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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[1]

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.

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  • $\begingroup$ Easy with biopython if Ur open to answers outside of R $\endgroup$
    – Liam McIntyre
    Feb 1, 2021 at 20:21
  • $\begingroup$ @LiamMcIntyre Sure! I would like to know your suggestion. $\endgroup$
    – Lumimoto
    Feb 23, 2021 at 12:29

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