Append usvi data

nextstrain · Nov 21, 2023 · 94b7590 · 94b7590
1 parent a53b5e4
commit 94b7590
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Showing 7 changed files with 235 additions and 43 deletions.
diff --git a/phylogenetic/Snakefile b/phylogenetic/Snakefile
@@ -16,6 +16,8 @@ rule files:
 
 files = rules.files.params
 
+include: "workflow/snakemake_rules/usvi.smk"
+
 rule download:
     """Downloading sequences and metadata from data.nextstrain.org"""
     output:
@@ -53,8 +55,8 @@ rule filter:
       - minimum genome length of {params.min_length} (50% of Zika virus genome)
     """
     input:
-        sequences = "data/sequences.fasta",
-        metadata = "data/metadata.tsv",
+        sequences = "data/sequences_all.fasta",
+        metadata = "data/metadata_all.tsv",
         exclude = files.dropped_strains
     output:
         sequences = "results/filtered.fasta"
@@ -122,7 +124,7 @@ rule refine:
     input:
         tree = "results/tree_raw.nwk",
         alignment = "results/aligned.fasta",
-        metadata = "data/metadata.tsv"
+        metadata = "data/metadata_all.tsv"
     output:
         tree = "results/tree.nwk",
         node_data = "results/branch_lengths.json"
@@ -189,7 +191,7 @@ rule traits:
     """
     input:
         tree = "results/tree.nwk",
-        metadata = "data/metadata.tsv"
+        metadata = "data/metadata_all.tsv"
     output:
         node_data = "results/traits.json",
     params:
@@ -212,7 +214,7 @@ rule export:
     """Exporting data files for for auspice"""
     input:
         tree = "results/tree.nwk",
-        metadata = "data/metadata.tsv",
+        metadata = "data/metadata_all.tsv",
         branch_lengths = "results/branch_lengths.json",
         traits = "results/traits.json",
         nt_muts = "results/nt_muts.json",
@@ -242,7 +244,7 @@ rule export:
 rule final_strain_name:
     input:
         auspice_json="results/raw_zika.json",
-        metadata="data/metadata.tsv",
+        metadata="data/metadata_all.tsv",
         root_sequence="results/raw_zika_root-sequence.json",
     output:
         auspice_json="auspice/zika.json",

diff --git a/phylogenetic/config/config_zika.yaml b/phylogenetic/config/config_zika.yaml
@@ -1,2 +1,2 @@
-strain_id_field: "genbank_accession"
+strain_id_field: "accession"
 display_strain_field: "strain"
diff --git a/phylogenetic/example_data/metadata.tsv b/phylogenetic/example_data/metadata.tsv
@@ -1,35 +1,35 @@
-strain	virus	genbank_accession	date	region	country	division	city	db	segment	authors	url
-PAN/CDC_259359_V1_V3/2015	zika	KX156774	2015-12-18	North America	Panama	Panama	Panama	genbank	genome	Shabman et al	https://www.ncbi.nlm.nih.gov/nuccore/KX156774
-COL/FLR_00024/2015	zika	MF574569	2015-12-XX	South America	Colombia	Colombia	Colombia	genbank	genome	Pickett et al	https://www.ncbi.nlm.nih.gov/nuccore/MF574569
-PRVABC59	zika	KU501215	2015-12-XX	North America	Puerto Rico	Puerto Rico	Puerto Rico	genbank	genome	Lanciotti et al	https://www.ncbi.nlm.nih.gov/nuccore/KU501215
-COL/FLR_00008/2015	zika	MF574562	2015-12-XX	South America	Colombia	Colombia	Colombia	genbank	genome	Pickett et al	https://www.ncbi.nlm.nih.gov/nuccore/MF574562
-Colombia/2016/ZC204Se	zika	KY317939	2016-01-06	South America	Colombia	Colombia	Colombia	genbank	genome	Quick et al	https://www.ncbi.nlm.nih.gov/nuccore/KY317939
-ZKC2/2016	zika	KX253996	2016-02-16	Oceania	American Samoa	American Samoa	American Samoa	genbank	genome	Wu et al	https://www.ncbi.nlm.nih.gov/nuccore/KX253996
-VEN/UF_1/2016	zika	KX702400	2016-03-25	South America	Venezuela	Venezuela	Venezuela	genbank	genome	Blohm et al	https://www.ncbi.nlm.nih.gov/nuccore/KX702400
-DOM/2016/BB_0059	zika	KY785425	2016-04-04	North America	Dominican Republic	Dominican Republic	Dominican Republic	genbank	genome	Metsky et al	https://www.ncbi.nlm.nih.gov/nuccore/KY785425
-BRA/2016/FC_6706	zika	KY785433	2016-04-08	South America	Brazil	Brazil	Brazil	genbank	genome	Metsky et al	https://www.ncbi.nlm.nih.gov/nuccore/KY785433
-DOM/2016/BB_0183	zika	KY785420	2016-04-18	North America	Dominican Republic	Dominican Republic	Dominican Republic	genbank	genome	Metsky et al	https://www.ncbi.nlm.nih.gov/nuccore/KY785420
-EcEs062_16	zika	KX879603	2016-04-XX	South America	Ecuador	Ecuador	Ecuador	genbank	genome	Marquez et al	https://www.ncbi.nlm.nih.gov/nuccore/KX879603
-HND/2016/HU_ME59	zika	KY785418	2016-05-13	North America	Honduras	Honduras	Honduras	genbank	genome	Metsky et al	https://www.ncbi.nlm.nih.gov/nuccore/KY785418
-DOM/2016/MA_WGS16_011	zika	KY785484	2016-06-06	North America	Dominican Republic	Dominican Republic	Dominican Republic	genbank	genome	Metsky et al	https://www.ncbi.nlm.nih.gov/nuccore/KY785484
-DOM/2016/BB_0433	zika	KY785441	2016-06-13	North America	Dominican Republic	Dominican Republic	Dominican Republic	genbank	genome	Metsky et al	https://www.ncbi.nlm.nih.gov/nuccore/KY785441
-USA/2016/FL022	zika	KY075935	2016-07-22	North America	Usa	Usa	Usa	genbank	genome	Grubaugh et al	https://www.ncbi.nlm.nih.gov/nuccore/KY075935
-SG_027	zika	KY241697	2016-08-27	Southeast Asia	Singapore	Singapore	Singapore	genbank	genome	Ho et al	https://www.ncbi.nlm.nih.gov/nuccore/KY241697
-SG_074	zika	KY241744	2016-08-28	Southeast Asia	Singapore	Singapore	Singapore	genbank	genome	Ho et al	https://www.ncbi.nlm.nih.gov/nuccore/KY241744
-SG_056	zika	KY241726	2016-08-28	Southeast Asia	Singapore	Singapore	Singapore	genbank	genome	Ho et al	https://www.ncbi.nlm.nih.gov/nuccore/KY241726
-USA/2016/FLUR022	zika	KY325473	2016-08-31	North America	Usa	Usa	Usa	genbank	genome	Grubaugh et al	https://www.ncbi.nlm.nih.gov/nuccore/KY325473
-Aedes_aegypti/USA/2016/FL05	zika	KY075937	2016-09-09	North America	Usa	Usa	Usa	genbank	genome	Grubaugh et al	https://www.ncbi.nlm.nih.gov/nuccore/KY075937
-SG_018	zika	KY241688	2016-09-13	Southeast Asia	Singapore	Singapore	Singapore	genbank	genome	Ho et al	https://www.ncbi.nlm.nih.gov/nuccore/KY241688
-USA/2016/FLWB042	zika	KY325478	2016-09-26	North America	Usa	Usa	Usa	genbank	genome	Grubaugh et al	https://www.ncbi.nlm.nih.gov/nuccore/KY325478
-COL/PRV_00028/2015	zika	MF574578	2016-12-XX	South America	Colombia	Colombia	Colombia	genbank	genome	Pickett et al	https://www.ncbi.nlm.nih.gov/nuccore/MF574578
-Thailand/1610acTw	zika	MF692778	2016-10-XX	Southeast Asia	Thailand	Thailand	Thailand	genbank	genome	Lin et al	https://www.ncbi.nlm.nih.gov/nuccore/MF692778
-1_0087_PF	zika	KX447509	2013-12-XX	Oceania	French Polynesia	French Polynesia	French Polynesia	genbank	genome	Pettersson et al	https://www.ncbi.nlm.nih.gov/nuccore/KX447509
-1_0199_PF	zika	KX447519	2013-11-XX	Oceania	French Polynesia	French Polynesia	French Polynesia	genbank	genome	Pettersson et al	https://www.ncbi.nlm.nih.gov/nuccore/KX447519
-1_0181_PF	zika	KX447512	2013-12-XX	Oceania	French Polynesia	French Polynesia	French Polynesia	genbank	genome	Pettersson et al	https://www.ncbi.nlm.nih.gov/nuccore/KX447512
-Brazil/2015/ZBRC301	zika	KY558995	2015-05-13	South America	Brazil	Brazil	Brazil	genbank	genome	Faria et al	https://www.ncbi.nlm.nih.gov/nuccore/KY558995
-Brazil/2015/ZBRA105	zika	KY558989	2015-02-23	South America	Brazil	Brazil	Brazil	genbank	genome	Faria et al	https://www.ncbi.nlm.nih.gov/nuccore/KY558989
-Brazil/2016/ZBRC16	zika	KY558991	2016-01-19	South America	Brazil	Brazil	Brazil	genbank	genome	Faria et al	https://www.ncbi.nlm.nih.gov/nuccore/KY558991
-V8375	zika	KU501217	2015-11-01	North America	Guatemala	Guatemala	Guatemala	genbank	genome	Lanciotti et al	https://www.ncbi.nlm.nih.gov/nuccore/KU501217
-Nica1_16	zika	KX421195	2016-01-19	North America	Nicaragua	Nicaragua	Nicaragua	genbank	genome	Tabata et al	https://www.ncbi.nlm.nih.gov/nuccore/KX421195
-Brazil/2015/ZBRC303	zika	KY558997	2015-05-14	South America	Brazil	Brazil	Brazil	genbank	genome	Faria et al	https://www.ncbi.nlm.nih.gov/nuccore/KY558997
-SMGC_1	zika	KX266255	2016-02-14	Oceania	American Samoa	American Samoa	American Samoa	genbank	genome	Bi et al	https://www.ncbi.nlm.nih.gov/nuccore/KX266255
+strain	virus	genbank_accession	date	region	country	division	city	db	segment	authors
+PAN/CDC_259359_V1_V3/2015	zika	KX156774	2015-12-18	North America	Panama	Panama	Panama	genbank	genome	Shabman et al
+COL/FLR_00024/2015	zika	MF574569	2015-12-XX	South America	Colombia	Colombia	Colombia	genbank	genome	Pickett et al
+PRVABC59	zika	KU501215	2015-12-XX	North America	Puerto Rico	Puerto Rico	Puerto Rico	genbank	genome	Lanciotti et al
+COL/FLR_00008/2015	zika	MF574562	2015-12-XX	South America	Colombia	Colombia	Colombia	genbank	genome	Pickett et al
+Colombia/2016/ZC204Se	zika	KY317939	2016-01-06	South America	Colombia	Colombia	Colombia	genbank	genome	Quick et al
+ZKC2/2016	zika	KX253996	2016-02-16	Oceania	American Samoa	American Samoa	American Samoa	genbank	genome	Wu et al
+VEN/UF_1/2016	zika	KX702400	2016-03-25	South America	Venezuela	Venezuela	Venezuela	genbank	genome	Blohm et al
+DOM/2016/BB_0059	zika	KY785425	2016-04-04	North America	Dominican Republic	Dominican Republic	Dominican Republic	genbank	genome	Metsky et al
+BRA/2016/FC_6706	zika	KY785433	2016-04-08	South America	Brazil	Brazil	Brazil	genbank	genome	Metsky et al
+DOM/2016/BB_0183	zika	KY785420	2016-04-18	North America	Dominican Republic	Dominican Republic	Dominican Republic	genbank	genome	Metsky et al
+EcEs062_16	zika	KX879603	2016-04-XX	South America	Ecuador	Ecuador	Ecuador	genbank	genome	Marquez et al
+HND/2016/HU_ME59	zika	KY785418	2016-05-13	North America	Honduras	Honduras	Honduras	genbank	genome	Metsky et al
+DOM/2016/MA_WGS16_011	zika	KY785484	2016-06-06	North America	Dominican Republic	Dominican Republic	Dominican Republic	genbank	genome	Metsky et al
+DOM/2016/BB_0433	zika	KY785441	2016-06-13	North America	Dominican Republic	Dominican Republic	Dominican Republic	genbank	genome	Metsky et al
+USA/2016/FL022	zika	KY075935	2016-07-22	North America	Usa	Usa	Usa	genbank	genome	Grubaugh et al
+SG_027	zika	KY241697	2016-08-27	Southeast Asia	Singapore	Singapore	Singapore	genbank	genome	Ho et al
+SG_074	zika	KY241744	2016-08-28	Southeast Asia	Singapore	Singapore	Singapore	genbank	genome	Ho et al
+SG_056	zika	KY241726	2016-08-28	Southeast Asia	Singapore	Singapore	Singapore	genbank	genome	Ho et al
+USA/2016/FLUR022	zika	KY325473	2016-08-31	North America	Usa	Usa	Usa	genbank	genome	Grubaugh et al
+Aedes_aegypti/USA/2016/FL05	zika	KY075937	2016-09-09	North America	Usa	Usa	Usa	genbank	genome	Grubaugh et al
+SG_018	zika	KY241688	2016-09-13	Southeast Asia	Singapore	Singapore	Singapore	genbank	genome	Ho et al
+USA/2016/FLWB042	zika	KY325478	2016-09-26	North America	Usa	Usa	Usa	genbank	genome	Grubaugh et al
+COL/PRV_00028/2015	zika	MF574578	2016-12-XX	South America	Colombia	Colombia	Colombia	genbank	genome	Pickett et al
+Thailand/1610acTw	zika	MF692778	2016-10-XX	Southeast Asia	Thailand	Thailand	Thailand	genbank	genome	Lin et al
+1_0087_PF	zika	KX447509	2013-12-XX	Oceania	French Polynesia	French Polynesia	French Polynesia	genbank	genome	Pettersson et al
+1_0199_PF	zika	KX447519	2013-11-XX	Oceania	French Polynesia	French Polynesia	French Polynesia	genbank	genome	Pettersson et al
+1_0181_PF	zika	KX447512	2013-12-XX	Oceania	French Polynesia	French Polynesia	French Polynesia	genbank	genome	Pettersson et al
+Brazil/2015/ZBRC301	zika	KY558995	2015-05-13	South America	Brazil	Brazil	Brazil	genbank	genome	Faria et al
+Brazil/2015/ZBRA105	zika	KY558989	2015-02-23	South America	Brazil	Brazil	Brazil	genbank	genome	Faria et al
+Brazil/2016/ZBRC16	zika	KY558991	2016-01-19	South America	Brazil	Brazil	Brazil	genbank	genome	Faria et al
+V8375	zika	KU501217	2015-11-01	North America	Guatemala	Guatemala	Guatemala	genbank	genome	Lanciotti et al
+Nica1_16	zika	KX421195	2016-01-19	North America	Nicaragua	Nicaragua	Nicaragua	genbank	genome	Tabata et al
+Brazil/2015/ZBRC303	zika	KY558997	2015-05-14	South America	Brazil	Brazil	Brazil	genbank	genome	Faria et al
+SMGC_1	zika	KX266255	2016-02-14	Oceania	American Samoa	American Samoa	American Samoa	genbank	genome	Bi et al
diff --git a/phylogenetic/example_data/metadata_usvi.tsv b/phylogenetic/example_data/metadata_usvi.tsv
@@ -0,0 +1,2 @@
+genbank_accession	genbank_accession_rev	accession	strain	date	region	country	division	location	length	host	release_date	update_date	sra_accessions	authors	institution	url
+USVI/37/2016		VI37	USVI/37/2016	2016-10-06	North America	Usvi	Saint Croix	Saint Croix	10807	Homo sapiens				Black et al	FH	https://github.com/blab/zika-usvi/
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		genbank_accession genbank_accession_rev accession strain date region country division location length host release_date update_date sra_accessions authors institution url
		USVI/37/2016 VI37 USVI/37/2016 2016-10-06 North America Usvi Saint Croix Saint Croix 10807 Homo sapiens Black et al FH https://github.com/blab/zika-usvi/