Looking at How to dump genes from GenBank in GFF3 format? ? i've tried to download the full record of CM000760.3 as XML using Efetch, but it seems that the annotations are not downloaded (which is a new "feature" to me ):
wget -O - "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=CM000760.3&rettype=gb&retmode=xml"
while https://www.ncbi.nlm.nih.gov/nuccore/CM000760?report=gbwithparts shows the full annotation table.
What would be the correct EFetch URL do get the full table ?
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Pierre Lindenbaum
i haven't found efetch retmode, but sviewer.cgi can output gff: curl 'https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=gff3&id=1174565284&extrafeat=976&maxplex=1' id param also takes accession.
it doesn't answer my needs but you should post this to : How to dump genes from GenBank in GFF3 format?
i haven't found efetch retmode, but sviewer.cgi can output gff
If you do this you will undoubtedly be blocked, and receive the following from NCBI:
The site was blocked because of an excessive rate of access to the NCBI sequence servers. The NCBI web pages are a public >service and we need to make it available to a large number of different users. Single sites with very high rates of access can >impact and cause degradation of our performance. This site made over 50,000 NCBI requests, at a rate at or exceeding one per >second.
Additionally these request were using the source code for a web page pull down menu. This is an unauthorized, insecure and >inefficient method of obtaining data.
NCBI does not permit scripting against the main web servers. We have servers, APIs and other tools for bulk access of the >data: https://www.ncbi.nlm.nih.gov/home/develop/
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@Pierre: how about this?
wget -O - "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=CM000760.3&rettype=gbfull&retmode=xml"@genomax: closer but it's not GBXML ( https://www.ncbi.nlm.nih.gov/dtd/NCBI_GBSeq.mod.dtd ) it's Bioseq-set : ( https://www.ncbi.nlm.nih.gov/dtd/NCBI_Seqset.mod.dtd )
and it matters because I can generate a java parser for genbank:
but not for the other one: