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Fix phylo input #40

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Merged
joverlee521 merged 3 commits into from
Apr 15, 2024
Merged

Fix phylo input #40

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4226f0c
phylogenetic: Use latest ingest data
joverlee521 Apr 11, 2024
c6a0f3a
phylogenetic: Update example data
joverlee521 Apr 11, 2024
9b9d1b2
phylogenetic: Update Auspice configs to include `genbank_accession`
joverlee521 Apr 12, 2024
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5 changes: 4 additions & 1 deletion phylogenetic/config/auspice_config_all.json
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Expand Up @@ -3,7 +3,7 @@
"maintainers": [
{"name": "Trevor Bedford", "url": "http://bedford.io/team/trevor-bedford/"}
],
"build_url": "https://github.com/nextstrain/dengue",
"build_url": "https://github.com/nextstrain/dengue",
"colorings": [
{
"key": "gt",
Expand Down Expand Up @@ -44,5 +44,8 @@
"country",
"region",
"author"
],
"metadata_columns": [
"genbank_accession"
]
}
3 changes: 3 additions & 0 deletions phylogenetic/config/auspice_config_denv1.json
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Expand Up @@ -43,5 +43,8 @@
"country",
"region",
"author"
],
"metadata_columns": [
"genbank_accession"
]
}
3 changes: 3 additions & 0 deletions phylogenetic/config/auspice_config_denv2.json
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Expand Up @@ -43,5 +43,8 @@
"country",
"region",
"author"
],
"metadata_columns": [
"genbank_accession"
]
}
3 changes: 3 additions & 0 deletions phylogenetic/config/auspice_config_denv3.json
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Expand Up @@ -43,5 +43,8 @@
"country",
"region",
"author"
],
"metadata_columns": [
"genbank_accession"
]
}
3 changes: 3 additions & 0 deletions phylogenetic/config/auspice_config_denv4.json
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Expand Up @@ -43,5 +43,8 @@
"country",
"region",
"author"
],
"metadata_columns": [
"genbank_accession"
]
}
2 changes: 1 addition & 1 deletion phylogenetic/config/config_dengue.yaml
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@@ -1,4 +1,4 @@
strain_id_field: "accession"
strain_id_field: "genbank_accession"
display_strain_field: "strain"

filter:
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2 changes: 1 addition & 1 deletion phylogenetic/example_data/metadata_all.tsv
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@@ -1,4 +1,4 @@
strain virus accession date region country division city db segment authors url title journal paper_url
strain virus genbank_accession date region country division city db segment authors url title journal paper_url
DENV1/VIETNAM/BIDV1862/2008 dengue FJ410220 2008-XX-XX Southeast Asia Vietnam Vietnam Vietnam ? genome Alvarado et al. ? ? ? ?
DENV3/WALLIS_AND_FUTUNA/1404838/1989 dengue JQ920487 1989-08-14 ? Wallis And Futuna French Overseas Collectivity Wallis And Futuna ? genome Aubry et al. ? ? ? ?
DENV/BRAZIL/SJRP778/2013 dengue KT438585 2013-02-04 South America Brazil Brazil Brazil ? genome Araujo et al. ? ? ? ?
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2 changes: 1 addition & 1 deletion phylogenetic/example_data/metadata_denv1.tsv
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@@ -1,4 +1,4 @@
strain virus accession date region country division city db segment authors url title journal paper_url
strain virus genbank_accession date region country division city db segment authors url title journal paper_url
DENV1/INDIA/237/1962 dengue JF297572 1962-XX-XX South Asia India India India ? genome Cecilia et al. ? ? ? ?
DENV1/CHINA/RL6/2013 dengue KJ470727 2013-09-XX China China China China ? genome Guo et al. ? ? ? ?
DENV1/THAILAND/AILANDKPPKDV08491NC04528V0L/2007 dengue JQ993108 2007-XX-XX Southeast Asia Thailand Thailand Thailand ? genome Aldstadt et al. ? ? ? ?
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2 changes: 1 addition & 1 deletion phylogenetic/example_data/metadata_denv2.tsv
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@@ -1,4 +1,4 @@
strain virus accession date region country division city db segment authors url title journal paper_url
strain virus genbank_accession date region country division city db segment authors url title journal paper_url
DENV2/INDONESIA/MKS0084/2007 dengue KC762660 2007-11-21 Southeast Asia Indonesia Makassar Makassar ? genome Bifani et al. ? ? ? ?
DENV2/TAIWAN/71/2002 dengue EF016253 2002-XX-XX China Taiwan Taiwan Taiwan ? genome Ke et al. ? ? ? ?
DENV2/PAKISTAN/8D/2011 dengue JX042512 2011-XX-XX West Asia Pakistan Pakistan Pakistan ? genome Alvi et al. ? ? ? ?
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2 changes: 1 addition & 1 deletion phylogenetic/example_data/metadata_denv3.tsv
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@@ -1,4 +1,4 @@
strain virus accession date region country division city db segment authors url title journal paper_url
strain virus genbank_accession date region country division city db segment authors url title journal paper_url
DENV3/PUERTO_RICO/BIDV1615/2004 dengue FJ373302 2004-XX-XX North America Puerto Rico Puerto Rico Puerto Rico ? genome Alvarado et al. ? ? ? ?
DENV3/THAILAND/BIDV2323/2001 dengue FJ744734 2001-XX-XX Southeast Asia Thailand Kamphaeng Phet Kamphaeng Phet ? genome Alvarado et al. ? ? ? ?
DENV3/BANGLADESH/JACOB/NA dengue AY656673 ? South Asia Bangladesh Bangladesh Bangladesh ? genome Aaskov et al. ? ? ? ?
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2 changes: 1 addition & 1 deletion phylogenetic/example_data/metadata_denv4.tsv
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@@ -1,4 +1,4 @@
strain virus accession date region country division city db segment authors url title journal paper_url
strain virus genbank_accession date region country division city db segment authors url title journal paper_url
DENV4/ECUADOR/FSE2098/2006 dengue GQ139572 2006-XX-XX South America Ecuador Ecuador Ecuador ? genome Alava et al. ? ? ? ?
DENV4/BRAZIL/SJRP580/2012 dengue KP188562 2012-12-10 South America Brazil Brazil Brazil ? genome Araujo et al. ? ? ? ?
DENV4/BRAZIL/GUSP0670/2013 dengue KP704043 2013-03-17 South America Brazil Brazil Brazil ? genome Balarini et al. ? ? ? ?
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4 changes: 2 additions & 2 deletions phylogenetic/rules/prepare_sequences.smk
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Expand Up @@ -21,8 +21,8 @@ rule download:
metadata = "data/metadata_{serotype}.tsv.zst"

params:
sequences_url = "https://data.nextstrain.org/files/dengue/sequences_{serotype}.fasta.zst",
metadata_url = "https://data.nextstrain.org/files/dengue/metadata_{serotype}.tsv.zst"
sequences_url = "https://data.nextstrain.org/files/workflows/dengue/sequences_{serotype}.fasta.zst",
metadata_url = "https://data.nextstrain.org/files/workflows/dengue/metadata_{serotype}.tsv.zst"
shell:
"""
curl -fsSL --compressed {params.sequences_url:q} --output {output.sequences}
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