I'm trying to extract the host field from the features table using the biofiles package. From what I understand, the function filter (from the same package) could be of help but I can't extract the information of interest. This is the simplified series of steps that I'm following:
library(biofiles) x_search <- reutils::esearch(db = "nuccore", #retmax = 9999, term = "((bacteria[ORGN]) AND host[ALL]) AND Loripes[ALL]") x_fetch <- reutils::efetch(x_search[1:3], "nuccore",rettype = "gbwithparts", retmode = "text") x_rec <- biofiles::gbRecord(x_fetch) x_ft <- biofiles::getFeatures(x_rec) x_ft
The last output should show the list of features for that entry, including the source with the qualifier "host", which I would like to retrieve for all the ids.
EDIT: I'm open to solutions outside the biofiles package.