1967.1223463088595, - 1973.4459390457255 - ], - "strain": "NODE_0000005" - 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"A4116G", - "G4314A", - "A4917G", - "C5313T", - "G5730A", - "G6039T", - "G6075A", - "C6231T", - "A6355C", - "C6504T", - "T6609C", - "T6762C", - "C7134T", - "T7251C", - "T7788C", - "T7839C", - "C8049T", - "G8106A", - "T8244A", - "T8256C", - "T8271A", - "T8782C", - "A8919G", - "C9072T", - "T9102C", - "C9319T", - "T9354C", - "C9450T", - "C9483T", - "A9564G", - "G9603C", - "A9756G", - "T9759C", - "A9852G" - ], - "strain": "NODE_0000000", - "yvalue": 106.24062521755695 - } - ], - "clade": 208, - "muts": [ - "T270C", - "G426A", - "G483A", - "T657C", - "T1071C", - "A1493G", - "C2166T", - "A2262C", - "T2331C", - "C2733T", - "A4726C", - "G4788A", - "G4875A", - "C5436T", - "C5550T", - "C5628T", - "G5889A", - "T6517C", - "G6534A", - "C6744T", - "T7647C", - "G7770A", - "C8307T", - "T9303C", - "C9684T", - "C9873T", - "T10062C", - "G10130A" - ], - "strain": "NODE_0000001", - "yvalue": 108.12031260877848 - } - ], - "clade": 209, - "muts": [], - "strain": "NODE_0000003", - "yvalue": 109.56015630438924 - } - ], - "clade": 210, - "muts": [], - "strain": "NODE_0000130", - "yvalue": 111.84257815219462 -} \ No newline at end of file diff --git a/_LEGACY/config/YFV112.gb b/_LEGACY/config/YFV112.gb deleted file mode 100644 index 6dcf657..0000000 --- a/_LEGACY/config/YFV112.gb +++ /dev/null @@ -1,290 +0,0 @@ -LOCUS MF465805 10948 bp RNA linear VRL 07-AUG-2018 -DEFINITION Yellow fever virus strain YFV112, complete genome. -ACCESSION MF465805 -VERSION MF465805.1 -KEYWORDS . -SOURCE Yellow fever virus (YFV) - ORGANISM Yellow fever virus - Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA - stage; Flaviviridae; Flavivirus; Yellow fever virus group. -REFERENCE 1 (bases 1 to 10948) - AUTHORS Meneguin,C.B., Di Paola,N., Cunha,M.D.P., Jesus,M.J.R., - Silveira,V.B., Silva,M.V., Zanotto,P.M.A., Durigon,E.L. and - Oliveira,D.B.L. - TITLE Diagnosis and molecular characterization of yellow fever virus - detected from urine and semen in a convalescent patient - JOURNAL Unpublished -REFERENCE 2 (bases 1 to 10948) - AUTHORS Meneguin,C.B., Di Paola,N., Cunha,M.D.P., Jesus,M.J.R., - Silveira,V.B., Silva,M.V., Zanotto,P.M.A., Durigon,E.L. and - Oliveira,D.B.L. - TITLE Direct Submission - JOURNAL Submitted (09-JUL-2017) Microbiology, Institute of Biological - Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 1374, - Sao Paulo, SP 05508-000, Brazil -COMMENT ##Assembly-Data-START## - Assembly Method :: Bowtie v. 2 - Coverage :: 112.6 - Sequencing Technology :: Illumina - ##Assembly-Data-END## -FEATURES Location/Qualifiers - source 1..10948 - /organism="Yellow fever virus" - /mol_type="genomic RNA" - /strain="YFV112" - /isolation_source="urine" - /host="Homo sapiens" - /db_xref="taxon:11089" - /country="Brazil" - /collection_date="17-Jan-2017" - /note="genotype: South America I" - CDS 109..10344 - /codon_start=1 - /product="polyprotein" - /protein_id="ATN45408.1" - /translation="MSGRKAQGKTLGVNMVRRGVRSLSSKIKQKTKQIGSRPGPSRGV - QGFVFFFLFNVLTGKKITAHLKKLWRMLDPRQGLVVLRKVKRVVASLMRGLSSRKRRS - QDVLTIQFLILGMLLMVGGVTLVRRNRWLLLNVTSEDLGKTFSVGTGNCTTNILEAKY - WCPDSMEYNCPNLSPREEPDDIDCWCYGVENVRVAYGKCDSAGRSRRSRRAIDLPTHE - NHGLKTRQEKWMTGRMGERQLQKIERWLVRNPFFAATALAIAYLVGSNMTQRVVIALL - VLAVGPAYSAHCIGITDRDFIEGVHGGTWVSATLEQDKCVTVMAPDKPSLDISLETVA - IDGPAEARKVCYSAVLTNVKINDKCPSTGEAHLEEENEGDNACKRTYSDRGWGNGCGL - FGKGSIVACAKFTCAKSMSLFEVDQTKIQYVIRAQLHVGAKQENWNTDIKTLKFDALS - GSQEAEFTGYGRATLECQVQTAVDFSNSYIAEMEKESWIVDKQWAQDLTLPWQSGSGG - VWREMHHLVEFEPPHAATIKVLALGNQEGSLKTALTGAMRVTKDTNNSKLYKLHGGHV - ACRVKLSALTLKGTSYKMCTDKMSFVKNPTDTGHGTAVMQVKVPKGAPCRIPVMVADD - LTAAVNKGILVTVNPIASTNDDEVLIEVNPPFGDSYIIVGTGDSRLTYQWHKEGSSIG - KLFTQTMKGAERLAVMGDAAWDFGSAGGFFTSVGKGIHTVFGSAFQGLFGGLSWITKV - IMGVVLIWVGINTRNMTMSMSMILVGVIMMFLSLGVGADQGCAINFGKRELKCGDGIF - VFRDSDDWLNKYSYYPEDPVKLASIVKASFEEGKCGLNSVDSLEHEMWRSRADEINAI - LEENEVDISVVVQDSKNIYQRGTHPFSRIRDGLQYGWKTWGKNLVFSPGRKNGSFIID - GKSRKECPFSNRVWNSFQIEEFGTGVFTTRVYMDAVFEYTMDCDGSILGAAVNGKKSA - HGSPTFWMGSHEVNGTWMIHTLETLDYKECEWPLTHTIGTSVEESDMFMPRSIGGPVS - SHNHIPGYKVQTNGPWMQVPLEVKREACPGTSVVVDGGCDGRGKSTRSTTDSGKIIPE - WCCRSCTMPPVSFHGSDGCWYPMEIRPKKTHDSHLVRSWVTAGEIHAIPFGLVSMMIA - MEVVLRKRQGPKQILVGGMVLLGAMLVGQVTILDLLKLTVAVGLHFHEMNNGGDAMYM - ALIAAFSIRPGLLIGFGLRTLWSPRERLVLTLGAAMVEIALGGMMGGLWKYLNAVSLC - ILTINAVASRKASNVILPLMALLTPVTMAEVRLATMLFCTVVIIGVLHQNSKDTSMQK - TIPLVALTLTSYLGLTQPFLGLCAFMATRIFGRRSIPVNEALAAAGLVGVLAGLAFQE - MENFLGPVAVGGILMMLVSVAGRVDGLELRKLGEVSWEEEAEISGSSARYDVTLSEQG - EFKLLSEEKVPWDQVVMTSLALVGAAIHPFALLLVLAGWLFHVKGARRSGDVLWDIPT - PKIIEECEYLEDGIYGIFQSTFLGASQRGVGVAQGGVFHTMWHVTRGAFLVRNGKKLV - PSWASVKEDLVAYGGSWKLDGRWDGEEEVQLIAAAPGKNVVNVQTKPSLFKVKNGGEI - GAVALDYPSGTSGSPIVNRNGEVIGLYGNGILVGDNSFVSAISQTEVKEEGKEELQEI - PTMLKKGMTTILDFHPGAGKTRRFLPQILAECARRRLRTLVLAPTRVVLSEMKEAFHG - LDVKFHTQAFSAHGSGKEVIDAMCHATLTYRMLEPTRVVNWEVIIMDEAHFLDPASIA - ARGWAAHRARANESATILMTATPPGTSDEFPHSNGEIEDVQTDIPSEPWNTGHDWILA - DKRPTAWFLPSIRAANVMAASLRKAGKSVVVLNRKTFEKEYPTIKQKKPDFILATDIA - EMGANLCVERVLDCRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGD - SYYYSEPTSEDNAHHVCWLEASMLLDNMEVRGGMVAPLYGIEGTKTPVSPGEMRLRDD - QRRVFRELVRNCDLPVWLSWQVAKAGLKTNDRRWCFEGPEEHEILNDSGETVKCRAPG - GAKKPLRPRWCDERVSSDQSALADFIKFAEGRRGAAEMLVVLSELPDFLAKKGGEAVD - TISVLLHSEEGSRAYRNALSMMPEAMTTVMLFVLAGLLTSGMVIFFMSPKGISRMSMA - MGTMAGCGYLMFLGGVKPTHISYIMLIFFVLMVVVVPEPGQQRTIQDNQVAYLIIGIL - TLISVVAANELGMLEKTKEDLFGKKNLIPSSAAPWSWPDLDLKPGAAWTVYVGIVTML - SPMLHHWIKVEYGNLSLSGIAQSASVLSFMDKGIPFMKMNISVIILLVSGWNSITVMP - LLCGIGCAMLHWTLILPGIKAQQSKLAQRRVFHGVAKNPVVDGNPTVDIEEAPEMPAL - YEKKLALYLLLALSLASVAMCRTPFSLAEGIVLASAALGPLIEGNTSLLWNGPMAVSM - TGVMRGNYYAFVGVMYNLWKMKTGRRGRANGKTLGEVWKRELNLLDKQQFELYKRTDI - VEVDRDTARRHLAEGKVDTGVAVSRGTAKLRWFHERGYVKLEGRVTDLGCGRGGWCYY - AAAQREVSGVRGFTLGKEGHEKPMNVQSLGWNIITFKDKTDVHRLEPIKCDTLLCDIG - ESSPSSVTEGERTMRVLDTVEKWLSCGVESFCVKVLAPYMPDVLEKLELLQRRFGGTV - IRNPLSRNSTHEMYYVSGARSNITFTVNQTSRLLMRRMRRPTGKVTLEADVILPIGTR - SVETDKGPLDRAAIEERVERIKSEYTATWFHDSDNPYRTWHYCGSYVTRTSGSAASMI - NGVIKILTYPWDRIEEVTRMAMTDTTPFGQQRVFKEKVDTRAKDPPAGTRKIMKVVNR - WLFRHLAREKNPRLCTKEEFIAKVRSHAAIGAFLEEQEQWKTANEAVQDPKFWELVDE - ERRLHQQGRCRTCVYNMMGKREKKLSEFGKAKGSRAIWYMWLGARYLEFEALGFLNED - HWASRENSGGGVEGIGLQYLGYVIRDLAALEGGGFYADDTAGWDTRITEADLDDEQEI - LNYMSPHHRKLALAVMEMTYKNKVVKVLRPAPGGKAYMDVISRRDQRGSGQVVTYALN - TITNLKVQLIRMAEAEMVIHHQHVQDCDDTALTKLEAWLAEHGCDRLKRMAVSGDDCV - VRPIDDRFGLALSHLNAMSKVRKDISEWQPSKGWDDWESVPFCSHHFHELQLKDGRRI - VVPCRDQDELVGRGRVSPGNGWMIKETACLSKAYANMWSLMYFHKRDMRLLSLAVSSA - VPTSWVPQGRTTWSVHGKGEWMTTEDMLEVWNRVWITNNPHMQDKTTVKEWRDIPYLT - KRQDKLCGSLIGMTNRATWASHIHLVIHRIRTLIGKERYTDYLTVMDRYSADADLQPG - ELI" -ORIGIN - 1 gtgtgctaat tgaggtgcat tggtctgcaa atcgagttgc taggcaataa acacatttgg - 61 attaattttg atcgttcgtt gagcgattag cagagaattg accagaaaat gtctggtcgt - 121 aaagctcagg gaaaaaccct gggcgtcaat atggttcgac gaggagtccg ctccttgtca - 181 agcaaaataa aacaaaaaac aaaacaaatt ggaagtagac ctggaccttc aagaggcgtt - 241 caaggatttg tttttttctt tttgttcaac gttttgactg gaaagaagat tactgctcat - 301 ctgaagaaac tatggagaat gctggaccca agacagggct tagttgtcct gaggaaggtt - 361 aagagggtgg tggcgagtct gatgagaggt ttgtcctcga ggaaacgccg atcccaagat - 421 gttttgacta ttcaattttt aattctggga atgctgctga tggttggtgg agtgaccctg - 481 gtacgcagaa acagatggtt acttctgaat gttacatctg aggaccttgg gaaaaccttc - 541 tccgttggca caggcaactg cacaaccaac attctggagg ccaaatactg gtgtccagat - 601 tccatggaat acaactgccc caatctcagt ccaagagaag agcctgatga catagactgt - 661 tggtgctatg gagtggaaaa tgtcagagtc gcttatggca agtgtgattc agcgggtagg - 721 tcaagaaggt ccagaagggc cattgactta cccacacatg aaaatcatgg cttaaagacc - 781 cggcaagaaa agtggatgac tggaagaatg ggcgagagac agctgcagaa aattgaaaga - 841 tggctggtga ggaacccctt ctttgcggca acagccttgg ccattgccta cctggtgggg - 901 agcaacatga cgcaacgagt tgtcattgcc ctgctagtct tggctgttgg cccagcctat - 961 tcggctcact gtataggaat aaccgacagg gatttcattg agggggtgca tgggggaacc - 1021 tgggtttcag ccaccttgga acaggacaag tgtgtcactg tgatggcccc cgacaagcct - 1081 tcactagaca tatcactaga aacagttgcc attgatggac ctgctgaggc aaggaaggtg - 1141 tgctacagtg cagtcttgac caacgtgaag atcaatgaca agtgccccag cactggtgaa - 1201 gcccacttgg aagaagaaaa tgaaggagac aatgcttgca agcgaactta ctccgataga - 1261 ggttggggaa atggttgtgg cttgtttgga aaaggaagca ttgtggcatg tgccaagttt - 1321 acctgtgcca aatccatgag tctatttgag gttgatcaga ccaaaattca gtatgtcatt - 1381 agggcacagc tacatgtcgg agccaagcag gagaactgga acactgacat caaaactctc - 1441 aagtttgatg ccctgtcggg ctctcaggaa gctgagttca ctggatacgg gagggccaca - 1501 ctggagtgcc aggtgcagac cgcagtggac ttcagtaaca gttacattgc agagatggag - 1561 aaagagagct ggattgtgga taaacagtgg gcccaagacc tgaccctacc ttggcagagt - 1621 ggaagtggcg gcgtgtggag agagatgcat catctcgtgg aatttgagcc tccacatgcc - 1681 gcaactatca aagtgttagc ccttggaaac caagaaggat ccttgaagac tgctctcact - 1741 ggtgcaatgc gagtcacaaa agacacaaac aacagcaagc tgtataagct gcatgggggg - 1801 catgtcgcgt gtagggtgaa gttgtcagct ctcacactta agggaacatc ctacaagatg - 1861 tgtaccgaca aaatgtcttt tgtcaagaac ccaactgaca ctggacatgg cactgcagtg - 1921 atgcaagtga aggtgccaaa aggagcaccc tgcaggattc cagtaatggt cgccgatgat - 1981 ctcacagcgg cagtcaacaa gggcatcttg gtcacagtca atccaatagc ctccaccaat - 2041 gatgatgaag tgttgatcga ggtgaatcct ccctttgggg atagttacat catagttggg - 2101 acaggggatt cacgcctgac ttaccagtgg cacaaggaag gcagctcaat agggaagttg - 2161 tttactcaga ccatgaaggg cgcagagcgt ctggccgtca tgggagatgc tgcctgggac - 2221 tttggttctg ctggaggatt cttcacatca gtcggaaaag gcatacacac tgtgtttggc - 2281 tctgccttcc aagggctgtt tggtggcttg agctggataa caaaggtcat catgggggta - 2341 gtcctcatat gggttggcat taacacaagg aatatgacaa tgtccatgag catgatccta - 2401 gttggagtca tcatgatgtt cctgtcccta ggagttgggg cggaccaagg atgtgcaata - 2461 aactttggca agagagaact caagtgtggg gatggcatct tcgtctttag agattcagat - 2521 gactggctga acaagtattc atactatcca gaggacccag taaaacttgc ttcaatagtg - 2581 aaagcttcct ttgaggaagg gaagtgtggc ctgaactcag tcgactccct ggaacatgag - 2641 atgtggagaa gcagggcaga tgagatcaat gccattcttg aggaaaatga ggtagacatc - 2701 tcagtggtgg tccaagactc aaaaaacatt tatcagagag ggacacatcc gttttccaga - 2761 atacgtgatg gcctacaata cggctggaag acttggggca aaaaccttgt gttctcccca - 2821 ggaagaaaga atggaagctt catcatagat gggaagtcca ggaaagagtg tccgttctca - 2881 aacagagtgt ggaattcctt ccagatagaa gagtttggga caggagtgtt caccacccga - 2941 gtgtacatgg atgcagtctt tgagtacact atggattgtg atggatccat cctgggtgca - 3001 gcagtgaatg gaaagaagag cgcgcatggg tccccaacat tctggatggg aagccatgag - 3061 gtgaatggaa catggatgat tcatactcta gagacactgg actacaagga atgtgaatgg - 3121 ccgctgacac acacgattgg aacatcagtt gaagagagtg acatgttcat gccgaggtca - 3181 attgggggtc cagttagctc ccacaaccac attccgggat ataaggtcca gacaaacgga - 3241 ccctggatgc aggtgccact agaggtgaaa agggaagctt gcccaggaac cagtgtggtt - 3301 gttgacggag gctgtgatgg gcgtgggaag tcgaccagat cgaccactga cagcgggaag - 3361 atcattcctg aatggtgttg ccgctcatgc acaatgccac cagtgagctt ccacgggagt - 3421 gatggttgct ggtatcctat ggagattaga ccaaagaaga cacatgacag ccacctggtc - 3481 cgctcatggg taacggctgg agagatccat gcaatcccct ttgggttggt gagcatgatg - 3541 atagccatgg aagtggtatt gaggaagaga cagggaccca agcaaatact ggttgggggc - 3601 atggtgcttc taggagccat gctagttgga caggtgacta tcttggactt gctgaagctc - 3661 acagtggcgg ttggactgca ctttcatgag atgaataatg gaggggatgc catgtatatg - 3721 gccctgatcg ctgctttctc aatcagacca gggctgctca tcggctttgg attgaggacg - 3781 ctgtggagcc cccgagaacg cctcgtgctg accctggggg ccgccatggt ggagattgct - 3841 ttgggtggca tgatgggagg tctgtggaag tacctgaacg cagtgtccct ttgcatcctg - 3901 acaataaacg ctgttgcctc cagaaaagca tcaaatgtca tcctgccctt gatggctctg - 3961 ttaacacctg tgacaatggc tgaggtgaga cttgcaacaa tgctcttctg cactgtggtc - 4021 atcatcggcg ttctccatca gaactcaaag gacacttcca tgcagaagac catacccctg - 4081 gtggccctca cactgacatc ctacctggga ctgacgcagc ccttcttggg cttgtgtgcc - 4141 ttcatggcaa cccgaatatt cgggcgaagg agcatcccag tgaatgaagc gcttgcagct - 4201 gctggtctcg tgggagtctt ggcagggcta gctttccagg agatggaaaa ttttctaggt - 4261 ccagttgcag ttggaggaat cctgatgatg ctggtcagtg tggctgggag ggtagatgga - 4321 cttgaactca ggaagcttgg ggaagtttct tgggaagaag aagctgagat cagtggaagt - 4381 tctgcccgtt atgatgtaac tctcagtgag caaggggaat ttaaactact ctctgaagag - 4441 aaggtgccat gggatcaggt tgtgatgact tcactggctt tggtcggagc tgccatccat - 4501 ccatttgcac ttttattggt tcttgctggc tggttgttcc acgtcaaagg agccagaaga - 4561 agtggggatg tcctttggga cattcccaca cctaaaatca ttgaggagtg tgaatatcta - 4621 gaggatggaa tctacggcat attccagtca acattcctag gggcctctca acggggagtg - 4681 ggagtggcgc agggaggggt cttccatacg atgtggcacg tcacgcgagg ggcctttctc - 4741 gttagaaatg gtaaaaagct ggttccatcc tgggcctcag tcaaggaaga ccttgttgct - 4801 tatggcggct catggaagtt ggatggtaga tgggatggag aagaggaggt tcagttgata - 4861 gcagctgccc ccggaaaaaa cgtagtgaat gtccaaacaa agccaagcct attcaaggtt - 4921 aagaatggag gagaaattgg ggcggttgcc cttgactacc caagtggcac ttctggttct - 4981 cccatcgtca acaggaatgg tgaggtaata gggctgtatg gcaatggaat tcttgttggt - 5041 gacaactctt ttgtgtctgc catatcccaa actgaggtga aagaggaggg gaaagaggag - 5101 ctacaggaaa tcccgacaat gttgaagaaa gggatgacaa ccattcttga tttccatcct - 5161 ggagctggga aaacaagacg ttttcttcct cagatcctgg ctgaatgcgc acgaagacgg - 5221 ttgcgcacac ttgtgctggc tcctactaga gttgtccttt ctgaaatgaa ggaagccttt - 5281 cacggtttag atgtcaagtt tcacacacag gctttctctg ctcacggtag cggaaaagag - 5341 gtcattgacg ccatgtgtca tgccaccctg acatatagaa tgttggaacc aaccagagtg - 5401 gtcaattggg aagtgatcat catggacgaa gcacattttt tggatccggc tagcatagca - 5461 gccagaggct gggcggcaca tagagccaga gcaaatgaaa gtgcaacaat cttgatgact - 5521 gctacccctc cgggaaccag tgatgaattt ccacattcaa atggggaaat agaggatgtc - 5581 caaacggaca ttcctagtga gccttggaac acaggtcatg actggatttt ggcggacaaa - 5641 aggcccacgg cctggtttct tccatccatc agggcagcaa atgtcatggc agcctctttg - 5701 cgcaaagctg gaaagagtgt ggtggtgcta aacaggaaaa cctttgagaa agaatacccc - 5761 acaattaaac agaaaaaacc tgatttcatc ttggccactg acatagctga gatgggagcc - 5821 aatctctgcg tggagagagt gttggattgt aggacggctt tcaaacctgt gcttgtggat - 5881 gaagggagaa aggtggcaat aaaagggcca ctccggattt cagcttcctc cgctgctcaa - 5941 aggagggggc gcattggaag gaaccctaac agagacgggg attcatacta ctactctgag - 6001 cccacaagtg aagacaatgc gcatcatgtc tgctggcttg aggcctcaat gctcctagac - 6061 aacatggagg tgagaggtgg gatggttgct ccactttatg gcatagaagg aacaaagaca - 6121 ccagtttccc caggtgaaat gaggctaaga gatgaccaga ggagagtctt ccgagagctg - 6181 gtgaggaatt gtgacctgcc tgtttggctc tcatggcaag tggctaaggc tggattgaag - 6241 acgaatgacc gaaggtggtg ctttgagggc ccagaagaac atgagatctt gaatgacagt - 6301 ggtgagacag taaagtgcag agcccctgga ggagccaaga agcctctgcg tccacggtgg - 6361 tgcgatgaaa gggtgtcgtc tgaccagagt gcgcttgccg acttcataaa gtttgctgag - 6421 ggcaggagag gggctgctga gatgctggtc gtgctgagtg aactcccaga cttcttggcc - 6481 aagaaaggtg gagaggcggt ggatactatc agcgtgctct tgcactctga ggaaggttcc - 6541 agagcttacc gcaatgcatt gtcaatgatg cctgaggcaa tgacaacagt catgctgttt - 6601 gttctggccg ggctgctgac gtctggaatg gttatctttt tcatgtctcc caagggtatc - 6661 agcagaatgt ctatggcaat gggcacgatg gctggttgtg gatacctcat gtttcttgga - 6721 ggcgtcaaac ccacccacat ctcttacatc atgctaatat tctttgtctt gatggtggtt - 6781 gtggttccgg agccggggca gcagagaacc attcaggaca atcaagtggc ttatcttatt - 6841 attggcatcc tgacgctgat ttctgtggtg gcagccaatg aactaggcat gctggaaaag - 6901 actaaggaag acctctttgg aaaaaagaat ttgattccat ctagtgccgc accttggagc - 6961 tggccagatc ttgacttgaa accaggagct gcttggactg tctatgttgg cattgtcaca - 7021 atgctctccc caatgctgca ccactggatc aaggttgagt atggtaatct gtctttgtct - 7081 ggaattgcac agtcagcctc agttttgtca ttcatggaca agggcatccc gtttatgaag - 7141 atgaacatct cggtcataat tctactggtc agtggctgga attcaataac ggtgatgccc - 7201 ctgctttgtg gcattggatg cgccatgcta cactggactc tcatcctgcc cggaataaaa - 7261 gcgcagcagt caaagctggc acagaggagg gtgtttcatg gtgttgctaa gaatccggtg - 7321 gttgatggga atccaacagt cgacattgag gaagccccgg aaatgcctgc cctctatgag - 7381 aagaagttgg cattgtatct tctgcttgcc cttagcttgg cctctgttgc catgtgtaga - 7441 acacccttct cactggctga aggcattgtg ctggcatcag cagccctggg accgctcatc - 7501 gagggaaata ccagcctctt gtggaatgga cccatggctg tgtccatgac aggagtcatg - 7561 cgggggaact actatgcttt tgtgggtgtt atgtacaatc tctggaagat gaagactgga - 7621 cgcaggggga gagcgaatgg gaagaccctg ggtgaggtct ggaaaaggga gctgaacctg - 7681 ctggacaaac agcagtttga gctgtataaa cggacagaca ttgtggaggt ggaccgtgac - 7741 acagctcgcc gacacctggc tgaagggaaa gtggacaccg gagtggccgt ctcgagaggg - 7801 accgcaaaat tgagatggtt ccatgaacgt ggctatgtca agttggaagg aagagtgact - 7861 gacctgggat gtgggcgtgg tggctggtgc tactacgctg ctgcacagag agaagtgagt - 7921 ggggtcaggg gattcaccct tggaaaggaa ggccacgaaa agcccatgaa tgtgcagagc - 7981 ctggggtgga acatcatcac cttcaaggac aagactgatg tccatcgcct tgagccgata - 8041 aagtgtgata ccctgctgtg cgacattgga gagtcgtccc catcatcagt gaccgaaggg - 8101 gaaagaacca tgagagttct tgacactgtt gagaaatggt tgagctgtgg tgttgaaagc - 8161 ttctgtgtga aggtgttggc tccatacatg cctgatgtgc ttgaaaagtt agagttgctc - 8221 caaaggaggt ttggtggaac ggtaatcagg aatcccctct ctagaaattc aacccacgag - 8281 atgtattatg tgtcgggagc ccgcagtaac atcacgttca ctgtgaatca aacatcccgc - 8341 ctcttaatga ggagaatgag gcgcccgaca ggcaaggtga ctcttgaagc cgatgtcatc - 8401 ctcccaattg gaacacgcag tgtggaaaca gacaaaggac cacttgatag ggcagccatt - 8461 gaagagaggg ttgaaagaat aaaatcagaa tacaccgcca cttggttcca tgatagtgac - 8521 aacccttaca ggacttggca ttattgtggt tcctacgtca caagaacctc agggagtgca - 8581 gcaagcatga ttaacggggt gattaagatc ttgacatacc cctgggacag gatagaggaa - 8641 gtcacgagaa tggcaatgac agacacaact ccttttggac aacaaagagt gttcaaggaa - 8701 aaagttgaca ccagagcaaa ggatccacca gcagggacca ggaaaatcat gaaggttgtc - 8761 aataggtggc tattccgtca cttggccaga gaaaagaacc ccaggttgtg cacaaaggag - 8821 gagtttatag caaaagttcg cagtcatgca gccatcggag ctttcctgga agagcaagaa - 8881 cagtggaaga ctgccaatga agctgtccaa gatccgaagt tctgggaatt agtggatgaa - 8941 gaacgacggc tgcatcagca gggcaggtgc cgaacttgtg tgtacaacat gatggggaag - 9001 agagaaaaga agctgtcaga gtttggaaag gcgaagggaa gccgtgccat ctggtacatg - 9061 tggctgggag cccgatatct tgagtttgaa gccctgggat tcctgaatga ggaccactgg - 9121 gcatccaggg agaactcagg gggaggggtt gaaggtatcg gtctacaata tctaggctac - 9181 gtgatcaggg acctggctgc actagagggt ggtggattct atgcggatga cacagctgga - 9241 tgggacacac gcataacaga ggcggatctg gatgatgaac aggaaatctt gaactacatg - 9301 agcccacacc ataggaagtt ggcgctggct gtaatggaaa tgacatacaa aaacaaagtg - 9361 gtgaaagtcc tgaggccagc tccaggtggg aaagcttaca tggatgtcat aagccggcgg - 9421 gaccagagag gatctgggca ggtggtgact tacgccttga acaccatcac caacctgaag - 9481 gttcaactga ttaggatggc ggaggcagag atggtgatac accaccagca tgtccaggac - 9541 tgtgacgaca cggctttgac caagcttgaa gcatggctcg ctgagcatgg ctgcgacagg - 9601 cttaagagga tggcagtgag tggagatgac tgtgttgtcc gacccattga tgacaggttt - 9661 ggcctggctc tgtcccatct caatgccatg tcaaaggtgc gaaaagacat atctgaatgg - 9721 cagccatcaa aaggatggga tgactgggag agtgtgccct tttgctctca ccactttcat - 9781 gaactgcaat tgaaggatgg caggagaatt gtagtgcctt gccgggatca agatgagctg - 9841 gttggcaggg ggagagtgtc tccagggaat ggttggatga tcaaggagac agcatgcctt - 9901 agcaaggcct acgccaacat gtggtcactg atgtactttc acaagaggga catgaggctg - 9961 ctttcactgg ctgtttcttc tgctgttccc acatcttggg ttccacaggg acgcaccacg - 10021 tggtctgttc atgggaaggg agagtggatg accacagaag acatgcttga ggtgtggaac - 10081 agagtgtgga taaccaacaa tccacacatg caggacaaaa cgacggtgaa ggagtggcga - 10141 gacatccctt acctgaccaa gagacaggac aagctttgtg gatcactgat tgggatgacc - 10201 aacagagcca cttgggcatc tcacatccac ttggtaatac accgcatccg gacactgatt - 10261 gggaaagaga gatacactga ctacctgaca gtcatggata ggtactctgc ggatgctgat - 10321 ctgcagcccg gtgagctcat ttgagacacc gttccaagaa caatcaagaa ctagactttg - 10381 tacatagaac aaaactgaaa ccgggataaa aactacggat ggagaaccgg actccacaca - 10441 tcaaacacaa gaggatgtca gcccagaaac ccgcgtgggt tctgccactg ctaagctgtg - 10501 aggcagtgca ggctgggaca gccgccttcc aggctgcgaa aacctggttt ctgagacttc - 10561 ccacctcaga gtaaaaccaa atggagcctc cgctaccacc cccccacgtg gtggtagaaa - 10621 gatggggtct agaggttaga ggagaccctc cagggaacaa atagtgggat gtcagcccag - 10681 aaacccgcgt gggttctgtc actgctaagc tgtgaggcag tgcaggctgg gacagccgcc - 10741 ctccatgttg cgaaaaacct ggtttctgag acttcccacc tcagagttaa accaaatgga - 10801 gcctccgcta ccacctcccc acgtggtggt agaaagacgg ggtctagagg ttagaggaga - 10861 ccctccaggg aataaatagt gggaccatat tgacgccagg gaaagaccgg agtggttctc - 10921 tgcttttcct ccagaggtct gtgagcac -// - diff --git a/_LEGACY/config/auspice_config.json b/_LEGACY/config/auspice_config.json deleted file mode 100644 index 3a7cb19..0000000 --- a/_LEGACY/config/auspice_config.json +++ /dev/null @@ -1,79 +0,0 @@ -{ - "title": "Yellow Fever Virus SA1", - "color_options": { - "gt": { - "menuItem": "genotype", - "legendTitle": "Genotype", - "type": "discrete", - "key": "genotype" - }, - "country": { - "type": "discrete" - }, - "num_date": { - "menuItem": "date", - "legendTitle": "Sampling date", - "type": "continuous" - }, - "collection_year": { - "menuItem": "Collection Year", - "legendTitle": "Collection Year", - "type": "continuous" - }, - "sample_type": { - "menuItem": "Sample Type", - "legendTitle": "Sample Type", - "type": "discrete" - }, - "municipality": { - "type": "discrete" - }, - "municipality_code": { - "menuItem": "Municipality Code", - "legendTitle": "Municipality Code", - "type": "discrete" - }, - "host": { - "type": "discrete" - }, - "host_genus": { - "menuItem": "Host Genus", - "legendTitle": "Host Genus", - "type": "discrete" - }, - "host_species": { - "menuItem": "Host Species", - "legendTitle": "Host Species", - "type": "discrete" - }, - "source_file": { - "menuItem": "Source File", - "legendTitle": "Source File", - "type": "discrete" - } - }, - "geo": [ - "strain" - ], - "defaults": { - "mapTriplicate": false, - "distanceMeasure": "div", - "geoResolution": "strain", - "colorBy": "source_file" - }, - "maintainer": [ - "Sarah Hill", - "http://evolve.zoo.ox.ac.uk/Evolve/Sarah_Hill.html" - ], - "filters": [ - "country", - "collection_year", - "sample_type", - "municipality", - "municipality_code", - "host", - "host_genus", - "host_species", - "source_file" - ] -} diff --git a/_LEGACY/config/genome_annotation_file.json b/_LEGACY/config/genome_annotation_file.json deleted file mode 100644 index 74712ab..0000000 --- a/_LEGACY/config/genome_annotation_file.json +++ /dev/null @@ -1,9 +0,0 @@ -{ - "annotations": { - "nuc": { - "end": 10948, - "start": 0, - "strand": 1 - } - } -} \ No newline at end of file diff --git a/_LEGACY/scripts/parseMetadata.py b/_LEGACY/scripts/parseMetadata.py deleted file mode 100644 index b7c73f3..0000000 --- a/_LEGACY/scripts/parseMetadata.py +++ /dev/null @@ -1,113 +0,0 @@ -import argparse -import csv -from Bio import SeqIO -from treetime.utils import numeric_date -from datetime import datetime -import os - -""" -We expect the input CSV files to have these headers: - "","Sequence_name","Sample_type","Municipality","Host","Host_genus","Host_species","Longitude","Latitude","Municipality_code","Date_collection" -Where sequence name looks like (e.g.) "JF912179|Brazil|GO|Uruacu|MO|Haemagogus||1980" - -""" - -def parse_args(): - parser = argparse.ArgumentParser(description="Process YFV metadata into a format for analysis with augur") - parser.add_argument('--metadataIn', metavar='CSV', type=str, nargs="+", required=True, help="input CSV file(s) of YFV metadata") - parser.add_argument('--sequencesIn', metavar='FASTA', type=str, nargs="+", required=True, help="input FASTA file(s) of YFV sequences") - parser.add_argument('--metadataOut', metavar='TSV', type=str, required=True, help="output TSV file for augur") - parser.add_argument('--sequencesOut', metavar='FASTA', type=str, required=True, help="output FASTA file for augur") - parser.add_argument('--latlongs', metavar='TSV', type=str, required=True, help="output lat/long file for augur") - return parser.parse_args() - -def convert_date_fields_to_numeric(date_fields): - nXX = date_fields.count("XX") - if nXX == 0: - return numeric_date(datetime.strptime("-".join(date_fields), "%Y-%M-%d")) - elif nXX == 1: - return numeric_date(datetime.strptime("-".join(date_fields[0:2])+"-15", "%Y-%M-%d")) - elif nXX == 2: - return date_fields[0] - else: - raise Exception("Unknown date format -- ", date_fields) - -def parse_metadata(metadataIn): - tsv_header = ["strain", "date", "num_date", "collection_year", "sample_type", "country", "municipality", "municipality_code", "host", "host_genus", "host_species", "source_file", "authors"] - tsv_data = [] - strains = set() - lat_long_data = {} - for csv_path in args.metadataIn: - with open(csv_path, "rU") as fh: - reader = csv.DictReader(fh) - for row in reader: - # manually extract strain from sequence name - strain = row.get("Sequence_name").split("|")[0] - # country is encoded in the sequence name, not a CSV field (!) - country = row.get("Sequence_name").split("|")[1] - # store lat/longs if they are present - if row.get("Latitude") and row.get("Longitude"): - try: - lat_long_data[strain] = [float(row.get("Latitude")), float(row.get("Longitude"))] - except ValueError: - # Non numeric values, e.g. "NA" shouldn't be added to the dictionary - pass - # parse the (sample) date information into the format augur expects: - # YYYY-MM-DD, with "XX" for missing fields - date_fields = row.get("Date_collection").split("-") - if not len(date_fields) or len(date_fields) > 3: - print("WARNING: strain {} is missing date information. Skipping".format(strain)) - continue - while len(date_fields) != 3: - date_fields.append("XX") - # num_date = numeric_date(datetime.strptime(date.split("-")[0], "YYYY")) if "XX" in date else numeric_date(datetime.strptime(date, "YYYY-MM-DD")) - # store for export - strains.add(strain) - tsv_data.append([ - strain, - "-".join(date_fields), - str(convert_date_fields_to_numeric(date_fields)), - str(date_fields[0]), - row.get("Sample_type"), - country, - row.get("Municipality"), - row.get("Municipality_code"), - row.get("Host"), - row.get("Host_genus"), - row.get("Host_species"), - os.path.basename(csv_path), - "" # adding a blank authors field stops `augur export` errors - ]) - return (tsv_header, tsv_data, lat_long_data, strains) - -def parse_fasta(fasta_paths, metadata_strains): - data = [] - for fasta_path in fasta_paths: - for seq_record in SeqIO.parse(fasta_path, "fasta"): - # turn 'HM582851|TrinidadAndTobago|NotApplicable|TrinidadAndTobago|NP|Alouatta_seniculus||2009' into "HM582851" - seq_record.id = seq_record.id.split("|")[0] - seq_record.description = seq_record.id - if not seq_record.id in metadata_strains: - print("WARNING: sequence {} in {} has no metadata in the CSV(s). Skipping.") - continue - data.append(seq_record) - return data - - - -if __name__ == "__main__": - args = parse_args() - tsv_header, tsv_data, lat_long_data, strains = parse_metadata(args.metadataIn) - sequences = parse_fasta(args.sequencesIn, strains) - - ## write out files for augur - with open(args.metadataOut, "w") as fh: - print("\t".join(tsv_header), file=fh) - for row in tsv_data: - print("\t".join(row), file=fh) - - with open(args.latlongs, "w") as fh: - for strain, lat_long in lat_long_data.items(): - print("strain\t{}\t{}\t{}".format(strain, lat_long[0], lat_long[1]), file=fh) - - SeqIO.write(sequences, args.sequencesOut, "fasta") \ No newline at end of file