Map host genus and host type

[DOH-LMT2303]

WNV NCBI records contain a column Host which has some information about the genus and species (i.e Culex pipiens). Create two categories to group and visualize the data in auspice. One category with the genus (i.e. Culex) to group all species under that genus, and another category with a host type (i.e mosquito). Similar categories have been incorporated in other WNV builds: WNV-Foco and WNV-Global

[DOH-LMT2303]

Downloaded metadata for 23,333 WNV sequences available in NCBI as of 11-1-2024. Explored and wrangled the data in R. Added two columns Host_Genus and Host_Type to the dataset excluding where Host is blank

[DOH-LMT2303]

Created a csv mapping file that contains three columns, Host from NCBI download as of 11-1-2024, Host_Genus which is populated with the first word of the Host column, and Host_Type which classifies Host_Genus as either Mosquito, Bird, Tick, Horse, Human, or Other.
WNVhostgenus_hosttype.csv

[j23414]

Thanks @DOH-LMT2303! Mind converting the csv to a tsv and placing the file in the ingest/defaults folder? Can commit to created branch map-host-genus-and-host-type.

After which we can draft a generalized transform-new-columns script that takes any mapping file and apply them to the metadata.tsv. Thanks for sharing your R code offline! We may be able to use parts of it as a starting point for the python script