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Drop GenBank accession version number
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Follows changes made in nextstrain/pathogen-repo-guide@ceb7fbc

Resolves #24
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@kimandrews
kimandrews committed Apr 19, 2024
1 parent 6bed278 commit 6dc1603
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32 changes: 16 additions & 16 deletions ingest/defaults/annotations.tsv
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Expand Up @@ -8,19 +8,19 @@
# Vaccine strain information from Parks et al. Comparison of predicted amino acid
# sequences of measles virus strains in the Edmonston vaccine lineage
# https://doi.org/10.1128/jvi.75.2.910-920.2001
AF266288.2 strain Measles strain Edmonston WT
AF266288.2 date 1954
AF266288.2 region North America
AF266288.2 country USA
AF266288.2 division Massachusetts
AF266288.2 location Boston
AF266287.1 strain Measles vaccine strain Moraten
AF266287.1 date 1954
AF266290.1 strain Measles vaccine strain Zagreb
AF266290.1 date 1954
AF266289.1 strain Measles vaccine strain Rubeovax
AF266289.1 date 1954
AF266291.1 strain Measles vaccine strain Schwarz
AF266291.1 date 1954
AF266286.1 strain Measles vaccine strain AIK-C
AF266286.1 date 1954
AF266288 strain Measles strain Edmonston WT
AF266288 date 1954
AF266288 region North America
AF266288 country USA
AF266288 division Massachusetts
AF266288 location Boston
AF266287 strain Measles vaccine strain Moraten
AF266287 date 1954
AF266290 strain Measles vaccine strain Zagreb
AF266290 date 1954
AF266289 strain Measles vaccine strain Rubeovax
AF266289 date 1954
AF266291 strain Measles vaccine strain Schwarz
AF266291 date 1954
AF266286 strain Measles vaccine strain AIK-C
AF266286 date 1954
2 changes: 2 additions & 0 deletions ingest/defaults/config.yaml
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Expand Up @@ -45,6 +45,7 @@ curate:
# This is the first step in the pipeline, so any references to field names in the configs below should use the new field names
field_map:
accession: accession
accession_version: accession_version
sourcedb: database
sra-accs: sra_accessions
isolate-lineage: strain
Expand Down Expand Up @@ -100,6 +101,7 @@ curate:
# The list of metadata columns to keep in the final output of the curation pipeline.
metadata_columns: [
'accession',
'accession_version',
'strain',
'virus_name',
'date',
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5 changes: 4 additions & 1 deletion ingest/rules/fetch_from_ncbi.smk
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Expand Up @@ -75,6 +75,9 @@ rule format_ncbi_dataset_report:
--fields {params.ncbi_datasets_fields:q} \
--elide-header \
| csvtk add-header -t -l -n {params.ncbi_datasets_fields:q} \
| csvtk rename -t -f accession -n accession_version \
| csvtk -tl mutate -f accession_version -n accession -p "^(.+?)\." \
| tsv-select -H -f accession --rest last \
> {output.ncbi_dataset_tsv}
"""

Expand All @@ -98,7 +101,7 @@ rule format_ncbi_datasets_ndjson:
augur curate passthru \
--metadata {input.ncbi_dataset_tsv} \
--fasta {input.ncbi_dataset_sequences} \
--seq-id-column accession \
--seq-id-column accession_version \
--seq-field sequence \
--unmatched-reporting warn \
--duplicate-reporting warn \
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4 changes: 2 additions & 2 deletions phylogenetic/defaults/dropped_strains.txt
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@@ -1,2 +1,2 @@
HM562901.1 # temara.MOR/24.03
HM562900.1 # Mvs/Toulon.FRA/08.07
HM562901 # temara.MOR/24.03
HM562900 # Mvs/Toulon.FRA/08.07
40 changes: 20 additions & 20 deletions phylogenetic/example_data/metadata.tsv
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@@ -1,21 +1,21 @@
accession strain virus_name date region country division location length host date_released date_updated sra_accessions authors abbr_authors institution
MK161348.1 D8 2018-08-04 South America Brazil Boa Vista Roraima State 15894 Homo sapiens 2018-11-20 2019-04-10 Meneses,C.A.,Nascimento,V.A.,Souza,V.C.,Maito,R.M.,Gomes,M.A.,Cunha,C.R.,Antony,I.A.,Silva,M.E.,Campos,D.P.,Corado,A.L.,Pessoa,K.P.,Monteiro,D.C.,Okumoto,O.,Cunha,M.C.,Pacheco,F.C.,Naveca,F.G.,Corado,A.G. Meneses et al Instituto Leonidas e Maria Deane - Fiocruz Amazonia, Laboratorio de Ecologia de Doencas Transmissiveis na Amazonia
MH173047.1 D8 2017-11-XX Europe Italy 15872 Homo sapiens 2018-06-06 2018-06-06 Marinelli,K.,Caucci,S.,Vincenzi,C.,Ferreri,M.,Magurano,F.,Bagnarelli,P.,Menzo,S. Marinelli et al Virologia, Ao Ospedali Riuniti Di Ancona
MF449469.1 G2V D4 2011-05-03 Europe France 15894 Homo sapiens 2017-08-28 2017-08-28 Mura,M.,Combredet,C.,Najburg,V.,Sanchez David,R.Y.,Tangy,F.,Komarova,A.V.,Sanchez-David,R.Y.,Komarova,A. Mura et al Institut Pasteur, Virology
KT732255.1 D8 2013-04-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service
KT732253.1 D8 2013-04-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service
KT732251.1 D8 2013-04-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service
KT732241.1 D8 2012-11-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service
KT732226.1 D4 2011-05-XX Europe United Kingdom 15684 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service
KT732223.1 B3 2014-01-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service
KT732221.1 B3 2014-01-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service
KT732220.1 B3 2014-01-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service
KT732219.1 B3 2014-01-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service
KJ755980.1 H1 2009-03-18 Asia China 15894 Homo sapiens 2016-05-02 2016-05-02 Jin,Q.,Xu,C.,Li,H.,Zhong,S.,Zheng,B.,Lu,Y. Jin et al Centre for Disease Control and Prevention of Zhejiang Province (ZJ CDC), Institute of Microbiology
KJ755979.1 H1 2008-03-20 Asia China 15894 Homo sapiens 2016-05-02 2016-05-02 Jin,Q.,Xu,C.,Li,H.,Zhong,S.,Zheng,B.,Lu,Y. Jin et al Centre for Disease Control and Prevention of Zhejiang Province (ZJ CDC), Institute of Microbiology
JN635408.1 2005-11-05 North America USA New Jersey 15894 Homo sapiens 2011-09-29 2012-01-26 Kirkness,E.F.,Halpin,R.,Bera,J.,Fedorova,N.,Overton,L.,Stockwell,T.,Amedeo,P.,Bishop,B.,Chen,H.,Edworthy,P.,Gupta,N.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Bankamp,B.,Byrd,L.,Bellini,W.,Rota,P. Kirkness et al J. Craig Venter Institute
JN635406.1 2008-03-11 North America USA Arizona 15894 Homo sapiens 2011-09-29 2012-01-26 Kirkness,E.F.,Halpin,R.,Bera,J.,Fedorova,N.,Overton,L.,Stockwell,T.,Amedeo,P.,Bishop,B.,Chen,H.,Edworthy,P.,Gupta,N.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Bankamp,B.,Byrd,L.,Bellini,W.,Rota,P. Kirkness et al J. Craig Venter Institute
FJ416067.1 15894 2009-05-21 2009-11-05 Zhang,Y.,Zhou,J.,Bellini,W.J.,Xu,W.,Rota,P.A.,Bamkamp,B. Zhang et al National Institute for Viral Disease Control and Prevention, China Centers for Disease Control and Prevention, WHO WPRO Regional Reference Measles Lab
EF565859.1 G954-PBL 1993-XX-XX Africa 6552 2008-04-02 2008-04-02 Druelle,J.,Sellin,C.I.,Waku-Kouomou,D.,Horvat,B.,Wild,F.T.,Sellin,C.,Wild,T. Druelle et al Inserm U404, Immunite et Vaccination
AB481088.1 1989-XX-XX Asia Japan 15894 2009-08-14 2009-08-14 Okada,H.,Itoh,M.,Nagata,K.,Takeuchi,K.,Ito,M. Okada et al Graduate School of Comprehensive Human Sciences; Tennodai 1-1-1, Tsukuba, Ibaraki 305-8575
AB012949.1 9301V 15894 Homo sapiens 1998-10-19 2008-12-04 Takeda,M.,Kato,A.,Kobune,F.,Sakata,H.,Li,Y.,Shioda,T.,Sakai,Y.,Asakawa,M.,Nagai,Y. Takeda et al University of Tokyo, Viral Infection; Shirokanedai 4-6-1, Minato-ku, Tokyo 108
MK161348 D8 2018-08-04 South America Brazil Boa Vista Roraima State 15894 Homo sapiens 2018-11-20 2019-04-10 Meneses,C.A.,Nascimento,V.A.,Souza,V.C.,Maito,R.M.,Gomes,M.A.,Cunha,C.R.,Antony,I.A.,Silva,M.E.,Campos,D.P.,Corado,A.L.,Pessoa,K.P.,Monteiro,D.C.,Okumoto,O.,Cunha,M.C.,Pacheco,F.C.,Naveca,F.G.,Corado,A.G. Meneses et al Instituto Leonidas e Maria Deane - Fiocruz Amazonia, Laboratorio de Ecologia de Doencas Transmissiveis na Amazonia
MH173047 D8 2017-11-XX Europe Italy 15872 Homo sapiens 2018-06-06 2018-06-06 Marinelli,K.,Caucci,S.,Vincenzi,C.,Ferreri,M.,Magurano,F.,Bagnarelli,P.,Menzo,S. Marinelli et al Virologia, Ao Ospedali Riuniti Di Ancona
MF449469 G2V D4 2011-05-03 Europe France 15894 Homo sapiens 2017-08-28 2017-08-28 Mura,M.,Combredet,C.,Najburg,V.,Sanchez David,R.Y.,Tangy,F.,Komarova,A.V.,Sanchez-David,R.Y.,Komarova,A. Mura et al Institut Pasteur, Virology
KT732255 D8 2013-04-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service
KT732253 D8 2013-04-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service
KT732251 D8 2013-04-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service
KT732241 D8 2012-11-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service
KT732226 D4 2011-05-XX Europe United Kingdom 15684 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service
KT732223 B3 2014-01-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service
KT732221 B3 2014-01-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service
KT732220 B3 2014-01-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service
KT732219 B3 2014-01-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service
KJ755980 H1 2009-03-18 Asia China 15894 Homo sapiens 2016-05-02 2016-05-02 Jin,Q.,Xu,C.,Li,H.,Zhong,S.,Zheng,B.,Lu,Y. Jin et al Centre for Disease Control and Prevention of Zhejiang Province (ZJ CDC), Institute of Microbiology
KJ755979 H1 2008-03-20 Asia China 15894 Homo sapiens 2016-05-02 2016-05-02 Jin,Q.,Xu,C.,Li,H.,Zhong,S.,Zheng,B.,Lu,Y. Jin et al Centre for Disease Control and Prevention of Zhejiang Province (ZJ CDC), Institute of Microbiology
JN635408 2005-11-05 North America USA New Jersey 15894 Homo sapiens 2011-09-29 2012-01-26 Kirkness,E.F.,Halpin,R.,Bera,J.,Fedorova,N.,Overton,L.,Stockwell,T.,Amedeo,P.,Bishop,B.,Chen,H.,Edworthy,P.,Gupta,N.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Bankamp,B.,Byrd,L.,Bellini,W.,Rota,P. Kirkness et al J. Craig Venter Institute
JN635406 2008-03-11 North America USA Arizona 15894 Homo sapiens 2011-09-29 2012-01-26 Kirkness,E.F.,Halpin,R.,Bera,J.,Fedorova,N.,Overton,L.,Stockwell,T.,Amedeo,P.,Bishop,B.,Chen,H.,Edworthy,P.,Gupta,N.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Bankamp,B.,Byrd,L.,Bellini,W.,Rota,P. Kirkness et al J. Craig Venter Institute
FJ416067 15894 2009-05-21 2009-11-05 Zhang,Y.,Zhou,J.,Bellini,W.J.,Xu,W.,Rota,P.A.,Bamkamp,B. Zhang et al National Institute for Viral Disease Control and Prevention, China Centers for Disease Control and Prevention, WHO WPRO Regional Reference Measles Lab
EF565859 G954-PBL 1993-XX-XX Africa 6552 2008-04-02 2008-04-02 Druelle,J.,Sellin,C.I.,Waku-Kouomou,D.,Horvat,B.,Wild,F.T.,Sellin,C.,Wild,T. Druelle et al Inserm U404, Immunite et Vaccination
AB481088 1989-XX-XX Asia Japan 15894 2009-08-14 2009-08-14 Okada,H.,Itoh,M.,Nagata,K.,Takeuchi,K.,Ito,M. Okada et al Graduate School of Comprehensive Human Sciences; Tennodai 1-1-1, Tsukuba, Ibaraki 305-8575
AB012949 9301V 15894 Homo sapiens 1998-10-19 2008-12-04 Takeda,M.,Kato,A.,Kobune,F.,Sakata,H.,Li,Y.,Shioda,T.,Sakai,Y.,Asakawa,M.,Nagai,Y. Takeda et al University of Tokyo, Viral Infection; Shirokanedai 4-6-1, Minato-ku, Tokyo 108
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