I want to extract the country location of a bunch of sequences in the NCBI using renterz. I have their accession numbers but I have the trouble of getting the country info. For example, I have this accession number MH939154 and I need to extract Romania using rentrez.
source 1..10976
/organism="West Nile virus"
/mol_type="genomic RNA"
/strain="DD84c"
/host="Culex pipiens s.l."
/db_xref="taxon:11082"
/country="Romania"
/collection_date="2014"
/note="lineage 2"
I have tried the code below but it seems like it will only extract the countries related to publication. So I wonder if there is any way to get the country under the source.
id = "MH939154.1"
db = entrez_fetch(db= "pubmed", id = id, rettype = "xml")
xml <- read_xml(db)
recs <- xml_find_all(xml, "//Country")
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kelvinfrog75 •
i don't know r+xml , so using a XPATH expression:
$ wget -q -O - "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=MH939154&rettype=gb&retmode=xml" | xmllint --xpath '//GBQualifier[GBQualifier_name="country"]/GBQualifier_value/text()' - && echo
Romania
This seems to work fine. I can run this command inside R. Just wonder how do you get this link "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=MH939154&rettype=gb&retmode=xml" ? Thanks.
Just wonder how do you get this link
Great. I am able to integrate the command script and get the country info. Thanks!
This can also be obtained by using Entrez Direct:
$ esearch -db nuccore -query "MH939154" | esummary | xtract -pattern DocumentSummary -element SubName
DD84c|Culex pipiens s.l.|WNV|Romania|2014|lineage 2
4th field is Country. I will leave it for you to extract that.
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GenoMax
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