From 26b66b27d38993b7d6d6529e2fd1071ad7f098da Mon Sep 17 00:00:00 2001 From: eharkins Date: Thu, 27 Aug 2020 19:37:54 -0700 Subject: [PATCH] fix gisaid annotations; these were raising a flag in https://github.com/nextstrain/ncov-ingest/pull/88 --- source-data/gisaid_annotations.tsv | 95 ++++++++++++++---------------- 1 file changed, 44 insertions(+), 51 deletions(-) diff --git a/source-data/gisaid_annotations.tsv b/source-data/gisaid_annotations.tsv index 58448edb..ecaced6c 100644 --- a/source-data/gisaid_annotations.tsv +++ b/source-data/gisaid_annotations.tsv @@ -793,10 +793,10 @@ Australia/VIC01/2020 EPI_ISL_406844 country_exposure China # ? Australia/VIC01/2020 EPI_ISL_406844 genbank_accession MT007544 Australia/VIC01/2020 EPI_ISL_406844 region_exposure Asia # ? Australia/VIC01/2020 EPI_ISL_406844 division_exposure Hubei # ? -Australia/SAP472/2020 EPI_ISL_508605 location -Australia/SAP473/2020 EPI_ISL_508606 location -Australia/SAP474/2020 EPI_ISL_508607 location -Australia/SAP475/2020 EPI_ISL_508608 location +Australia/SAP472/2020 EPI_ISL_508605 location +Australia/SAP473/2020 EPI_ISL_508606 location +Australia/SAP474/2020 EPI_ISL_508607 location +Australia/SAP475/2020 EPI_ISL_508608 location Australia/NSW2153/2020 EPI_ISL_509505 region_exposure Asia Australia/NSW2153/2020 EPI_ISL_509505 country_exposure China Australia/NSW2153/2020 EPI_ISL_509505 division_exposure Hubei @@ -3208,38 +3208,38 @@ Canada/SK_63/2020 EPI_ISL_429822 division Saskatchewan Canada/SHSC1/2020 EPI_ISL_450747 division_exposure Iran Canada/SHSC1/2020 EPI_ISL_450747 country_exposure Iran Canada/SHSC1/2020 EPI_ISL_450747 region_exposure Asia -Canada/Qc-L00240587/2020 location Montérégie -Canada/Qc-L00240587/2020 division Quebec -Canada/Qc-L00240652/2020 location Montérégie -Canada/Qc-L00240652/2020 division Quebec -Canada/Qc-L00240685/2020 location Montérégie -Canada/Qc-L00240685/2020 division Quebec -Canada/Qc-L00240857/2020 location Montérégie -Canada/Qc-L00240857/2020 division Quebec -Canada/Qc-L00240954/2020 location Montérégie -Canada/Qc-L00240954/2020 division Quebec -Canada/Qc-L00240979/2020 location Montérégie -Canada/Qc-L00240979/2020 division Quebec -Canada/Qc-L00241026/2020 location Montérégie -Canada/Qc-L00241026/2020 division Quebec -Canada/Qc-L00241042/2020 location Montérégie -Canada/Qc-L00241042/2020 division Quebec -Canada/Qc-L00241168/2020 location Montérégie -Canada/Qc-L00241168/2020 division Quebec -Canada/Qc-L00241192/2020 location Montérégie -Canada/Qc-L00241192/2020 division Quebec -Canada/Qc-L00241205/2020 location Montérégie -Canada/Qc-L00241205/2020 division Quebec -Canada/Qc-L00241208/2020 location Montérégie -Canada/Qc-L00241208/2020 division Quebec -Canada/Qc-L00241245/2020 location Montérégie -Canada/Qc-L00241245/2020 division Quebec -Canada/Qc-L00241292/2020 location Lanaudière -Canada/Qc-L00241292/2020 division Quebec -Canada/Qc-L00241344/2020 location Montérégie -Canada/Qc-L00241344/2020 division Quebec -Canada/Qc-L00241355/2020 location Montérégie -Canada/Qc-L00241355/2020 division Quebec +Canada/Qc-L00240587/2020 EPI_ISL_450303 location Montérégie +Canada/Qc-L00240587/2020 EPI_ISL_450303 division Quebec +Canada/Qc-L00240652/2020 EPI_ISL_450304 location Montérégie +Canada/Qc-L00240652/2020 EPI_ISL_450304 division Quebec +Canada/Qc-L00240685/2020 EPI_ISL_450305 location Montérégie +Canada/Qc-L00240685/2020 EPI_ISL_450305 division Quebec +Canada/Qc-L00240857/2020 EPI_ISL_450306 location Montérégie +Canada/Qc-L00240857/2020 EPI_ISL_450306 division Quebec +Canada/Qc-L00240954/2020 EPI_ISL_450307 location Montérégie +Canada/Qc-L00240954/2020 EPI_ISL_450307 division Quebec +Canada/Qc-L00240979/2020 EPI_ISL_450308 location Montérégie +Canada/Qc-L00240979/2020 EPI_ISL_450308 division Quebec +Canada/Qc-L00241026/2020 EPI_ISL_450309 location Montérégie +Canada/Qc-L00241026/2020 EPI_ISL_450309 division Quebec +Canada/Qc-L00241042/2020 EPI_ISL_450310 location Montérégie +Canada/Qc-L00241042/2020 EPI_ISL_450310 division Quebec +Canada/Qc-L00241168/2020 EPI_ISL_450311 location Montérégie +Canada/Qc-L00241168/2020 EPI_ISL_450311 division Quebec +Canada/Qc-L00241192/2020 EPI_ISL_450312 location Montérégie +Canada/Qc-L00241192/2020 EPI_ISL_450312 division Quebec +Canada/Qc-L00241205/2020 EPI_ISL_450313 location Montérégie +Canada/Qc-L00241205/2020 EPI_ISL_450313 division Quebec +Canada/Qc-L00241208/2020 EPI_ISL_450314 location Montérégie +Canada/Qc-L00241208/2020 EPI_ISL_450314 division Quebec +Canada/Qc-L00241245/2020 EPI_ISL_450315 location Montérégie +Canada/Qc-L00241245/2020 EPI_ISL_450315 division Quebec +Canada/Qc-L00241292/2020 EPI_ISL_450316 location Lanaudière +Canada/Qc-L00241292/2020 EPI_ISL_450316 division Quebec +Canada/Qc-L00241344/2020 EPI_ISL_450317 location Montérégie +Canada/Qc-L00241344/2020 EPI_ISL_450317 division Quebec +Canada/Qc-L00241355/2020 EPI_ISL_450318 location Montérégie +Canada/Qc-L00241355/2020 EPI_ISL_450318 division Quebec Canada/ON_MU-S1/2020 EPI_ISL_463970 division Ontario # previously Toronto Canada/ON_MU-S1/2020 EPI_ISL_463970 location Toronto Canada/ON_MU-S13/2020 EPI_ISL_463971 division Ontario # previously Toronto @@ -25395,11 +25395,8 @@ SouthAfrica/KRISP-0190/2020 EPI_ISL_482709 division KwaZulu-Natal SouthAfrica/KRISP-0191/2020 EPI_ISL_482710 division KwaZulu-Natal SouthAfrica/KRISP-0192/2020 EPI_ISL_482711 division KwaZulu-Natal SouthAfrica/KRISP-0193/2020 EPI_ISL_482848 division KwaZulu-Natal -SouthAfrica/KRISP-0193/2020 EPI_ISL_482848 location SouthAfrica/KRISP-0194/2020 EPI_ISL_482849 division KwaZulu-Natal -SouthAfrica/KRISP-0194/2020 EPI_ISL_482849 location SouthAfrica/KRISP-0195/2020 EPI_ISL_482850 division KwaZulu-Natal -SouthAfrica/KRISP-0195/2020 EPI_ISL_482850 location SouthAfrica/KRISP-0196/2020 EPI_ISL_482712 division KwaZulu-Natal SouthAfrica/KRISP-0197/2020 EPI_ISL_482713 division KwaZulu-Natal SouthAfrica/KRISP-0198/2020 EPI_ISL_482851 division KwaZulu-Natal @@ -25826,10 +25823,6 @@ SouthAfrica/KRISP-0485/2020 EPI_ISL_495561 division KwaZulu-Natal # previously K SouthAfrica/KRISP-0487/2020 EPI_ISL_495562 division KwaZulu-Natal # previously Kzn SouthAfrica/KRISP-0141/2020 EPI_ISL_467492 location KwaDukuza # previously Stanger SouthAfrica/KRISP-0143/2020 EPI_ISL_467493 location KwaDukuza # previously Stanger -SouthAfrica/KRISP-0191/2020 EPI_ISL_482710 location -SouthAfrica/KRISP-0192/2020 EPI_ISL_482711 location -SouthAfrica/KRISP-0196/2020 EPI_ISL_482712 location -SouthAfrica/KRISP-0197/2020 EPI_ISL_482713 location SouthAfrica/KRISP-0198/2020 EPI_ISL_482851 location eThekwini # previously Ethekwini SouthAfrica/KRISP-0203/2020 EPI_ISL_482852 location eThekwini # previously Ethekwini SouthAfrica/KRISP-0259/2020 EPI_ISL_482729 location eThekwini # previously Ethekwini @@ -31103,19 +31096,19 @@ USA/TX-HMH096/2020 EPI_ISL_434801 location Greater Houston Area USA/TX-HMH097/2020 EPI_ISL_434802 location Greater Houston Area USA/TX-HMH098/2020 EPI_ISL_434803 location Greater Houston Area USA/TX-HMH099/2020 EPI_ISL_434804 location Greater Houston Area -USA/UN-UW-1266/2020 EPI_ISL_476904 division +USA/UN-UW-1266/2020 EPI_ISL_476904 division USA/UN-UW-1266/2020 EPI_ISL_476904 location # previously Unknown -USA/UN-UW-629/2020 EPI_ISL_476910 division +USA/UN-UW-629/2020 EPI_ISL_476910 division USA/UN-UW-629/2020 EPI_ISL_476910 location # previously Unknown -USA/UN-UW-659/2020 EPI_ISL_476919 division +USA/UN-UW-659/2020 EPI_ISL_476919 division USA/UN-UW-659/2020 EPI_ISL_476919 location # previously Unknown -USA/UN-UW-666/2020 EPI_ISL_476922 division +USA/UN-UW-666/2020 EPI_ISL_476922 division USA/UN-UW-666/2020 EPI_ISL_476922 location # previously Unknown -USA/UN-UW-667/2020 EPI_ISL_476923 division +USA/UN-UW-667/2020 EPI_ISL_476923 division USA/UN-UW-667/2020 EPI_ISL_476923 location # previously Unknown -USA/UN-UW-672/2020 EPI_ISL_476926 division +USA/UN-UW-672/2020 EPI_ISL_476926 division USA/UN-UW-672/2020 EPI_ISL_476926 location # previously Unknown -USA/UN-UW-686/2020 EPI_ISL_476932 division +USA/UN-UW-686/2020 EPI_ISL_476932 division USA/UN-UW-686/2020 EPI_ISL_476932 location # previously Unknown USA/UPHL-01/2020 EPI_ISL_415539 country_exposure Japan # duncan USA/UPHL-01/2020 EPI_ISL_415539 division_exposure Diamond Princess # duncan @@ -31128,7 +31121,7 @@ USA/UPHL-04/2020 EPI_ISL_415542 division_exposure Grand Princess # duncan USA/UPHL-04/2020 EPI_ISL_415542 region_exposure North America # duncan USA/VT-CDC-0303/2020 EPI_ISL_447846 region North America USA/VT-UW-MAYO49/2020 EPI_ISL_491004 division Vermont # previously Vt -USA/WA-S214/2020 EPI_ISL_430252 location +USA/WA-S214/2020 EPI_ISL_430252 location USA/WA-S316/2020 EPI_ISL_434076 location Franklin County WA USA/WA-S320/2020 EPI_ISL_434080 location Franklin County WA USA/WA-S380/2020 EPI_ISL_434140 location Franklin County WA