From fbdfbe85fa5fb816bdae4f7393d6b4025589b8a3 Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Wed, 11 Dec 2024 17:26:52 -0800 Subject: [PATCH] Update example data --- phylogenetic/example_data/metadata.tsv | 70 ++++++++++----------- phylogenetic/example_data/metadata_usvi.tsv | 4 +- 2 files changed, 37 insertions(+), 37 deletions(-) diff --git a/phylogenetic/example_data/metadata.tsv b/phylogenetic/example_data/metadata.tsv index 3d39cf9..928289c 100644 --- 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 -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 +strain virus 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 diff --git a/phylogenetic/example_data/metadata_usvi.tsv b/phylogenetic/example_data/metadata_usvi.tsv index 96d3d52..42a3a08 100644 --- a/phylogenetic/example_data/metadata_usvi.tsv +++ b/phylogenetic/example_data/metadata_usvi.tsv @@ -1,2 +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/ +accession accession_version strain date region country division location length host release_date update_date sra_accessions authors institution url +VI37 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/ \ No 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