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Add notes on FH Zika sequences and update geo synonyms for USVI

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1 parent 2ae5853 commit afe09625c8ba41769a1dbcd604321f9520e5a245 @trvrb trvrb committed Jan 3, 2017
Showing with 21 additions and 5 deletions.
  1. +8 −0 ZIKA.md
  2. +1 −0 source-data/geo_ISO_code.tsv
  3. +4 −2 source-data/geo_lat_long.tsv
  4. +1 −0 source-data/geo_regions.tsv
  5. +7 −3 source-data/geo_synonyms.tsv
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@@ -52,3 +52,11 @@ Upload with: `python vdb/zika_upload.py -db vdb -v zika --source broad --locus g
Regex replace: `^>([^_]+)_[^_]+_[^_]+_(\S+)`
With: `>\1|\1|\2|human|usa|florida|florida`
Upload with: `python vdb/zibra_upload.py -db vdb -v zika --source usamriid --locus genome --authors "Ladner et al" --fname RIID_ZIKV_FL_10-27-16.fasta`
+
+# FH sequences
+
+## Upload documents to VDB
+Upload with:
+
+* `python vdb/zibra_upload.py -db vdb -v zika --source fh --locus genome --authors "Black et al" --fname ZIKA_good.fasta`
+* `python vdb/zibra_upload.py -db vdb -v zika --source fh --locus genome --authors "Black et al" --fname ZIKA_partial.fasta`
@@ -243,6 +243,7 @@ ukraine UA
united_arab_emirates AE
united_kingdom GB
usa US
+usvi VI
uruguay UY
uzbekistan UZ
vanuatu VU
@@ -1857,8 +1857,6 @@ antioquia CO 7.0000085 -75.5000085
guaviare CO 1.6894444 -72.8202863
nayarit MX 22.0000001 -105.0
chiapas MX 16.5000001 -92.5
-st_thomas US 18.34290815 -64.9188996006
-st_croix US 45.0312388 -92.4679304
kuala_lumpur MY 2.74378195 101.711611883
easter_island CL -27.1260191 -109.349674206
masaya NI 11.9763955 -86.0882611
@@ -1896,3 +1894,7 @@ pocone BR -16.2634093 -56.6229716
cambe BR -23.2782856 -51.2799828
vasteras SE 59.6110992 16.5463679
cherkessk RU 44.2250248 42.056765
+saint_thomas VI 18.34290815 -64.9188996006
+saint_croix VI 45.0312388 -92.4679304
+st_thomas VI 18.34290815 -64.9188996006
+st_croix VI 45.0312388 -92.4679304
@@ -133,6 +133,7 @@ trinidad_tobago north_america
turks_and_caicos north_america
usa north_america
united_states north_america
+usvi north_america
american_samoa oceania
australia oceania
canberra oceania
@@ -2328,9 +2328,6 @@ Texas USA Texas Texas
Utah USA Utah Utah
Vermont USA Vermont Vermont
Virginia USA Virginia Virginia
-VirginIslands USA VirginIslands VirginIslands
-Usvirginislandssaintthomas USA VirginIslands StThomas
-usvirginislandssaintcroix USA VirginIslands StCroix
Washington USA Washington Washington
WestVirginia USA WestVirginia WestVirginia
Wisconsin USA Wisconsin Wisconsin
@@ -2391,6 +2388,13 @@ Springfield USA Illinois Springfield
Sophia USA WestVirginia Sophia
StLouis USA Missouri StLouis
+# US Virgin Islands
+USVI USVI USVI USVI
+USVirginIslands USVI USVI USVI
+Usvirginislandssaintthomas USVI SaintThomas SaintThomas
+usvirginislandssaintcroix USVI SaintCroix SaintCroix
+SaintCroix USVI SaintCroix SaintCroix
+SaintThomas USVI SaintThomas SaintThomas
# Uruguay
Uruguay Uruguay Uruguay Uruguay

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